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Sample records for included flair sequences

  1. Detection of lesions in multiple sclerosis by 2D FLAIR and single-slab 3D FLAIR sequences at 3.0 T: initial results

    International Nuclear Information System (INIS)

    Bink, Andrea; Gaa, Jochen; Lanfermann, Heinrich; Zanella, Friedhelm E.; Schmitt, Melanie; Mugler, John P.

    2006-01-01

    The aim of this study was to compare conventional 2D FLAIR and single-slab 3D FLAIR sequences in the detection of lesions in patients with multiple sclerosis. Eight patients with MS were examined at 3.0 T by using a 2D FLAIR sequence and a single-slab 3D FLAIR sequence. A comparison of lesion detectability was performed for the following regions: periventricular, nonperiventricular/juxtacortical and infratentorial. The contrast-to-noise ratios (CNRs) between lesions and brain tissue and CSF were calculated for each sequence. A total of 424 lesions were found using the 2D FLAIR sequence, while with the 3D FLAIR sequence 719 lesions were found. With the 2D FLAIR sequence, 41% fewer lesions were detected than with the 3D FLAIR sequence. Further, 40% fewer supratentorial and 62.5% fewer infratentorial lesions were found with the 2D FLAIR sequence. In images acquired with the 3D FLAIR sequence, the lesions had significantly higher CNRs than in images acquired with the 2D FLAIR sequence. These are the first results using a single-slab 3D FLAIR sequence at 3.0 T for detection of lesions in patients with MS. With the 3D FLAIR sequence significantly higher CNRs were achieved and significantly more lesions in patients with MS were detected. (orig.)

  2. Clinical usefulness of FLAIR MR sequence in the diagnosis of cerebral disease

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    Lee, Sang Hyun; Chang, Kee Hyun; Park, Hong Suk; Sim, Jung Suk; Cho, Seong Whi; Yu, In Kyu; Han, Moon Hee [Seoul National Univ. College of Medicine, Seoul (Korea, Republic of)

    1997-07-01

    To evaluate the clinical usefulness and limitation of FLAIR(fluid attenuated inversion recovery) MR sequence in various intracranial pathologic conditions. In prospective fashion, we used a 1.0T MR unit to obtain FLAIR sequence MR images, together with T1-weighted (T1WI), proton-density weighted (PDWI), and T2-weighted spin echo images (T2WI) in 24 patients with various intracranial diseases. Forty-two lesions in 24 patients were classified into three categories : nonhemorrhagic noncavitary lesions (n=20), hemorrhagic lesions (n=10), and cavitary lesions (n=12). Hemorrhagic lesion was divided into two types; type 1 showed high signal intensity on both T1WI and T2WI and type 2 showed marked low signal intensity on T2WI such as hemosiderin. Cavitary lesion was defined as one with signal intensity which paralleled CSF on all pulse sequences. Visually, we compared the lesion conspicuity on FLAIR with that on T2WI. Quantitatively, we also compared lesion/white matter (WM) contrast, lesion/WM contrast to noise ratio(CNR), lesion/CSF contrast, and lesion/CSF CNR on FLAIR with those on T2WI. For visual conspicuity of nonhemorrhagic noncavitary lesions and type 1 hemorrhagic lesions, FLAIR was superior to PDWI and T2WI, but for type 2 hemorrhangic lesions, PDWI and T2WI were superior to FLAIR. For cavitary lesions, there was no significant difference between T2WI and FLAIR. In the quantitative assessment of nonhemorrhagic noncavitary lesions, FLAIR was superior to PDWI for lesion/CSF cnotrast, and CNR, and lesion/WM contrast, but for lesion/WM CNR FLAIR was inferior to PDWI. For lesion/CSF contrast in cavitary lesions, FLAIR was superior to PDWI. There was no significant difference between PDWI and FLAIR for hemorrhagic lesions types 1 and 2. In assessing nonhemorrhagic noncavitary lesions, FLAIR was superior to T2WI for lesion/CSF contrast, but for lesion/WM CNR, FLAIR was inferior to T2WI. In cavitary lesions, T2WI was superior to FLAIR for lesion/WM contrast and CNR. In

  3. Comparison of 3D double inversion recovery and 2D STIR FLAIR MR sequences for the imaging of optic neuritis: pilot study

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    Hodel, Jerome; Bocher, Anne-Laure; Pruvo, Jean-Pierre; Leclerc, Xavier [Hopital Roger Salengro, Department of Neuroradiology, Lille (France); Outteryck, Olivier; Zephir, Helene; Vermersch, Patrick [Hopital Roger Salengro, Department of Neurology, Lille (France); Lambert, Oriane [Fondation Ophtalmologique Rothschild, Department of Neuroradiology, Paris (France); Benadjaoud, Mohamed Amine [Radiation Epidemiology Team, Inserm, CESP Centre for Research in Epidemiology and Population Health, U1018, Villejuif (France); Chechin, David [Philips Medical Systems, Suresnes (France)

    2014-12-15

    We compared the three-dimensional (3D) double inversion recovery (DIR) magnetic resonance imaging (MRI) sequence with the coronal two-dimensional (2D) short tau inversion recovery (STIR) fluid-attenuated inversion recovery (FLAIR) for the detection of optic nerve signal abnormality in patients with optic neuritis (ON). The study group consisted of 31 patients with ON (44 pathological nerves) confirmed by visual-evoked potentials used as the reference. MRI examinations included 2D coronal STIR FLAIR and 3D DIR with 3-mm coronal reformats to match with STIR FLAIR. Image artefacts were graded for each portion of the optic nerves. Each set of MR images (2D STIR FLAIR, DIR reformats and multiplanar 3D DIR) was examined independently and separately for the detection of signal abnormality. Cisternal portion of optic nerves was better delineated with DIR (p < 0.001), while artefacts impaired analysis in four patients with STIR FLAIR. Inter-observer agreement was significantly improved (p < 0.001) on 3D DIR (κ = 0.96) compared with STIR FLAIR images (κ = 0.60). Multiplanar DIR images reached the best performance for the diagnosis of ON (95 % sensitive and 94 % specific). Our study showed a high sensitivity and specificity of 3D DIR compared with STIR FLAIR for the detection of ON. These findings suggest that the 3D DIR sequence may be more useful in patients suspected of ON. (orig.)

  4. 3D-Flair sequence at 3T in cochlear otosclerosis

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    Lombardo, Francesco; De Cori, Sara; Aghakhanyan, Gayane; Montanaro, Domenico; De Marchi, Daniele; Frijia, Francesca; Canapicchi, Raffaello [Fondazione CNR Regione Toscana ' ' G. Monasterio' ' , Neuroradiology Unit, Pisa (Italy); Fortunato, Susanna; Forli, Francesca; Berrettini, Stefano [University of Pisa, ENT Audiology Phoniatry Unit, Department of Neuroscience, Pisa (Italy); Chiappino, Dante [Fondazione CNR Regione Toscana ' ' G. Monasterio' ' , Department of Radiology, Massa (Italy)

    2016-10-15

    To assess the capability of three-dimensional fluid-attenuated inversion recovery (3D-FLAIR) sequences in detecting signal alterations of the endolabyrinthine fluid in patients with otosclerosis. 3D-FLAIR before and after (-/+) gadolinium (Gd) administration was added to the standard MR protocol and acquired in 13 patients with a clinical/audiological diagnosis of severe/profound hearing loss in otosclerosis who were candidates for cochlear implantation and in 11 control subjects using 3-T magnetic resonance imaging (MRI) equipment. The MRI signal of the fluid-filled cochlea was assessed both visually and calculating the signal intensity ratio (SIR = signal intensity cochlea/brainstem). We revealed no endocochlear signal abnormalities on T1-weighted -/+ Gd images for either group, while on 3D-FLAIR we found bilateral hyperintensity with enhancement after Gd administration in eight patients and bilateral hyperintensity without enhancement in one patient. No endocochlear signal abnormalities were detected in other patients or the control group. Using 3-T MRI equipment, the 3D-FLAIR -/+ Gd sequence is able to detect the blood-labyrinth barrier (BLB) breakdown responsible for alterations of the endolabyrinthine fluid in patients with cochlear otosclerosis. We believe that 3D-FLAIR +/- Gd is an excellent imaging modality to assess the intra-cochlear damage in otosclerosis patients. (orig.)

  5. Usefulness of turbo-fluid-attenuated inversion-recovery (tFLAIR) sequence in diagnosing meningioma

    International Nuclear Information System (INIS)

    Shimizu, Teruhiko; Miki, Hitoshi; Takeguchi, Takashi; Kikuchi, Keiichi; Mochizuki, Teruhito; Ikezoe, Junpei

    2003-01-01

    We evaluated qualitatively and quantitatively the usefulness of turbo-fluid-attenuated inversion-recovery (tFLAIR) in diagnosing meningioma in comparison with the T2-weighted turbo spin echo (T2W-TSE) sequence. Forty-eight patients diagnosed with meningioma were studied. In the qualitative study, we evaluated tumor delineation, contrast (Co) of tumor-to-CSF (cerebrospinal fluid), Co of tumor-to-brain parenchyma, Co of peripheral edema-to-brain parenchyma, and detectability of tumor margin. In quantitative study-1, using signal intensity (SI), we measured SI and calculated Co-SI of tumor-to-gray matter, Co-SI of tumor-to-white matter, Co-SI of peripheral edema-to-white matter, and Co-SI of tumor-to-CSF. In quantitative study-2, using film density, we measured density (De) on hard-copy film images and calculated Co-De for the same items as in quantitative study-1. In the qualitative study, tFLAIR was superior to T2W-TSE in tumor delineation, Co of tumor-to-CSF, Co of tumor-to-brain parenchyma, and Co of peripheral edema-to-brain parenchyma. In quantitative study-1, tFLAIR was superior to T2W-TSE in Co-SI of tumor-to-CSF, however, T2W-TSE was superior to tFLAIR in Co-SI of tumor-to-white matter. In quantitative study-2, tFLAIR was superior to T2W-TSE in all Co-De. tFLAIR was superior to T2W-TSE in the depiction of meningioma. (author)

  6. Usefulness of turbo-fluid-attenuated inversion-recovery (tFLAIR) sequence in diagnosing meningioma

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    Shimizu, Teruhiko; Miki, Hitoshi; Takeguchi, Takashi; Kikuchi, Keiichi; Mochizuki, Teruhito; Ikezoe, Junpei [Ehime Univ., Shigenobu (Japan). School of Medicine

    2003-04-01

    We evaluated qualitatively and quantitatively the usefulness of turbo-fluid-attenuated inversion-recovery (tFLAIR) in diagnosing meningioma in comparison with the T2-weighted turbo spin echo (T2W-TSE) sequence. Forty-eight patients diagnosed with meningioma were studied. In the qualitative study, we evaluated tumor delineation, contrast (Co) of tumor-to-CSF (cerebrospinal fluid), Co of tumor-to-brain parenchyma, Co of peripheral edema-to-brain parenchyma, and detectability of tumor margin. In quantitative study-1, using signal intensity (SI), we measured SI and calculated Co-SI of tumor-to-gray matter, Co-SI of tumor-to-white matter, Co-SI of peripheral edema-to-white matter, and Co-SI of tumor-to-CSF. In quantitative study-2, using film density, we measured density (De) on hard-copy film images and calculated Co-De for the same items as in quantitative study-1. In the qualitative study, tFLAIR was superior to T2W-TSE in tumor delineation, Co of tumor-to-CSF, Co of tumor-to-brain parenchyma, and Co of peripheral edema-to-brain parenchyma. In quantitative study-1, tFLAIR was superior to T2W-TSE in Co-SI of tumor-to-CSF, however, T2W-TSE was superior to tFLAIR in Co-SI of tumor-to-white matter. In quantitative study-2, tFLAIR was superior to T2W-TSE in all Co-De. tFLAIR was superior to T2W-TSE in the depiction of meningioma. (author)

  7. Accuracy of the Compressed Sensing Accelerated 3D-FLAIR Sequence for the Detection of MS Plaques at 3T.

    Science.gov (United States)

    Toledano-Massiah, S; Sayadi, A; de Boer, R; Gelderblom, J; Mahdjoub, R; Gerber, S; Zuber, M; Zins, M; Hodel, J

    2018-01-18

    The use of 3D FLAIR improves the detection of brain lesions in MS patients, but requires long acquisition times. Compressed sensing reduces acquisition time by using the sparsity of MR images to randomly undersample the k-space. Our aim was to compare the image quality and diagnostic performance of 3D-FLAIR with and without compressed sensing for the detection of multiple sclerosis lesions at 3T. Twenty-three patients with relapsing-remitting MS underwent both conventional 3D-FLAIR and compressed sensing 3D-FLAIR on a 3T scanner (reduction in scan time 1 minute 25 seconds, 27%; compressed sensing factor of 1.3). Two blinded readers independently evaluated both conventional and compressed sensing FLAIR for image quality (SNR and contrast-to-noise ratio) and the number of MS lesions visible in the periventricular, intra-juxtacortical, infratentorial, and optic nerve regions. The volume of white matter lesions was measured with automatic postprocessing segmentation software for each FLAIR sequence. Image quality and the number of MS lesions detected by the readers were similar between the 2 FLAIR acquisitions ( P = .74 and P = .094, respectively). Almost perfect agreement was found between both FLAIR acquisitions for total MS lesion count (Lin concordance correlation coefficient = 0.99). Agreement between conventional and compressed sensing FLAIR was almost perfect for periventricular and infratentorial lesions and substantial for intrajuxtacortical and optic nerve lesions. Postprocessing with the segmentation software did not reveal a significant difference between conventional and compressed sensing FLAIR in total MS lesion volume ( P = .63) or the number of MS lesions ( P = .15). With a compressed sensing factor of 1.3, 3D-FLAIR is 27% faster and preserves diagnostic performance for the detection of MS plaques at 3T. © 2018 by American Journal of Neuroradiology.

  8. van der Knaap syndrome: MR imaging findings including FLAIR, diffusion imaging, and proton MR spectroscopy

    International Nuclear Information System (INIS)

    Sener, R.N.

    2000-01-01

    A patient is reported with diffuse leukoencephalopathy associated with cystic degeneration of the white matter of the brain (van der Knaap syndrome). The changes were studied by fluid attenuated inversion recovery (FLAIR), and diffusion-weighted MR imaging. The FLAIR sequence revealed suppressed signal of the cysts, and widespread high-signal white matter changes associated with thinned cortices. On diffusion-weighted MR imaging, apparent diffusion coefficient (ADC) values ranged from 3.0 x 10 -3 to 2.7 x 10 -3 mm 2 /s in the temporal cysts, similar to that of CSF. The ADC values within the parenchyma ranged between 2 x 10 -3 and 2.1 x 10 -3 mm 2 /s, a value falling between normal parenchyma and cerebrospinal fluid, compared with a control group of three healthy subjects. The changes were also evaluated by proton MR spectroscopy, and were compared with a control group of 12 cases. Magnetic resonance spectroscopy revealed apparently increased NAA/Cr ratios in most parts of the brain. The NAA/Cho ratios were either high or low, and the Cho/Cr ratios were increased or normal in different regions. (orig.)

  9. Comparison of 3D cube FLAIR with 2D FLAIR for multiple sclerosis imaging at 3 tesla

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    Patzig, M.; Brueckmann, H.; Fesl, G. [Muenchen Univ. (Germany). Dept. of Neuroradiology; Burke, M. [GE Healthcare, Solingen (Germany)

    2014-05-15

    Purpose: Three-dimensional (3 D) MRI sequences allow improved spatial resolution with good signal and contrast properties as well as multiplanar reconstruction. We sought to compare Cube, a 3 D FLAIR sequence, to a standard 2 D FLAIR sequence in multiple sclerosis (MS) imaging. Materials and Methods: Examinations were performed in the clinical routine on a 3.0 Tesla scanner. 12 patients with definite MS were included. Lesions with MS-typical properties on the images of Cube FLAIR and 2 D FLAIR sequences were counted and allocated to different brain regions. Signal-to-noise ratios (SNR) and contrast-to-noise ratios (CNR) were calculated. Results: With 384 the overall number of lesions found with Cube FLAIR was significantly higher than with 2 D FLAIR (N = 221). The difference was mostly accounted for by supratentorial lesions (N = 372 vs. N = 216) while the infratentorial lesion counts were low in both sequences. SNRs and CNRs were significantly higher in CUBE FLAIR with the exception of the CNR of lesion to gray matter, which was not significantly different. Conclusion: Cube FLAIR showed a higher sensitivity for MS lesions compared to a 2 D FLAIR sequence. 3 D FLAIR might replace 2 D FLAIR sequences in MS imaging in the future. (orig.)

  10. Uso da sequência FLAIR-EPI na análise da esclerose mesial temporal EPI-FLAIR sequence in the evaluation of mesial temporal sclerosis

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    Marcos Alberto da Costa Machado Júnior

    2001-06-01

    Full Text Available O objetivo deste estudo é analisar as alterações morfológicas e de intensidade de sinal das regiões hipocampais em pacientes, com epilepsia temporal fármaco-resistente. Para tal, estudamos 8 pacientes com esclerose mesial temporal, utilizando aparelhagem de RM de 1,5T, com sequências Spin Eco - SE, Fast Spin Eco - FSE, Fluid Atenuation Inversion Recovery, com Eco Planar Imaging - FLAIR-EPI. Observamos a superioridade da sequência FLAIR na detecção do aumento da intensidade de sinal da região hipocampal, particularmente com cortes coronais, em relação às sequências SE e FSE, com a vantagem de ser uma técnica de rápida execução. A sequência STIR evidenciou adelgaçamento da cortical do hipocampo, na metade dos casos que apresentavam alteração de sinal.The purpose of this study is to evaluate morpholologycal and signal intensity changes in the hippocampus in patients with medically intractable temporal lobe epilepsy. We studied 8 patients with mesial temporal sclerosis using a 1.5 -T MR and the following sequences Spin Eco- SE, Fast Spin Echo- FSE, Fluid Atenuation Inversion Recovery Echo Planar Imaging - FLAIR-EPI. We noticed a sensitive increase signal intensity on FLAIR- EPI sequences, particularly, in coronal images, than on SE and FSE sequences. The STIR sequence showed a cortical hippocampus atrophy in half of the cases, in whom signal abnormalities were present.

  11. Contrast enhancement of intracranial lesions at 1.5 T: comparison among 2D spin echo, black-blood (BB) Cube, and BB Cube-FLAIR sequences

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    Im, SungWoon; Ashikaga, Ryuichiro; Yagyu, Yukinobu; Hyodo, Tomoko; Imaoka, Izumi; Kumano, Seishi; Ishii, Kazunari; Murakami, Takamichi [Kinki University Faculty of Medicine, Department of Radiology, Osaka-Sayama, Osaka (Japan); Wakayama, Tetsuya; Miyoshi, Mitsuharu [GE Healthcare Japan, MR Applications and Workflow, Asia Pacific, Hino, Tokyo (Japan)

    2015-11-15

    The purpose of this study was to investigate the usefulness of T1W black-blood Cube (BB Cube) and T1W BB Cube fluid-attenuated inversion recovery (BB Cube-FLAIR) sequences for contrast-enhanced brain imaging, by evaluating flow-related artefacts, detectability, and contrast ratio (CR) of intracranial lesions among these sequences and T1W-SE. Phantom studies were performed to determine the optimal parameters of BB Cube and BB Cube-FLAIR. A clinical study in 23 patients with intracranial lesions was performed to evaluate the usefulness of these two sequences for the diagnosis of intracranial lesions compared with the conventional 2D T1W-SE sequence. The phantom study revealed that the optimal parameters for contrast-enhanced T1W imaging were TR/TE = 500 ms/minimum in BB Cube and TR/TE/TI = 600 ms/minimum/300 ms in BB Cube-FLAIR imaging. In the clinical study, the degree of flow-related artefacts was significantly lower in BB Cube and BB Cube-FLAIR than in T1W-SE. Regarding tumour detection, BB Cube showed the best detectability; however, there were no significant differences in CR among the sequences. At 1.5 T, contrast-enhanced BB Cube was a better imaging sequence for detecting brain lesions than T1W-SE or BB Cube-FLAIR. (orig.)

  12. MRI of head injury using FLAIR

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    Ashikaga, R. [Dept. of Radiology, Kinki Univ. School of Medicine, Osaka (Japan); Araki, Y. [Dept. of Radiology, Kinki Univ. School of Medicine, Osaka (Japan); Ishida, O. [Dept. of Radiology, Kinki Univ. School of Medicine, Osaka (Japan)

    1997-04-01

    We studied the utility of fluid-attenuated inversion-recovery (FLAIR) MRI in the investigation of head injury. We examined 56 patients with head injuries with T2-weighted spin-echo (SE) and FLAIR sequences. In all cases, the sensitivity of FLAIR images to equal or superior to that of conventional SE images to the traumatic lesions. In 9 cases, central diffuse axonal injury of the fornix and corpus callosum could be seen only on sagittal FLAIR images. (orig.). With 4 figs., 1 tab.

  13. MRI of head injury using FLAIR

    International Nuclear Information System (INIS)

    Ashikaga, R.; Araki, Y.; Ishida, O.

    1997-01-01

    We studied the utility of fluid-attenuated inversion-recovery (FLAIR) MRI in the investigation of head injury. We examined 56 patients with head injuries with T2-weighted spin-echo (SE) and FLAIR sequences. In all cases, the sensitivity of FLAIR images to equal or superior to that of conventional SE images to the traumatic lesions. In 9 cases, central diffuse axonal injury of the fornix and corpus callosum could be seen only on sagittal FLAIR images. (orig.). With 4 figs., 1 tab

  14. Assessment of Cochlea Endolymphatic Hydrops Using 3-D FLAIR and 3-D Real IR Sequence in Guinea Pigs via 3T MRI After Intratympanic Gadolinium: A Histopathological Comparison.

    Science.gov (United States)

    Wang, Feng; Lyu, Huiying; Zhao, Menglong; Sha, Yan; Zhang, Fang; Cheng, Yushu; Huang, Wenhu; Tang, Wenlin; Xie, Youzhou; Lu, Ping

    2017-04-01

    We assessed whether the three-dimensional fluid-attenuated inversion-recovery (3-D FLAIR) and three-dimensional inversion-recovery with real reconstruction (3-D real IR) sequences can be used to detect cochlea endolymphatic hydrops (EHs) in guinea pigs using 3 Tesla magnetic resonance imaging (3T MRI). The results of 3-D real IR imaging were compared with histopathological outcomes. Fourteen healthy men and women albino guinea pigs were used in this study. Their right ears received procedures that promoted EHs, and their left ears were used as untreated controls. High-resolution 3T MRI, combined with the intratympanic injection of gadolinium (Gd) in both ears, was performed 8 to 12 weeks after surgery. Both sides of the cochlea midmodiolar sections were observed under a light microscope and saved as the histopathological images. The signal-to-noise ratios (SNRs) and contrast-to-noise ratios (CNRs) between the T2-weighted 3-D FLAIR and T2-weighted 3-D real IR sequences were compared. The appearance of EHs in the basal, second, third, and apical turns of the cochlea was further evaluated using 3-D FLAIR, 3-D real IR, and the histopathological images. Moreover, the maximum scala media area ratios (SMRs) on the histopathological sections were compared with the grading of the EHs on the 3-D real IR sequence with regard to each turn of the cochlea. Significant differences were found between the 3-D FLAIR and 3-D-real IR sequences with regard to the SNRs and CNRs (p IR sequence (SNRROI: 86.71 ± 30.11; SNRB: 11.11 ± 3.45), whereas the 3-D real IR sequence showed higher CNRs (2.78 ± 0.58) compared with the 3-D FLAIR sequence (2.18 ± 0.55). Various degrees of EHs were observed in each turn of the cochlea in the experimental ears on the basis of the histopathological images. Thirteen, 10, 4, and 0 EHs were observed in the basal, second, third, and apical turns of the cochlear using 3-D FLAIR images, respectively, whereas 14, 14, 14, and 13 EHs were

  15. FLAIR images of brain diseases

    International Nuclear Information System (INIS)

    Segawa, Fuminori; Kinoshita, Masao; Kishibayashi, Jun; Kamada, Kazuhiko; Sunohara, Nobuhiko.

    1994-01-01

    The present study was designed to assess the usefulness of fluid-attenuated inversion recovery (FLAIR) images in diagnosing brain diseases. The subjects were 20 patients with multiple cerebral infarction, multiple sclerosis, temporal epilepsy, or brain trauma, and 20 other healthy adults. FLAIR images, with a long repetitive time of 6000 msec and a long inversion time of 1400-1600 msec, showed low signal intensity in the cerebrospinal fluid in the lateral ventricles and the cerebral sulci, and high signal intensity in brain tissues. Signal intensity on FLAIR images correlated well with T2 relaxation times under 100 msec. For multiple sclerosis and cerebral infarction, cystic lesions, which were shown on T2-weighted images with long relaxation times over 100 msec, appeared as low-signal areas; and the lesions surrounding the cystic lesions appeared as high-signal areas. For temporal lobe epilepsy, the hippocampus was visualized as a high-signal area. Hippocampal lesions were demonstrated better with FLAIR images than with conventional T2-weighted and proton-density images. In a patient with cerebral trauma, FLAIR images revealed the lobulated structure with the residual cortex shown as a high signal area. The lesions surrounding the cystic change were imaged as high signal areas. These structural changes were demonstrated better with FLAIR images than with conventional T2-weighted sequences. FLAIR images were useful in detecting white matter lesions surrounding the lateral ventricles and cortical and subcortical lesions near the brain surface, which were unclear on conventional T2-weighted and proton-density images. (N.K.)

  16. The Effects of DWI-Infarct Lesion Volume on DWI-FLAIR Mismatch: Is There a Need for Size Stratification?

    Science.gov (United States)

    Payabvash, Seyedmehdi; Taleb, Shayandokht; Benson, John C; Rykken, Jeffrey B; Oswood, Mark C; McKinney, Alexander M; Hoffman, Benjamin

    2017-07-01

    The lack of fluid-attenuated inversion-recovery (FLAIR) hyperintensity in areas of diffusion-weighted imaging (DWI) high signal, or DWI-FLAIR mismatch, is a potential imaging biomarker for timing of stroke onset. We aimed to determine the effects of DWI infarct lesion volume on DWI-FLAIR mismatch and its accuracy for identification of strokes within intravenous (IV) the thrombolytic therapy window. Acute ischemic stroke patients with magnetic resonance imaging scan within 12 hours of witnessed stroke were included. Two neuroradiologists independently reviewed DWI and FLAIR sequences for DWI-FLAIR mismatch in areas of restricted diffusion compared to the contralateral normal side. DWI-FLAIR mismatch was identified in 21/82 (26%) patients. Infarct lesions with DWI-FLAIR mismatch were scanned earlier (3.8 ± .3 vs. 7.5 ± .3 hours from onset, P mismatch. Multivariate regression analysis showed a significant interaction between lesion volume and time-from-onset in relationship with the presence of DWI-FLAIR mismatch (P = .045). The presence of DWI-FLAIR mismatch had 56% sensitivity, 83% specificity, 48% positive predictive value (PPV), and 87% negative predictive value (NPV) for identification of infarction within 4.5 hours of symptom onset; while for infarct lesions >15 mL, the DWI-FLAIR mismatch had 100% specificity and PPV for acute infarcts within 4.5 hours of onset. The effects of stroke onset-to-scan time gap on DWI-FLAIR mismatch are not the same for different DWI lesion volumes. At DWI lesion volumes >15 mL, the DWI-FLAIR mismatch is highly specific for acute infarcts within IV thrombolytic therapy time, and can identify wake-up stroke patients eligible for treatment. Copyright © 2016 by the American Society of Neuroimaging.

  17. Contrast-enhanced FLAIR in the early diagnosis of infectious meningitis

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    Splendiani, Alesssandra; Puglielli, Edoardo; Amicis, Rosanna De; Masciocchi, Carlo; Gallucci, Massimo [University of L' Aquila, Department of Radiology, L' Aquila (Italy); Necozione, Stefano [University of L' Aquila, Department of Statistic, L' Aquila (Italy)

    2005-08-01

    We investigated the accuracy of MRI in the early diagnosis of infectious meningitis with emphasis on the value of gadolinium-enhanced fluid-attenuated inversion recovery (FLAIR) sequence. Twenty-seven patients with clinical suspicion of infectious meningitis were included. MRI was performed within 3 h of clinical evaluation. For all patients, T1-weighted spin-echo, dual-echo T2-weighted fast-spin-echo and FLAIR sequences were performed, followed by gadolinium-enhanced T1-weighted spin-echo and FLAIR sequences. Final diagnosis was based on the clinical findings and the analysis of cerebrospinal fluid, obtained by lumbar puncture after the MRI. Infectious meningitis was confirmed in 12 patients. In all of these patients of the plain studies, FLAIR was positive in only four patients. MRI gadolinium-enhanced FLAIR showed abnormal meningeal enhancement in all 12 patients, while gadolinium-enhanced T1-weighted spin-echo was positive only in six cases. There were no false-positive or false-negative results. It is concluded that MRI could have an important role in the early screening for infectious meningitis, provided a gadolinium-enhanced FLAIR sequence is used. (orig.)

  18. Contrast-enhanced FLAIR in the early diagnosis of infectious meningitis

    International Nuclear Information System (INIS)

    Splendiani, Alesssandra; Puglielli, Edoardo; Amicis, Rosanna De; Masciocchi, Carlo; Gallucci, Massimo; Necozione, Stefano

    2005-01-01

    We investigated the accuracy of MRI in the early diagnosis of infectious meningitis with emphasis on the value of gadolinium-enhanced fluid-attenuated inversion recovery (FLAIR) sequence. Twenty-seven patients with clinical suspicion of infectious meningitis were included. MRI was performed within 3 h of clinical evaluation. For all patients, T1-weighted spin-echo, dual-echo T2-weighted fast-spin-echo and FLAIR sequences were performed, followed by gadolinium-enhanced T1-weighted spin-echo and FLAIR sequences. Final diagnosis was based on the clinical findings and the analysis of cerebrospinal fluid, obtained by lumbar puncture after the MRI. Infectious meningitis was confirmed in 12 patients. In all of these patients of the plain studies, FLAIR was positive in only four patients. MRI gadolinium-enhanced FLAIR showed abnormal meningeal enhancement in all 12 patients, while gadolinium-enhanced T1-weighted spin-echo was positive only in six cases. There were no false-positive or false-negative results. It is concluded that MRI could have an important role in the early screening for infectious meningitis, provided a gadolinium-enhanced FLAIR sequence is used. (orig.)

  19. Arterial hyperintensity on BLADE fluid-attenuated inversion recovery images (FLAIR) in hyperacute territorial infarction: comparison with conventional FLAIR

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    Kwag, Eujean; Lim, Soo Mee; Park, Ji Eun; Chae, In Hye [Ewha Womans University School of Medicine, Department of Radiology, Mokdong Hospital, Seoul (Korea, Republic of)

    2014-09-15

    To evaluate the utility of BLADE fluid-attenuated inversion recovery images (FLAIR) magnetic resonance (MR) imaging compared to conventional FLAIR for the detection of arterial hyperintensity (AH) in hyperacute territorial infarction. We retrospectively analysed MR images of patients with hyperacute (<6 h) territorial infarction over a 9-month study period. Special attention was paid to the presence or absence of AH in the frontal, parietal and temporal lobes and the number of AHs in the sylvian fissure. We also evaluated the presence of three kinds of artefacts on BLADE FLAIR and conventional FLAIR images. AH was seen in 41 (91 %) patients with conventional FLAIR and 45 (100 %) patients with BLADE FLAIR images. More instances of AH were detected in the frontal, parietal and temporal lobes and within the sylvian fissure using BLADE FLAIR. Motion artefacts, pulsation artefacts from the sigmoid sinus and incomplete cerebrospinal fluid (CSF) nulling that reduced image quality were observed more frequently on conventional FLAIR images than on BLADE FLAIR images. BLADE FLAIR sequences are more sensitive than conventional FLAIR for the detection of AH in hyperacute territorial infarctions and provide better image quality by reducing artefacts. They may be used in place of conventional FLAIR for patients with hyperacute stroke. (orig.)

  20. Contrast enhancement of intracranial lesions at 1.5 T: comparison among 2D spin echo, black-blood (BB) Cube, and BB Cube-FLAIR sequences.

    Science.gov (United States)

    Im, SungWoon; Ashikaga, Ryuichiro; Yagyu, Yukinobu; Wakayama, Tetsuya; Miyoshi, Mitsuharu; Hyodo, Tomoko; Imaoka, Izumi; Kumano, Seishi; Ishii, Kazunari; Murakami, Takamichi

    2015-11-01

    The purpose of this study was to investigate the usefulness of T1W black-blood Cube (BB Cube) and T1W BB Cube fluid-attenuated inversion recovery (BB Cube-FLAIR) sequences for contrast-enhanced brain imaging, by evaluating flow-related artefacts, detectability, and contrast ratio (CR) of intracranial lesions among these sequences and T1W-SE. Phantom studies were performed to determine the optimal parameters of BB Cube and BB Cube-FLAIR. A clinical study in 23 patients with intracranial lesions was performed to evaluate the usefulness of these two sequences for the diagnosis of intracranial lesions compared with the conventional 2D T1W-SE sequence. The phantom study revealed that the optimal parameters for contrast-enhanced T1W imaging were TR/TE = 500 ms/minimum in BB Cube and TR/TE/TI = 600 ms/minimum/300 ms in BB Cube-FLAIR imaging. In the clinical study, the degree of flow-related artefacts was significantly lower in BB Cube and BB Cube-FLAIR than in T1W-SE. Regarding tumour detection, BB Cube showed the best detectability; however, there were no significant differences in CR among the sequences. At 1.5 T, contrast-enhanced BB Cube was a better imaging sequence for detecting brain lesions than T1W-SE or BB Cube-FLAIR. • Cube is a single-slab 3D FSE imaging sequence. • We applied a black-blood (BB) imaging technique to T1W Cube. • At 1.5 T, contrast-enhanced T1W BB Cube was valuable for detecting brain lesions.

  1. Contrast-enhanced FLAIR (fluid-attenuated inversion recovery for evaluating mild traumatic brain injury.

    Directory of Open Access Journals (Sweden)

    Soo Chin Kim

    Full Text Available PURPOSE: To evaluate whether adding a contrast-enhanced fluid-attenuated inversion recovery (FLAIR sequence to routine magnetic resonance imaging (MRI can detect additional abnormalities in the brains of symptomatic patients with mild traumatic brain injury. MATERIALS AND METHODS: Fifty-four patients with persistent symptoms following mild closed head injury were included in our retrospective study (M ∶ F =  32 ∶ 22, mean age: 59.8 ± 16.4, age range: 26-84 years. All MRI examinations were obtained within 14 days after head trauma (mean: 3.2 ± 4.1 days, range: 0.2-14 days. Two neuroradiologists recorded (1 the presence of traumatic brain lesions on MR images with and without contrast-enhanced FLAIR images and (2 the pattern and location of meningeal enhancement depicted on contrast-enhanced FLAIR images. The number of additional traumatic brain lesions diagnosed with contrast-enhanced FLAIR was recorded. Correlations between meningeal enhancement and clinical findings were also evaluated. RESULTS: Traumatic brain lesions were detected on routine image sequences in 25 patients. Three additional cases of brain abnormality were detected with the contrast-enhanced FLAIR images. Meningeal enhancement was identified on contrast-enhanced FLAIR images in 9 cases while the other routine image sequences showed no findings of traumatic brain injury. Overall, the additional contrast-enhanced FLAIR images revealed more extensive abnormalities than routine imaging in 37 cases (p<0.001. In multivariate logistic regression analysis, subdural hematoma and posttraumatic loss of consciousness showed a significant association with meningeal enhancement on contrast-enhanced FLAIR images, with odds ratios 13.068 (95% confidence interval 2.037 to 83.852, and 15.487 (95% confidence interval 2.545 to 94.228, respectively. CONCLUSION: Meningeal enhancement on contrast-enhanced FLAIR images can help detect traumatic brain lesions as well as additional abnormalities

  2. Clinical utility of MR FLAIR imaging for head injuries

    International Nuclear Information System (INIS)

    Ashikaga, Ryuichiro

    1996-01-01

    To study the utility of fluid attenuated inversion recovery (FLAIR) MR images in the evaluation of traumatic head injury, 56 patients with traumatic head injuries were examined with long TR/TE spin-echo (SE) sequences and FLAIR sequences. In 40 of them, long TR/short TE images were added to those sequences. Careful readings of MR images were done by two well-trained neuroradiologists. The chi-square test was used for statistical evaluation of our results. The relative sensitivities of FLAIR images were significantly better than those of long TR/TE, long TR/short TE images for the detection of diffuse axonal injury (p<0.01), cortical contusion (p<0.01), and subdural hematoma (p<0.01 for long TR/TE, p<0.05 for long TR/short TE). The number of cases of epidural hematoma and brainstem injury was too small for statistical significance to be determined. In 9 patients with corpus callosum injuries. FLAIR images demonstrated the lesions as abnormally high signal intensity in the septum pellucidum and fornix. Only sagittal FLAIR images could definitely discriminate the traumatic lesions of the fornix from the surrounding CSF. In addition, FLAIR images could easily discriminate DAI of the corpus callosum from CSF of the cavum velli interpositi. MR FLAIR images were found to be useful for detecting traumatic head injuries. (author)

  3. Clinical utility of MR FLAIR imaging for head injuries

    Energy Technology Data Exchange (ETDEWEB)

    Ashikaga, Ryuichiro [Kinki Univ., Osaka-Sayama, Osaka (Japan). School of Medicine

    1996-12-01

    To study the utility of fluid attenuated inversion recovery (FLAIR) MR images in the evaluation of traumatic head injury, 56 patients with traumatic head injuries were examined with long TR/TE spin-echo (SE) sequences and FLAIR sequences. In 40 of them, long TR/short TE images were added to those sequences. Careful readings of MR images were done by two well-trained neuroradiologists. The chi-square test was used for statistical evaluation of our results. The relative sensitivities of FLAIR images were significantly better than those of long TR/TE, long TR/short TE images for the detection of diffuse axonal injury (p<0.01), cortical contusion (p<0.01), and subdural hematoma (p<0.01 for long TR/TE, p<0.05 for long TR/short TE). The number of cases of epidural hematoma and brainstem injury was too small for statistical significance to be determined. In 9 patients with corpus callosum injuries. FLAIR images demonstrated the lesions as abnormally high signal intensity in the septum pellucidum and fornix. Only sagittal FLAIR images could definitely discriminate the traumatic lesions of the fornix from the surrounding CSF. In addition, FLAIR images could easily discriminate DAI of the corpus callosum from CSF of the cavum velli interpositi. MR FLAIR images were found to be useful for detecting traumatic head injuries. (author)

  4. Low-energy antiprotons physics and the FLAIR facility

    International Nuclear Information System (INIS)

    Widmann, E

    2015-01-01

    FLAIR, the Facility for low-energy antiproton and ion research has been proposed in 2004 as an extension of the planned FAIR facility at Darmstadt, Germany. FLAIR was not included into the modularized start version of FAIR, but the recent installation of the CRYRING storage ring at GSI Darmstadt has opened new perspectives for physics with low-energy antiprotons at FAIR. (paper)

  5. Regional Fluid-Attenuated Inversion Recovery (FLAIR) at 7 Tesla correlates with amyloid beta in hippocampus and brainstem of cognitively normal elderly subjects

    Science.gov (United States)

    Schreiner, Simon J.; Liu, Xinyang; Gietl, Anton F.; Wyss, Michael; Steininger, Stefanie C.; Gruber, Esmeralda; Treyer, Valerie; Meier, Irene B.; Kälin, Andrea M.; Leh, Sandra E.; Buck, Alfred; Nitsch, Roger M.; Pruessmann, Klaas P.; Hock, Christoph; Unschuld, Paul G.

    2014-01-01

    Background: Accumulation of amyloid beta (Aβ) may occur during healthy aging and is a risk factor for Alzheimer Disease (AD). While individual Aβ-accumulation can be measured non-invasively using Pittsburgh Compund-B positron emission tomography (PiB-PET), Fluid-attenuated inversion recovery (FLAIR) is a Magnetic Resonance Imaging (MRI) sequence, capable of indicating heterogeneous age-related brain pathologies associated with tissue-edema. In the current study cognitively normal elderly subjects were investigated for regional correlation of PiB- and FLAIR intensity. Methods: Fourteen healthy elderly subjects without known history of cognitive impairment received 11C-PiB-PET for estimation of regional Aβ-load. In addition, whole brain T1-MPRAGE and FLAIR-MRI sequences were acquired at high field strength of 7 Tesla (7T). Volume-normalized intensities of brain regions were assessed by applying an automated subcortical segmentation algorithm for spatial definition of brain structures. Statistical dependence between FLAIR- and PiB-PET intensities was tested using Spearman's rank correlation coefficient (rho), followed by Holm–Bonferroni correction for multiple testing. Results: Neuropsychological testing revealed normal cognitive performance levels in all participants. Mean regional PiB-PET and FLAIR intensities were normally distributed and independent. Significant correlation between volume-normalized PiB-PET signals and FLAIR intensities resulted for Hippocampus (right: rho = 0.86; left: rho = 0.84), Brainstem (rho = 0.85) and left Basal Ganglia vessel region (rho = 0.82). Conclusions: Our finding of a significant relationship between PiB- and FLAIR intensity mainly observable in the Hippocampus and Brainstem, indicates regional Aβ associated tissue-edema in cognitively normal elderly subjects. Further studies including clinical populations are necessary to clarify the relevance of our findings for estimating individual risk for age-related neurodegenerative

  6. Regional Fluid-Attenuated Inversion Recovery (FLAIR at 7 Tesla correlates with Amyloid beta in Hippocampus and Brainstem of cognitively normal elderly subjects.

    Directory of Open Access Journals (Sweden)

    Simon J Schreiner

    2014-09-01

    Full Text Available Background: Accumulation of amyloid beta (Aβ may occur during healthy aging and is a risk factor for Alzheimer Disease (AD. While individual Aβ-accumulation can be measured non-invasively using Pittsburgh compound-B positron-emission-tomography (PiB-PET, Fluid-Attenuated Inversion Recovery (FLAIR is a Magnetic Resonance Imaging (MRI sequence, capable of indicating heterogeneous age-related brain pathologies associated with tissue-edema. In the current study cognitively normal elderly subjects were investigated for regional correlation of PiB- and FLAIR- intensity. Methods: 14 healthy elderly subjects without known history of cognitive impairment received 11C-PiB-PET for estimation of regional Aβ-load. In addition, whole brain T1-MPRAGE and FLAIR-MRI sequences were acquired at high field strength of 7 Tesla (7T. Volume-normalized intensities of brain regions were assessed by applying an automated subcortical segmentation algorithm for spatial definition of brain structures. Statistical dependence between FLAIR- and PiB-PET intensities was tested using Spearman's rank correlation coefficient (rho, followed by Holm-Bonferroni correction for multiple testing. Results: Neuropsychological testing revealed normal cognitive performance levels in all participants. Mean regional PiB-PET and FLAIR intensities were normally distributed and independent. Significant correlation between volume-normalized PiB-PET signals and FLAIR intensities resulted for Hippocampus (right:rho=0.86; left:rho=0.84, Brainstem (rho=0.85 and left Basal Ganglia vessel region (rho=0.82. Conclusions: Our finding of a significant relationship between PiB- and FLAIR-intensity mainly observable in the Hippocampus and Brainstem, indicates regional Aβ associated tissue-edema in cognitively normal elderly subjects. Further studies including clinical populations are necessary to clarify the relevance of our findings for estimating individual risk for age-related neurodegenerative

  7. Contrast-enhanced flair imaging in the evaluation of infectious leptomeningeal diseases

    International Nuclear Information System (INIS)

    Parmar, Hemant; Sitoh, Y.-Y.; Anand, Pooja; Chua, Violet; Hui, Francis

    2006-01-01

    Purpose: The purpose of our study was to compare contrast-enhanced fluid-attenuated inversion recovery (FLAIR) images with contrast-enhanced T1 weighted images for infectious leptomeningitis. Materials and methods: We studied twenty-four patients with a clinical suspicion of infectious meningitis with unenhanced FLAIR, contrast-enhanced T1 weighted and contrast-enhanced FLAIR MR sequences. Twelve patients had cytologic and biochemical diagnosis of meningitis on cerebrospinal fluid (CSF) examination obtained 48 h before or after the MR study. Sequences were considered positive if abnormal signal was seen in the subarachnoid space (cistern or sulci) or along pial surface. Results: Twenty-seven examinations in 24 patients were performed. Of the 12 patients (thirteen studies) in whom cytology was positive, unenhanced FLAIR images were positive in six cases (sensitivity 46%), contrast-enhanced FLAIR images were positive in 11 (sensitivity 85%), and contrast-enhanced T1 weighted MR images were positive in 11 patients (sensitivity 85%). Of the 12 patients (14 studies) in whom cerebrospinal fluid study was negative, unenhanced FLAIR images were negative in 13, contrast-enhanced FLAIR images were negative in 11, and contrast-enhanced T1 weighted MR images were negative in eight. Thus, the specificity of unenhanced FLAIR, contrast-enhanced FLAIR and contrast-enhanced T1 weighted images was 93, 79 and 57%, respectively. Conclusion: Our results suggest that post-contrast FLAIR images have similar sensitivity but a higher specificity compared to contrast-enhanced T1 weighted images for detection of leptomeningeal enhancement. It can be a useful adjunct to post-contrast T1 weighted images in evaluation of infectious leptomeningitis

  8. Contrast-enhanced flair imaging in the evaluation of infectious leptomeningeal diseases

    Energy Technology Data Exchange (ETDEWEB)

    Parmar, Hemant [Department of Neuroradiology, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore 308433 (Singapore) and Department of Diagnostic Imaging, Hospital for Sick Children, Toronto (Canada)]. E-mail: parurad@hotmail.com; Sitoh, Y.-Y. [Department of Neuroradiology, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore 308433 (Singapore); Anand, Pooja [Department of Neurology, National Neuroscience Institute, 11 Jalan Tan Tock Seng (Singapore); Chua, Violet [Department of Neuroradiology, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore 308433 (Singapore); Hui, Francis [Department of Neuroradiology, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore 308433 (Singapore)

    2006-04-15

    Purpose: The purpose of our study was to compare contrast-enhanced fluid-attenuated inversion recovery (FLAIR) images with contrast-enhanced T1 weighted images for infectious leptomeningitis. Materials and methods: We studied twenty-four patients with a clinical suspicion of infectious meningitis with unenhanced FLAIR, contrast-enhanced T1 weighted and contrast-enhanced FLAIR MR sequences. Twelve patients had cytologic and biochemical diagnosis of meningitis on cerebrospinal fluid (CSF) examination obtained 48 h before or after the MR study. Sequences were considered positive if abnormal signal was seen in the subarachnoid space (cistern or sulci) or along pial surface. Results: Twenty-seven examinations in 24 patients were performed. Of the 12 patients (thirteen studies) in whom cytology was positive, unenhanced FLAIR images were positive in six cases (sensitivity 46%), contrast-enhanced FLAIR images were positive in 11 (sensitivity 85%), and contrast-enhanced T1 weighted MR images were positive in 11 patients (sensitivity 85%). Of the 12 patients (14 studies) in whom cerebrospinal fluid study was negative, unenhanced FLAIR images were negative in 13, contrast-enhanced FLAIR images were negative in 11, and contrast-enhanced T1 weighted MR images were negative in eight. Thus, the specificity of unenhanced FLAIR, contrast-enhanced FLAIR and contrast-enhanced T1 weighted images was 93, 79 and 57%, respectively. Conclusion: Our results suggest that post-contrast FLAIR images have similar sensitivity but a higher specificity compared to contrast-enhanced T1 weighted images for detection of leptomeningeal enhancement. It can be a useful adjunct to post-contrast T1 weighted images in evaluation of infectious leptomeningitis.

  9. Pre- and postcontrast FLAIR MR imaging in the diagnosis of intracranial meningeal pathology

    International Nuclear Information System (INIS)

    Tsuchiya, Kazuhiro; Katase, Shichiro; Yoshino, Ayako; Hachiya, Junichi

    2000-01-01

    Few reports address the use of fluid-attenuated inversion-recovery (FLAIR) images of the brain in the diagnosis of extraaxial lesions. Our purpose was to assess the value of FLAIR images, including postcontrast ones, in the diagnosis of intracranial meningeal diseases. We reviewed precontrast (n=24) and postcontrast (n=20) FLAIR images obtained from 25 patients with infectious meningitis (n=13), carcinomatous meningitis or dissemination of primary brain tumor (n=7), dural metastasis (n=3), and others (n=2) in comparison with fast spin-echo T2-weighted and postcontrast T1-weighted images. In lesion detectability, precontrast FLAIR images were significantly superior to fast spin-echo T2-weighted images but inferior to postcontrast T1-weighted images. There was no significant difference between postcontrast T1-weighted and FLAIR images. Precontrast FLAIR images can substitute for conventional fast spin-echo T2-weighted images. Postcontrast FLAIR images have diagnostic potential equivalent to conventional postcontrast T1-weighted images. (author)

  10. FLAIR images of mild head trauma with transient amnesia

    Energy Technology Data Exchange (ETDEWEB)

    Wakamoto, Hirooki; Miyazaki, Hiromichi; Inaba, Makoto; Ishiyama, Naomi [Hiratsuka City Hospital, Kanagawa (Japan); Kawase, Takeshi

    1998-11-01

    A newly advanced MRI pulse sequence, the FLAIR (fluid-attenuated inversion recovery) imaging, in which a long TE spin echo sequence is used with suppression of the CSF with an inversion pulse, displays the CSF space as a no signal intensity area. We examined 45 cases of mild head trauma with posttraumatic amnesia by FLAIR images and could detect some findings which could not be detected by CT scan and conventional MR images. These findings could be detected in many patients with long posttraumatic amnesia (over 2 hours), but they could not be detected in patients with short posttraumatic amnesia (within 30 mins). These findings existed surrounding lateral ventricles and we classified them into 3 types: type 1 is anterior horn of lateral ventricle, type 2 is the base of frontal lobe, and type 3 is cerebral deep white matter. Some of them were examined again by FLAIR images a month later, and these findings had disappeared. We suspect that these lesions were brain edema or mild contusion without hemorrhage. (author)

  11. FLAIR images of mild head trauma with transient amnesia

    International Nuclear Information System (INIS)

    Wakamoto, Hirooki; Miyazaki, Hiromichi; Inaba, Makoto; Ishiyama, Naomi; Kawase, Takeshi

    1998-01-01

    A newly advanced MRI pulse sequence, the FLAIR (fluid-attenuated inversion recovery) imaging, in which a long TE spin echo sequence is used with suppression of the CSF with an inversion pulse, displays the CSF space as a no signal intensity area. We examined 45 cases of mild head trauma with posttraumatic amnesia by FLAIR images and could detect some findings which could not be detected by CT scan and conventional MR images. These findings could be detected in many patients with long posttraumatic amnesia (over 2 hours), but they could not be detected in patients with short posttraumatic amnesia (within 30 mins). These findings existed surrounding lateral ventricles and we classified them into 3 types: type 1 is anterior horn of lateral ventricle, type 2 is the base of frontal lobe, and type 3 is cerebral deep white matter. Some of them were examined again by FLAIR images a month later, and these findings had disappeared. We suspect that these lesions were brain edema or mild contusion without hemorrhage. (author)

  12. Fast fluid-attenuated inversion recovery (FLAIR) magnetic resonance imaging of the brain: a comparison of multi-shot echo-planar and fast spin-echo techniques

    International Nuclear Information System (INIS)

    Sargent, M.A.; Poskitt, K.J.

    1997-01-01

    Purpose. To evaluate fast spin-echo and multi-shot echo-planar fluid-attenuated inversion recovery (FLAIR) sequences in paediatric brain imaging. Materials and methods. Matched images from 32 patients with suspected tumour or white matter disease were independently evaluated by two paediatric neuroradiologists. The observer preferences for image quality and lesion detection were analysed for differences between fast spin-echo FLAIR and multi-shot echo-planar FLAIR. Diagnostic quality was compared with that of fast spin-echo T2-weighted images. Results. Images of a diagnostic quality equivalent to that of fast spin-echo T2-weighted images were achieved with both FLAIR techniques. Grey and white matter differentiation and cerebrospinal fluid (CSF) nulling were significantly better on fast spin-echo FLAIR sequences. CSF flow artefact was reduced on multi-shot echo-planar FLAIR. There was no difference in lesion detection. Fast spin-echo FLAIR images were visually preferred at the expense of longer imaging time. Conclusion. Fast FLAIR techniques are complementary to fast spin-echo T2-weighted sequences in imaging of the paediatric brain. We find that the fast spin-echo FLAIR sequence is preferable to the multi-shot echo-planar technique. (orig.). With 5 figs., 2 tabs

  13. Volumetric relationship between 2-hydroxyglutarate and FLAIR hyperintensity has potential implications for radiotherapy planning of mutant IDH glioma patients.

    Science.gov (United States)

    Jafari-Khouzani, Kourosh; Loebel, Franziska; Bogner, Wolfgang; Rapalino, Otto; Gonzalez, Gilberto R; Gerstner, Elizabeth; Chi, Andrew S; Batchelor, Tracy T; Rosen, Bruce R; Unkelbach, Jan; Shih, Helen A; Cahill, Daniel P; Andronesi, Ovidiu C

    2016-11-01

    Gliomas with mutant isocitrate dehydrogenase (IDH) produce high levels of 2-hydroxyglutarate (2HG) that can be quantitatively measured by 3D magnetic resonance spectroscopic imaging (MRSI). Current glioma MRI primarily relies upon fluid-attenuated inversion recovery (FLAIR) hyperintensity for treatment planning, although this lacks specificity for tumor cells. Here, we investigated the relationship between 2HG and FLAIR in mutant IDH glioma patients to determine whether 2HG mapping is valuable for radiotherapy planning. Seventeen patients with mutant IDH1 gliomas were imaged by 3 T MRI. A 3D MRSI sequence was employed to specifically image 2HG. FLAIR imaging was performed using standard clinical protocol. Regions of interest (ROIs) were determined for FLAIR and optimally thresholded 2HG hyperintensities. The overlap, displacement, and volumes of 2HG and FLAIR ROIs were calculated. In 8 of 17 (47%) patients, the 2HG volume was larger than FLAIR volume. Across the entire cohort, the mean volume of 2HG was 35.3 cc (range, 5.3-92.7 cc), while the mean volume of FLAIR was 35.8 cc (range, 6.3-140.8 cc). FLAIR and 2HG ROIs had mean overlap of 0.28 (Dice coefficients range, 0.03-0.57) and mean displacement of 12.2 mm (range, 3.2-23.5 mm) between their centers of mass. Our results indicate that for a substantial number of patients, the 2HG volumetric assessment of tumor burden is more extensive than FLAIR volume. In addition, there is only partial overlap and asymmetric displacement between the centers of FLAIR and 2HG ROIs. These results may have important implications for radiotherapy planning of IDH mutant glioma. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Comparison of MR sequences in early cerebral infarction at 0.5 T

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    Saatci, I.; Baskan, O.; Cekirge, H.S.; Besim, A. [Hacettepe Univ. Hospital, Ankara (Turkey). Radiology Dept.

    2000-11-01

    To compare the diagnostic values of fluid-attenuated inversion recovery (FLAIR) and gradient spin-echo (GRASE) with those of conventional spin-echo (SE) and fast SE T2-weighted sequences in the evaluation of acute cerebrovascular lesions at 0.5 T. Material and Methods: Twenty-two consecutive patients with the clinical diagnosis of acute cerebrovascular accident were examined by MR imaging within the first 48 h of ictus. MR examination included 5-mm axial conventional SE and turbo SE (TSE) T2-weighted, dual-echo GRASE and FLAIR sequences. The patients also had pre- and postcontrast T1-weighted axial images. Two examiners evaluated the images and scored the conspicuity of the acute lesions. Results: Regardless of location, FLAIR provided the best lesion conspicuity in the detection of acute infarcts, followed by the GRASE sequence. In the posterior fossa, TSE and SE demonstrated the lesions better than GRASE and FLAIR techniques. In the detection of hemorrhagic elements within the ischemic region, TSE demonstrated statistically significant superiority over other sequences. Conclusion: In the detection of acute ischemic lesions in locations other than the posterior fossa, FLAIR provided the best lesion conspicuity among four T2-weighted sequences, including SE, TSE, GRASE and FLAIR. However, for the posterior fossa examination, preference of SE or TSE T2-weighted sequences is suggested.

  15. Comparison of MR sequences in early cerebral infarction at 0.5 T

    International Nuclear Information System (INIS)

    Saatci, I.; Baskan, O.; Cekirge, H.S.; Besim, A.

    2000-01-01

    To compare the diagnostic values of fluid-attenuated inversion recovery (FLAIR) and gradient spin-echo (GRASE) with those of conventional spin-echo (SE) and fast SE T2-weighted sequences in the evaluation of acute cerebrovascular lesions at 0.5 T. Material and Methods: Twenty-two consecutive patients with the clinical diagnosis of acute cerebrovascular accident were examined by MR imaging within the first 48 h of ictus. MR examination included 5-mm axial conventional SE and turbo SE (TSE) T2-weighted, dual-echo GRASE and FLAIR sequences. The patients also had pre- and postcontrast T1-weighted axial images. Two examiners evaluated the images and scored the conspicuity of the acute lesions. Results: Regardless of location, FLAIR provided the best lesion conspicuity in the detection of acute infarcts, followed by the GRASE sequence. In the posterior fossa, TSE and SE demonstrated the lesions better than GRASE and FLAIR techniques. In the detection of hemorrhagic elements within the ischemic region, TSE demonstrated statistically significant superiority over other sequences. Conclusion: In the detection of acute ischemic lesions in locations other than the posterior fossa, FLAIR provided the best lesion conspicuity among four T2-weighted sequences, including SE, TSE, GRASE and FLAIR. However, for the posterior fossa examination, preference of SE or TSE T2-weighted sequences is suggested

  16. Role of three-dimensional fluid-attenuated inversion recovery (3D FLAIR) and proton density magnetic resonance imaging for the detection and evaluation of lesion extent of focal cortical dysplasia in patients with refractory epilepsy

    International Nuclear Information System (INIS)

    Saini, Jitender; Kesavadas, Chandrasekharan; Thomas, Bejoy; Singh, Atampreet; Rathore, Chathurbhuj; Radhakrishnan, Ashalatha; Radhakrishnan, Kurupath; Bahuleyan, Biji

    2010-01-01

    Background: Focal cortical dysplasia (FCD) is often associated with epilepsy. Identification of FCD can be difficult due to subtle magnetic resonance imaging (MRI) changes. Though fluid-attenuated inversion recovery (FLAIR) sequence detects the majority of these lesions, smaller lesions may go unnoticed while larger lesions may be poorly delineated. Purpose: To determine the ability of a specialized epilepsy protocol in visualizing and delineating the extent of FCD. Material and Methods: We compared the imaging findings in nine patients with cortical malformation who underwent routine epilepsy MR imaging as well as a specialized epilepsy protocol. All imaging was done on a 1.5T MR unit. The specialized epilepsy protocol included 3D FLAIR in the sagittal plane as well as proton density (PD) and high-resolution T2-weighted (T2W) images in the transverse plane. Results: In all nine patients, the specialized protocol identified lesion anatomy better. In three patients in whom routine MRI was normal, the specialized epilepsy protocol including 3D FLAIR helped in identifying the lesions. One of these patients underwent surgery, and histo-pathology revealed a cortical dysplasia. In one patient, lesion characterization was improved, while in the remaining patients the extent of the FCD was more clearly demonstrated in the 3D FLAIR and PD images. Statistical analysis of images for cortical thickness, cortical signal intensity, adjacent white matter abnormalities, and gray-white matter junction showed significant statistical difference in the ability of 3D FLAIR to assess these aspects over conventional images. PD images were also found superior to the routine epilepsy protocol in assessment of cortical signal, adjacent white matter, and gray-white matter junction. Conclusion: Specialized MRI sequences and techniques should be performed whenever there is a high suspicion of cortical dysplasia, especially when they remain occult on conventional MR protocols. These techniques

  17. Comparison of T2 and FLAIR imaging for target delineation in high grade gliomas

    Directory of Open Access Journals (Sweden)

    Miller Robert W

    2010-01-01

    Full Text Available Abstract Background FLAIR and T2 weighted MRIs are used based on institutional preference to delineate high grade gliomas and surrounding edema for radiation treatment planning. Although these sequences have inherent physical differences there is limited data on the clinical and dosimetric impact of using either or both sequences. Methods 40 patients with high grade gliomas consecutively treated between 2002 and 2008 of which 32 had pretreatment MRIs with T1, T2 and FLAIR available for review were selected for this study. These MRIs were fused with the treatment planning CT. Normal structures, clinical tumor volume (CTV and planning tumor volume (PTV were then defined on the T2 and FLAIR sequences. A Venn diagram analysis was performed for each pair of tumor volumes as well as a fractional component analysis to assess the contribution of each sequence to the union volume. For each patient the tumor volumes were compared in terms of total volume in cubic centimeters as well as anatomic location using a discordance index. The overlap of the tumor volumes with critical structures was calculated as a measure of predicted toxicity. For patients with MRI documented failures, the tumor volumes obtained using the different sequences were compared with the recurrent gross tumor volume (rGTV. Results The FLAIR CTVs and PTVs were significantly larger than the T2 CTVs and PTVs (p Conclusions Although both T2 and FLAIR MRI sequences are used to define high grade glial neoplasm and surrounding edema, our results show that the volumes generated using these techniques are different and not interchangeable. These differences have bearing on the use of intensity modulated radiation therapy (IMRT and highly conformal treatment as well as on future clinical trials where the bias of using one technique over the other may influence the study outcome.

  18. CDNA encoding a polypeptide including a hevein sequence

    Science.gov (United States)

    Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

    1995-03-21

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74-79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  19. cDNA encoding a polypeptide including a hevein sequence

    Energy Technology Data Exchange (ETDEWEB)

    Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

    2000-07-04

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  20. Maturation of the limbic system revealed by MR FLAIR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Jacques F.; Vergesslich, Klara [University Children' s Hospital UKBB, Department of Paediatric Radiology, Basel (Switzerland)

    2007-04-15

    Cortical signal intensity (SI) of the limbic system in adults is known to be higher than in neocortical structures, but time-related changes in SI during childhood have not been described. To detect maturation-related SI changes within the limbic system using a fluid-attenuated inversion recovery (FLAIR) MR sequence. Twenty children (10 boys, 10 girls; age 3.5-18 years, mean 11.2 years) with no neurological abnormality and normal MR imaging examination were retrospectively selected. On two coronal FLAIR slices, ten regions of interest (ROI) with a constant area of 10 mm{sup 2} were manually placed in the archeocortex (hippocampus), periarcheocortex (parahippocampal gyrus, subcallosal area, cingulate gyrus) and in the neocortex at the level of the superior frontal gyrus on both sides. Significant SI gradients were observed with a higher intensity in the archeocortex, intermediate intensity in the periarcheocortex and low intensity in the neocortex. Significant higher SI values in hippocampal and parahippocampal structures were detected in children up to 10 years of age. These differences mainly reflected differences in cortical structure and myelination state. Archeocortical structures especially showed significant age-related intensity progression suggesting ongoing organization and/or myelination until early adolescence. (orig.)

  1. Thin isotropic FLAIR MR images at 1.5T increase the yield of focal cortical dysplasia transmantle sign detection in frontal lobe epilepsy.

    Science.gov (United States)

    Kokkinos, Vasileios; Kallifatidis, Alexandros; Kapsalaki, Eftychia Z; Papanikolaou, Nikolaos; Garganis, Kyriakos

    2017-05-01

    The transmantle sign is a distinctive imaging marker of focal cortical dysplasia (FCD) type II in frontal lobe epilepsy (FLE), which is revealed predominantly by fluid-attenuation inversion recovery (FLAIR) sequences. Although the transmantle sign detection yield is high by routine imaging protocols for epilepsy at 3T, most centers around the world have access to 1.5T MR technology and FLE patients often receive negative imaging reports. This study investigates the optimization of transmantle detection yield at 1.5T by introducing a 3D thin-slice isotropic FLAIR sequence in the epilepsy imaging protocol. Twenty FLE patients underwent diagnostic imaging for epilepsy with typical 2D thick-slice (3.0mm) coronal FLAIR sequences and a 3D thin-slice (1.0mm) isotropic FLAIR sequences at 1.5T, and transmantle sign detection yields and thickness measurements were derived. The 2D thick-slice FLAIR detected a transmantle sign in seven (35.0%) patients. The 3D isotropic thin-slice FLAIR detected a transmantle sign in eleven (55.0%) patients, thereby increasing the transmantle sign detection yield by 57.4%. The mean transmantle sign thickness by thick images was 12.3mm, by thin images was 8.9mm, and in the patients undetected by thick FLAIR was 3.5mm. This study showed that the extratemporal transmantle sign in FLE patients can be thin enough to be missed by thick-slice FLAIR sequences at 1.5T. By introducing 3D thin-slice isotropic FLAIR, false-negative reports can be reduced without reference for higher MR field structural scanning or other modalities, and more FLE patients can benefit from epilepsy surgery candidacy. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Comparison of T2 and FLAIR imaging for target delineation in high grade gliomas

    International Nuclear Information System (INIS)

    Stall, Bronwyn; Zach, Leor; Ning, Holly; Ondos, John; Arora, Barbara; Shankavaram, Uma; Miller, Robert W; Citrin, Deborah; Camphausen, Kevin

    2010-01-01

    FLAIR and T2 weighted MRIs are used based on institutional preference to delineate high grade gliomas and surrounding edema for radiation treatment planning. Although these sequences have inherent physical differences there is limited data on the clinical and dosimetric impact of using either or both sequences. 40 patients with high grade gliomas consecutively treated between 2002 and 2008 of which 32 had pretreatment MRIs with T1, T2 and FLAIR available for review were selected for this study. These MRIs were fused with the treatment planning CT. Normal structures, clinical tumor volume (CTV) and planning tumor volume (PTV) were then defined on the T2 and FLAIR sequences. A Venn diagram analysis was performed for each pair of tumor volumes as well as a fractional component analysis to assess the contribution of each sequence to the union volume. For each patient the tumor volumes were compared in terms of total volume in cubic centimeters as well as anatomic location using a discordance index. The overlap of the tumor volumes with critical structures was calculated as a measure of predicted toxicity. For patients with MRI documented failures, the tumor volumes obtained using the different sequences were compared with the recurrent gross tumor volume (rGTV). The FLAIR CTVs and PTVs were significantly larger than the T2 CTVs and PTVs (p < 0.0001 and p = 0.0001 respectively). Based on the discordance index, the abnormality identified using the different sequences also differed in location. Fractional component analysis showed that the intersection of the tumor volumes as defined on both T2 and FLAIR defined the majority of the union volume contributing 63.6% to the CTV union and 82.1% to the PTV union. T2 alone uniquely identified 12.9% and 5.2% of the CTV and PTV unions respectively while FLAIR alone uniquely identified 25.7% and 12% of the CTV and PTV unions respectively. There was no difference in predicted toxicity to normal structures using T2 or FLAIR. At the

  3. Cerebrospinal fluid changes after intravenous injection of gadolinium chelate: assessment by FLAIR MR imaging

    International Nuclear Information System (INIS)

    Bozzao, Alessandro; Floris, Roberto; Fasoli, Fabrizio; Simonetti, Giovanni; Fantozzi, Luigi Maria; Colonnese, Claudio

    2003-01-01

    Fluid-attenuated inversion recovery (FLAIR) sequence is currently used in clinical practice. Some reports emphasize the possibility that, in pathologic conditions, intravenous injection of gadolinium chelates may lead to an increased signal inside the cerebrospinal fluid (CSF). The aim of this study was to evaluate the presence of CSF signal changes in pathologic conditions causing blood-brain barrier disruption or neovascularization when imaging is performed after intravenous injection of gadolinium. We obtained FLAIR sequences after gadolinium injection from 33 patients affected by different intracranial pathologies and 10 control subjects. Patients were affected by ischemic stroke in the subacute phase, from 2 to 7 days from onset of symptoms (12 patients), meningiomas (8 patients), high-grade gliomas (5 patients), previous surgical procedures for intra-axial neoplasms (5 patients), and multiple sclerosis with active plaques (3 patients). Magnetic resonance imaging was performed in patients and controls using a 1.5-T magnet, using T2- and T1-weighted FLAIR sequences. The FLAIR sequence was acquired before and 1-3 h after injection of a standard dose of gadolinium. In those patients affected by ischemic lesions, FLAIR sequences were repeated the next days and 3-4 days later. The CSF signal was visually evaluated by two readers and scored from 0 to 3 depending by the degree of enhancement. The location of CSF signal changes (close to the lesion, hemispheric, or diffuse) was also considered. The CSF signal was markedly increased after 3 h from intravenous injection of gadolinium in all the patients with stroke, in those with previous surgery, and in those with high-grade gliomas whose neoplasm's surface was in contact with the subarachnoid spaces (SAS) or ventricles; a strong enhancement was also evident inside the necrotic component of the tumor. The CSF changes were more evident close to the pathology and/or in the hemisphere involved by the pathology. Moderate

  4. Comparative Analysis of Signal Intensity and Apparent Diffusion Coefficient at Varying b-values in the Brain : Diffusion Weighted-Echo Planar Image (T{sub 2} and FLAIR) Sequence

    Energy Technology Data Exchange (ETDEWEB)

    Oh, Jong Kap [Dept. of Radiology, Cheomdan Medical Center, Gwangju (Korea, Republic of); Im, Jung Yeol [Dept. of Digital Management Information Graduate School of Nambu Univesity, Gwangju (Korea, Republic of)

    2009-09-15

    Diffusion-weighted imaging (DWI) has been demonstrated to be a practical method for the diagnosis of various brain diseases such as acute infarction, brain tumor, and white matter disease. In this study, we used two techniques to examine the average signal intensity (SI) and apparent diffusion coefficient (ADC) of the brains of patients who ranged in age from 10 to 60 years. Our results indicated that the average SI was the highest in amygdala (as derived from DWI), whereas that in the cerebrospinal fluid was the lowest. The average ADC was the highest in the cerebrospinal fluid, whereas the lowest measurement was derived from the pons. The average SI and ADC were higher in T{sub 2}-DW-EPI than in FLAIR-DW-EPI. The higher the b-value, the smaller the average difference in both imaging techniques; the lower the b-value, the greater the average difference. Also, comparative analysis of the brains of patients who had experienced cerebral infarction showed no distinct lesion in the general MR image over time. However, there was a high SI in apparent weighted images. Analysis of other brain diseases (e.g., bleeding, acute, subacute, chronic infarction) indicated SI variance in accordance with characteristics of the two techniques. The higher the SI, the lower the ADC. Taken together, the value of SI and ADC in accordance with frequently occurring areas and various brain disease varies based on the b-value and imaging technique. Because they provide additional useful information in the diagnosis and treatment of patients with various brain diseases through signal recognition, the proper imaging technique and b-value are important for the detection and interpretation of subacute stroke and other brain diseases.

  5. New multispectral MRI data fusion technique for white matter lesion segmentation: method and comparison with thresholding in FLAIR images

    International Nuclear Information System (INIS)

    Del C Valdes Hernandez, Maria; Ferguson, Karen J.; Chappell, Francesca M.; Wardlaw, Joanna M.

    2010-01-01

    Brain tissue segmentation by conventional threshold-based techniques may have limited accuracy and repeatability in older subjects. We present a new multispectral magnetic resonance (MR) image analysis approach for segmenting normal and abnormal brain tissue, including white matter lesions (WMLs). We modulated two 1.5T MR sequences in the red/green colour space and calculated the tissue volumes using minimum variance quantisation. We tested it on 14 subjects, mean age 73.3 ± 10 years, representing the full range of WMLs and atrophy. We compared the results of WML segmentation with those using FLAIR-derived thresholds, examined the effect of sampling location, WML amount and field inhomogeneities, and tested observer reliability and accuracy. FLAIR-derived thresholds were significantly affected by the location used to derive the threshold (P = 0.0004) and by WML volume (P = 0.0003), and had higher intra-rater variability than the multispectral technique (mean difference ± SD: 759 ± 733 versus 69 ± 326 voxels respectively). The multispectral technique misclassified 16 times fewer WMLs. Initial testing suggests that the multispectral technique is highly reproducible and accurate with the potential to be applied to routinely collected clinical MRI data. (orig.)

  6. Flair MR imaging in the Detection of subarachnoid hemorrhage : comparison with CT and T1-weighted MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Min, Soo Hyun; Kim, Soo Youn; Lee, Ghi Jai; Shim, Jae Chan; Oh, Tae Kyung; Kim, Ho Kyun [College of Medicine, Jnje University, Seoul (Korea, Republic of)

    2000-03-01

    To compare the findings of fluid-attenuated inversion recovery (FLAIR) MR imaging in the detection of subarachnoid hemorrhage (SAH), with those of precontrast CT and T1-weighted MR imaging. In 13 patients (14 cases) with SAH, FLAIR MR images were retrospectively analyzed and compared with CT (10 patients, 11 cases) and T1-weighted MR images (9 cases). SAH was confirmed on the basis of high density along the subarachnoid space, as seen on precontrast CT, or lumbar puncture. MR imaging was performed on a 1.0T unit. FLAIR MR and CT images were obtained during the acute stage(less than 3 days after ictus) in 10 and 9 cases, respectively, during the subacute stage (4-14 days after ictus) in two cases and one, respectively, and during the chronic stage (more than 15 days after ictus) in two cases and one, respectively. CT was performed before FLAIR MR imaging, and the interval between CT and FLAIR ranged from 24 hours (6 cases) to 2-3 (2 cases) or 4-7 days (3 cases). In each study, the conspicuity of visualization of SAH was graded as excellent, good, fair, or negative at five locations (sylvian fissure, cortical sulci, anterior basal cistern, posterior basal cistern, and perimesencephalic cistern). In all cases, subarachnoid hemorrhages were demonstrated as high signal intensity areas on FLAIR images. The detection rates for SAH on CT and T1-weighted MR images were 100% (11/11) and 89% (8/9), respectively. FLAIR was superior to T1-weighted imaging in the detection of SAH at all sites except the anterior basal cistern (p less than 0.05) and superior to CT in the detection of SAH at the cortical sulci (p less than 0.05). On FLAIR MR images, subarachnoid hemorrhages at all stages are demonstrated as high signal intensity areas; the FLAIR MR sequence is thus considered useful in the detection of SAH. In particular FLAIR is more sensitive than CT for the detection of SAH in the cortical sulci. (author)

  7. Qualitative and quantitative comparison of contrast-enhanced fluid-attenuated inversion recovery, magnetization transfer spin echo, and fat-saturation T1-weighted sequences in infectious meningitis

    Energy Technology Data Exchange (ETDEWEB)

    Azad, Rajiv; Tayal, Mohit; Azad, Sheenam; Sharma, Garima; Srivastava, Rajendra Kumar [SGRR Institute of Medical and Health Sciences, Patel Nagar, Dehradun (India)

    2017-11-15

    To compare the contrast-enhanced fluid-attenuated inversion recovery (CE-FLAIR), the CE T1-weighted (CE-T1W) sequence with fat suppression (FS) and magnetization transfer (MT) for early detection and characterization of infectious meningitis. Fifty patients and 10 control subjects were evaluated with the CE-FLAIR and the CE-T1W sequences with FS and MT. Qualitative assessment was done by two observers for presence and grading of abnormal leptomeningeal enhancement. Quantitative assessment included computation of net meningeal enhancement, using single pixel signal intensity software. A newly devised FLAIR based scoring system, based on certain imaging features including ventricular dilatation, ependymal enhancement, infarcts and subdural effusions was used to indicate the etiology. Data were analysed using the Student's t test, Cohen's Kappa coefficient, Pearson's correlation coefficient, the intraclass correlation coefficient, one way analysis of variance, and Fisher's exact test with Bonferroni correction as the post hoc test. The CE-FLAIR sequence demonstrated a better sensitivity (100%), diagnostic accuracy (95%), and a stronger correlation with the cerebrospinal fluid, total leukocyte count (r = 0.75), protein (r = 0.77), adenosine deaminase (r = 0.81) and blood glucose (r = -0.6) values compared to the CE-T1W sequences. Qualitative grades and quantitative meningeal enhancement on the CE-FLAIR sequence were also significantly greater than those on the other sequences. The FLAIR based scoring system yielded a diagnostic accuracy of 91.6% and a sensitivity of 96%. A strong inverse Pearson's correlation (r = -0.95) was found between the assigned score and patient's Glasgow Coma Scale at the time of admission. The CE-FLAIR sequence is better suited for evaluating infectious meningitis and could be included as a part of the routine MR imaging protocol.

  8. Qualitative and quantitative comparison of contrast-enhanced fluid-attenuated inversion recovery, magnetization transfer spin echo, and fat-saturation T1-weighted sequences in infectious meningitis

    International Nuclear Information System (INIS)

    Azad, Rajiv; Tayal, Mohit; Azad, Sheenam; Sharma, Garima; Srivastava, Rajendra Kumar

    2017-01-01

    To compare the contrast-enhanced fluid-attenuated inversion recovery (CE-FLAIR), the CE T1-weighted (CE-T1W) sequence with fat suppression (FS) and magnetization transfer (MT) for early detection and characterization of infectious meningitis. Fifty patients and 10 control subjects were evaluated with the CE-FLAIR and the CE-T1W sequences with FS and MT. Qualitative assessment was done by two observers for presence and grading of abnormal leptomeningeal enhancement. Quantitative assessment included computation of net meningeal enhancement, using single pixel signal intensity software. A newly devised FLAIR based scoring system, based on certain imaging features including ventricular dilatation, ependymal enhancement, infarcts and subdural effusions was used to indicate the etiology. Data were analysed using the Student's t test, Cohen's Kappa coefficient, Pearson's correlation coefficient, the intraclass correlation coefficient, one way analysis of variance, and Fisher's exact test with Bonferroni correction as the post hoc test. The CE-FLAIR sequence demonstrated a better sensitivity (100%), diagnostic accuracy (95%), and a stronger correlation with the cerebrospinal fluid, total leukocyte count (r = 0.75), protein (r = 0.77), adenosine deaminase (r = 0.81) and blood glucose (r = -0.6) values compared to the CE-T1W sequences. Qualitative grades and quantitative meningeal enhancement on the CE-FLAIR sequence were also significantly greater than those on the other sequences. The FLAIR based scoring system yielded a diagnostic accuracy of 91.6% and a sensitivity of 96%. A strong inverse Pearson's correlation (r = -0.95) was found between the assigned score and patient's Glasgow Coma Scale at the time of admission. The CE-FLAIR sequence is better suited for evaluating infectious meningitis and could be included as a part of the routine MR imaging protocol

  9. Subcallosal Striations: the Role of FLAIR MR Imaging in Detecting ...

    African Journals Online (AJOL)

    FLAIR) in detection of subcallosal striations in clinical Multiple sclerosis (MS) patients and determine its role as a good noninvasive tool for the diagnosis of this disease. Material and Method: Forty patients with clinically proved MS were examined ...

  10. Contributions of an adiabatic initial inversion pulse and K-space Re-ordered by inversion-time at each slice position (KRISP) to control of CSF artifacts and visualization of the brain in FLAIR magnetic resonance imaging

    Energy Technology Data Exchange (ETDEWEB)

    Curati, Walter L.; Oatridge, Angela; Herlihy, Amy H.; Hajnal, Joseph V.; Puri, Basant K.; Bydder, Graeme M

    2001-05-01

    AIM: The aim of this study was to compare the performance of three fluid attenuated inversion recovery (FLAIR) pulse sequences for control of cerebrospinal fluid (CSF) and blood flow artifacts in imaging of the brain. The first of these sequences had an initial sinc inversion pulse which was followed by conventional k-space mapping. The second had an initial sinc inversion pulse followed by k-space re-ordered by inversion time at each slice position (KRISP) and the third had an adiabatic initial inversion pulse followed by KRISP. MATERIALS AND METHODS: Ten patients with established disease were studied with all three pulse sequences. Seven were also studied with the adiabatic KRISP sequence after contrast enhancement. Their images were evaluated for patient motion artifact, CSF and blood flow artifact as well as conspicuity of the cortex, meninges, ventricular system, brainstem and cerebellum. The conspicuity of lesions and the degree of enhancement were also evaluated. RESULTS: Both the sinc and adiabatic KRISP FLAIR sequences showed better control of CSF and blood flow artifacts than the conventional FLAIR sequence. In addition the adiabatic KRISP FLAIR sequence showed better control of CSF artifact at the inferior aspect of the posterior fossa. The lesion conspicuity was similar for each of the FLAIR sequences as was the degree of contrast enhancement to that shown with a T{sub 1}weighted spin echo sequence. CONCLUSION: The KRISP FLAIR sequence controls high signal artifacts from CSF flow and blood flow and the adiabatic pulse controls high signal artifacts due to inadequate inversion of the CSF magnetization at the periphery of the head transmitter coil. The KRISP FLAIR sequence also improves cortical and meningeal definition as a result of an edge enhancement effect. The effects are synergistic and can be usefully combined in a single pulse sequence. Curati, W.L. et al. (2001)

  11. Three-dimensional fluid-attenuated inversion recovery sequence for visualisation of subthalamic nucleus for deep brain stimulation in Parkinson's disease

    Energy Technology Data Exchange (ETDEWEB)

    Heo, Young Jin [University of Ulsan College of Medicine, Asan Medical Center, Department of Radiology, Research Institute of Radiology, Seoul (Korea, Republic of); Inje University, Department of Radiology, Busan Paik Hospital, Busan (Korea, Republic of); Kim, Sang Joon; Kim, Ho Sung; Choi, Choong Gon; Jung, Seung Chai [University of Ulsan College of Medicine, Asan Medical Center, Department of Radiology, Research Institute of Radiology, Seoul (Korea, Republic of); Lee, Jung Kyo [University of Ulsan College of Medicine, Asan Medical Center, Department of Neurosurgery, Seoul (Korea, Republic of); Lee, Chong Sik; Chung, Sun J. [University of Ulsan College of Medicine, Asan Medical Center, Department of Neurology, Seoul (Korea, Republic of); Cho, So Hyun [Department of Radiology, Busan (Korea, Republic of); Lee, Gyoung Ro [Philips HealthCare Korea, Seoul (Korea, Republic of)

    2015-09-15

    Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is an accepted treatment for advanced Parkinson's disease (PD). However, targeting the STN is difficult due to its relatively small size and variable location. The purpose of this study was to assess which of the following sequences obtained with the 3.0 T MR system can accurately delineate the STN: coronal 3D fluid-attenuated inversion recovery (FLAIR), 2D T2*-weighted fast-field echo (T2*-FFE) and 2D T2-weighted turbo spin-echo (TSE) sequences. We included 20 consecutive patients with PD who underwent 3.0 T MR for DBS targeting. 3D FLAIR, 2D T2*-FFE and T2-TSE images were obtained for all study patients. Image quality and demarcation of the STN were analysed using 4-point scales, and contrast ratio (CR) of the STN and normal white matter was calculated. The Friedman test was used to compare the three sequences. In qualitative analysis, the 2D T2*-FFE image showed more artefacts than 3D FLAIR or 2D T2-TSE, but the difference did not reach statistical significance. 3D FLAIR images showed significantly superior demarcation of the STN compared with 2D T2*-FFE and T2-TSE images (P < 0.001, respectively). The CR of 3D FLAIR was significantly higher than that of 2D T2*-FFE or T2-TSE images in multiple comparison correction (P < 0.001), but there was no significant difference in the CR between 2D T2*-FFE and T2-TSE images. Coronal 3D FLAIR images showed the most accurate demarcation of the STN for DBS targeting among coronal 3D FLAIR, 2D T2*-FFE and T2-TSE images. (orig.)

  12. Three-dimensional fluid-attenuated inversion recovery sequence for visualisation of subthalamic nucleus for deep brain stimulation in Parkinson's disease

    International Nuclear Information System (INIS)

    Heo, Young Jin; Kim, Sang Joon; Kim, Ho Sung; Choi, Choong Gon; Jung, Seung Chai; Lee, Jung Kyo; Lee, Chong Sik; Chung, Sun J.; Cho, So Hyun; Lee, Gyoung Ro

    2015-01-01

    Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is an accepted treatment for advanced Parkinson's disease (PD). However, targeting the STN is difficult due to its relatively small size and variable location. The purpose of this study was to assess which of the following sequences obtained with the 3.0 T MR system can accurately delineate the STN: coronal 3D fluid-attenuated inversion recovery (FLAIR), 2D T2*-weighted fast-field echo (T2*-FFE) and 2D T2-weighted turbo spin-echo (TSE) sequences. We included 20 consecutive patients with PD who underwent 3.0 T MR for DBS targeting. 3D FLAIR, 2D T2*-FFE and T2-TSE images were obtained for all study patients. Image quality and demarcation of the STN were analysed using 4-point scales, and contrast ratio (CR) of the STN and normal white matter was calculated. The Friedman test was used to compare the three sequences. In qualitative analysis, the 2D T2*-FFE image showed more artefacts than 3D FLAIR or 2D T2-TSE, but the difference did not reach statistical significance. 3D FLAIR images showed significantly superior demarcation of the STN compared with 2D T2*-FFE and T2-TSE images (P < 0.001, respectively). The CR of 3D FLAIR was significantly higher than that of 2D T2*-FFE or T2-TSE images in multiple comparison correction (P < 0.001), but there was no significant difference in the CR between 2D T2*-FFE and T2-TSE images. Coronal 3D FLAIR images showed the most accurate demarcation of the STN for DBS targeting among coronal 3D FLAIR, 2D T2*-FFE and T2-TSE images. (orig.)

  13. Approach to include load sequence effects in the design of an offshore wind turbine substructure

    NARCIS (Netherlands)

    Dragt, R.C.; Allaix, D.L.; Maljaars, J.; Tuitman, J.T.; Salman, Y.; Otheguy, M.E.

    2017-01-01

    Fatigue is one of the main design drivers for offshore wind substructures. Using Fracture Mechanics methods, load sequence effects such as crack growth retardation due to large load peaks can be included in the fatigue damage estimation. Due to the sequence dependency, a method is required that

  14. Ivy signs on FLAIR images before and after STA-MCA anastomosis in patients with Moyamoya disease

    International Nuclear Information System (INIS)

    Ideguchi, Reiko; Enokizono, Mikako; Uetani, Masataka; Morikawa, Minoru; Ogawa, Yoji; Nagata, Izumi

    2011-01-01

    Background: Leptomeningeal high signal intensity (ivy sign) on fluid-attenuated inversion-recovery (FLAIR) MR imaging is one of the features of Moyamoya disease. However, the correlation between ivy sign and cerebral perfusion status has not been fully evaluated. Purpose: To characterize ivy sign on FLAIR images in Moyamoya disease and compare this finding with hemodynamic alterations on perfusion single-photon emission CT (SPECT) obtained before and after bypass surgery. Material and Methods: Sixteen patients with angiographically confirmed Moyamoya disease who underwent superficial temporal artery-middle cerebral artery (STA-MCA) anastomosis were included in the study. The presence of ivy sign on FLAIR images was classified as 'negative', 'minimal' and 'positive'. We evaluated the relationship between ivy sign and findings of SPECT, including cerebral vascular reserve (CVR) before and after surgery. Results: Minimal or positive ivy sign was seen in 13 (81%) of 16 patients, and 21 (66%) of 32 hemispheres. CVR in the areas with positive or minimal ivy sign was lower than that in the areas with negative ivy sign. After STA-MCA anastomosis, ivy sign disappeared or decreased in all 21 hemispheres demonstrating ivy sign. SPECT demonstrated apparent hemodynamic improvement in areas demonstrating disappearance or decrease of ivy sign. Conclusion: Ivy sign on FLAIR image is seen in areas with decreased cerebral perfusion. The sign is useful for non-invasive assessment of cerebral hemodynamic status before and after surgery

  15. Evaluation of prospective motion correction of high-resolution 3D-T2-FLAIR acquisitions in epilepsy patients.

    Science.gov (United States)

    Vos, Sjoerd B; Micallef, Caroline; Barkhof, Frederik; Hill, Andrea; Winston, Gavin P; Ourselin, Sebastien; Duncan, John S

    2018-03-02

    T2-FLAIR is the single most sensitive MRI contrast to detect lesions underlying focal epilepsies but 3D sequences used to obtain isotropic high-resolution images are susceptible to motion artefacts. Prospective motion correction (PMC) - demonstrated to improve 3D-T1 image quality in a pediatric population - was applied to high-resolution 3D-T2-FLAIR scans in adult epilepsy patients to evaluate its clinical benefit. Coronal 3D-T2-FLAIR scans were acquired with a 1mm isotropic resolution on a 3T MRI scanner. Two expert neuroradiologists reviewed 40 scans without PMC and 40 with navigator-based PMC. Visual assessment addressed six criteria of image quality (resolution, SNR, WM-GM contrast, intensity homogeneity, lesion conspicuity, diagnostic confidence) on a seven-point Likert scale (from non-diagnostic to outstanding). SNR was also objectively quantified within the white matter. PMC scans had near-identical scores on the criteria of image quality to non-PMC scans, with the notable exception that intensity homogeneity was generally worse. Using PMC, the percentage of scans with bad image quality was substantially lower than without PMC (3.25% vs. 12.5%) on the other five criteria. Quantitative SNR estimates revealed that PMC and non-PMC had no significant difference in SNR (p=0.07). Application of prospective motion correction to 3D-T2-FLAIR sequences decreased the percentage of low-quality scans, reducing the number of scans that need to be repeated to obtain clinically useful data. Copyright © 2018. Published by Elsevier Masson SAS.

  16. Should abdominal sequences be included in prostate cancer MR staging studies?

    Energy Technology Data Exchange (ETDEWEB)

    McEvoy, S.H., E-mail: sineadhmcevoy@gmail.com [Department of Radiology, St. Vincent' s University Hospital, Dublin 4 (Ireland); Lavelle, L.P.; Purcell, Y.M. [Department of Radiology, St. Vincent' s University Hospital, Dublin 4 (Ireland); Quinlan, D.M. [Department of Urology, St. Vincent' s University Hospital, Dublin 4 (Ireland); Skehan, S.J.; Collins, C.D.; McMahon, C.J. [Department of Radiology, St. Vincent' s University Hospital, Dublin 4 (Ireland)

    2015-06-15

    Highlights: • ESUR guideline that abdominal MR sequences are reserved for high-risk prostate cancer is tested. • Routine abdominal sequences are of low yield in prostate cancer MR staging. • Routine abdominal staging sequences frequently result in incidental findings. • Abdominal staging sequences should be reserved for high-risk prostate cancer cases. - Abstract: Objectives: Prostate cancer staging MR examinations commonly include abdominal sequences to assess for non-regional (common iliac or para-aortic) nodal metastasis. In our experience the diagnostic yield of this is limited, but incidental findings are frequent, often necessitating further investigations. The aim of this study is to assess the diagnostic utility of abdominal sequences in routine prostate cancer MR staging studies. Methods: Findings on abdominal sequences of consecutive MRI prostate studies performed for staging newly diagnosed prostate cancer between September 2011 and September 2013 were reviewed with respect to adenopathy and additional incidental findings. Results were correlated with Gleason grade and serum prostate-specific antigen (PSA) level in each case. Results: 355 MRI prostate examinations were reviewed. 4 (1.1%) showed enlarged non-regional lymph nodes. Incidental findings were found in 82(23.1%) cases, neccessitating further investigation in 45 (12.7%) cases. Enlarged non-regional nodes were associated with higher PSA level and Gleason grade (p = 0.007, p = 0.005 respectively). With a combined threshold of PSA > 20 ng/mL and/or Gleason grade ≥8 the sensitivity, specificity, PPV and NPV were 100, 60, 3 and 100% respectively for predicting the presence of non-regional adenopathy. Conclusions: Routine abdominal sequences are of very low yield in routine prostate cancer MR staging, frequently resulting in incidental findings requiring further work-up and should be reserved for high-risk cases. Our experience supports the use of an abdominal staging sequence in high

  17. Post-trial sleep sequences including transition sleep are involved in avoidance learning of adult rats.

    Science.gov (United States)

    Mandile, P; Vescia, S; Montagnese, P; Piscopo, S; Cotugno, M; Giuditta, A

    2000-07-01

    High resolution computerized EEG analyses, and behavioral observations were used to identify slow wave sleep (SS), paradoxical sleep (PS) and transition sleep (TS) in adult male Wistar rats exposed to a session of two-way active avoidance training. Of the four sleep sequences that could be identified, two included TS (SS-->TS-->W and SS-->TS-->PS), while the other two did not (SS-->W and SS-->PS). Comparison of post-trial sleep variables between fast learning rats (FL, reaching criterion in the training session), slow learning rats (SL, reaching criterion in the retention session the following day), and non learning rats (NL, failing to reach criterion) indicated that the total amounts of SS, TS and PS of the SS-->TS-->PS sequence was markedly higher in FL rats than in SL rats. In addition, in comparison with the corresponding baseline period, the average duration and total amount of SS and TS episodes of the SS-->TS-->PS sequence increased in FL rats, while the number of SS-->TS-->W sequences decreased. On the other hand, the average duration of SS episodes increased in the SS-->TS-->W and SS-->W sequences of SL rats, and in the SS-->W and SS-->TS-->PS sequences of NL rats. Correlative analyses between number of avoidances and post-trial sleep variables demonstrated that avoidances were directly correlated with the duration of SS episodes of the SS-->TS-->PS sequence and with the duration of TS episodes of the SS-->TS-->W sequence, but inversely correlated with the number and amount of SS episodes of the SS-->W sequence and with the duration and amount of SS episodes of the SS-->PS sequence. On the whole, the data supported the view that TS-containing sleep sequences are involved in long-term storage of novel adaptive behavior, while sleep sequences lacking TS are involved in the maintenance of innate behavioral responses.

  18. MRI diagnosis of traumatic fornical injury. Investigation utilizing FLAIR Technique

    International Nuclear Information System (INIS)

    Asai, Toshiharu; Kataoka, Kazuo; Uejima, Toshifumi; Maruyama, Jiro; Sakata, Ikuhiro; Taneda, Mamoru

    1996-01-01

    We studied traumatic fornix injuries by using the fluid attenuated inversion recovery (FLAIR) technique which provides T 2 -weighted images without the unwanted influence of cerebrospinal fluid (CSF) signals. 5-21 days (average: 10.3) after injury, we performed MRI on 14 patients (mean age: 22.6 years) who were clinically diagnosed as having diffuse axonal injury (DAI). The mid-sagittal FLAIR images in seven of the 14 patients clearly revealed T 2 -prolonged fornix lesions and the concurrent corpus callosum lesions. The same fornix lesions, as detected by the spin echo technique, were blurred by the partial volume effects and motion artifacts derived from the surrounding CSF signals. The accompanying callosal lesions were mainly in the splenium. Of the seven patients with fornix injuries, three had T 2 -prolonged lesions in the septum pellucidum. With respect to the outcome, there was no difference between patients with and without fornix injury. In conclusion, the FLAIR technique is appropriate for detecting fornix injuries adjacent to the CSF space. (author)

  19. MRI diagnosis of traumatic fornical injury. Investigation utilizing FLAIR Technique

    Energy Technology Data Exchange (ETDEWEB)

    Asai, Toshiharu; Kataoka, Kazuo; Uejima, Toshifumi; Maruyama, Jiro; Sakata, Ikuhiro; Taneda, Mamoru [Kinki Univ., Sayama, Osaka (Japan) School of Medicine

    1996-06-01

    We studied traumatic fornix injuries by using the fluid attenuated inversion recovery (FLAIR) technique which provides T{sub 2}-weighted images without the unwanted influence of cerebrospinal fluid (CSF) signals. 5-21 days (average: 10.3) after injury, we performed MRI on 14 patients (mean age: 22.6 years) who were clinically diagnosed as having diffuse axonal injury (DAI). The mid-sagittal FLAIR images in seven of the 14 patients clearly revealed T{sub 2}-prolonged fornix lesions and the concurrent corpus callosum lesions. The same fornix lesions, as detected by the spin echo technique, were blurred by the partial volume effects and motion artifacts derived from the surrounding CSF signals. The accompanying callosal lesions were mainly in the splenium. Of the seven patients with fornix injuries, three had T{sub 2}-prolonged lesions in the septum pellucidum. With respect to the outcome, there was no difference between patients with and without fornix injury. In conclusion, the FLAIR technique is appropriate for detecting fornix injuries adjacent to the CSF space. (author)

  20. Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus

    Directory of Open Access Journals (Sweden)

    Boore Jeffrey L

    2007-06-01

    Full Text Available Abstract Background The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is often useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the genomes reported here: Nuphar advena (from a basal-most lineage and Ranunculus macranthus (a basal eudicot. We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs and longer dispersed repeats (SDR, and patterns of nucleotide composition. Results The Nuphar [GenBank:NC_008788] and Ranunculus [GenBank:NC_008796] plastid genomes share characteristics of gene content and organization with many other chloroplast genomes. Like other plastid genomes, these genomes are A+T-rich, except for rRNA and tRNA genes. Detailed comparisons of Nuphar with Nymphaea, another Nymphaeaceae, show that more than two-thirds of these genomes exhibit at least 95% sequence identity and that most SSRs are shared. In broader comparisons, SSRs vary among genomes in terms of abundance and length and most contain repeat motifs based on A and T nucleotides. Conclusion SSR and SDR abundance varies by genome and, for SSRs, is proportional to genome size. Long SDRs are rare in the genomes assessed. SSRs occur less frequently than predicted and, although the majority of the repeat motifs do include A and T nucleotides, the A+T bias in SSRs is less than that predicted from the underlying genomic nucleotide composition. In codon usage third positions show an A+T bias, however variation in codon usage does not correlate with differences in A+T-richness. Thus, although plastome nucleotide composition shows "A

  1. Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus.

    Science.gov (United States)

    Raubeson, Linda A; Peery, Rhiannon; Chumley, Timothy W; Dziubek, Chris; Fourcade, H Matthew; Boore, Jeffrey L; Jansen, Robert K

    2007-06-15

    The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is often useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (a basal eudicot). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition. The Nuphar [GenBank:NC_008788] and Ranunculus [GenBank:NC_008796] plastid genomes share characteristics of gene content and organization with many other chloroplast genomes. Like other plastid genomes, these genomes are A+T-rich, except for rRNA and tRNA genes. Detailed comparisons of Nuphar with Nymphaea, another Nymphaeaceae, show that more than two-thirds of these genomes exhibit at least 95% sequence identity and that most SSRs are shared. In broader comparisons, SSRs vary among genomes in terms of abundance and length and most contain repeat motifs based on A and T nucleotides. SSR and SDR abundance varies by genome and, for SSRs, is proportional to genome size. Long SDRs are rare in the genomes assessed. SSRs occur less frequently than predicted and, although the majority of the repeat motifs do include A and T nucleotides, the A+T bias in SSRs is less than that predicted from the underlying genomic nucleotide composition. In codon usage third positions show an A+T bias, however variation in codon usage does not correlate with differences in A+T-richness. Thus, although plastome nucleotide composition shows "A+T richness", an A+T bias is not apparent upon more in

  2. DNA sequence analyses of blended herbal products including synthetic cannabinoids as designer drugs.

    Science.gov (United States)

    Ogata, Jun; Uchiyama, Nahoko; Kikura-Hanajiri, Ruri; Goda, Yukihiro

    2013-04-10

    In recent years, various herbal products adulterated with synthetic cannabinoids have been distributed worldwide via the Internet. These herbal products are mostly sold as incense, and advertised as not for human consumption. Although their labels indicate that they contain mixtures of several potentially psychoactive plants, and numerous studies have reported that they contain a variety of synthetic cannabinoids, their exact botanical contents are not always clear. In this study, we investigated the origins of botanical materials in 62 Spice-like herbal products distributed on the illegal drug market in Japan, by DNA sequence analyses and BLAST searches. The nucleotide sequences of four regions were analyzed to identify the origins of each plant species in the herbal mixtures. The sequences of "Damiana" (Turnera diffusa) and Lamiaceae herbs (Mellissa, Mentha and Thymus) were frequently detected in a number of products. However, the sequences of other plant species indicated on the packaging labels were not detected. In a few products, DNA fragments of potent psychotropic plants were found, including marijuana (Cannabis sativa), "Diviner's Sage" (Salvia divinorum) and "Kratom" (Mitragyna speciosa). Their active constituents were also confirmed using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS), although these plant names were never indicated on the labels. Most plant species identified in the products were different from the plants indicated on the labels. The plant materials would be used mainly as diluents for the psychoactive synthetic compounds, because no reliable psychoactive effects have been reported for most of the identified plants, with the exception of the psychotropic plants named above. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  3. Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores.

    Science.gov (United States)

    de Boer, Paulo; Caspers, Martien; Sanders, Jan-Willem; Kemperman, Robèr; Wijman, Janneke; Lommerse, Gijs; Roeselers, Guus; Montijn, Roy; Abee, Tjakko; Kort, Remco

    2015-01-01

    Spoilage of food products is frequently caused by bacterial spores and lactic acid bacteria. Identification of these organisms by classic cultivation methods is limited by their ability to form colonies on nutrient agar plates. In this study, we adapted and optimized 16S rRNA amplicon sequencing for quantification of bacterial spores in a canned food matrix and for monitoring the outgrowth of spoilage microbiota in a ready-to-eat food matrix. The detection limit of bar-coded 16S rRNA amplicon sequencing was determined for the number of bacterial spores in a canned food matrix. Analysis of samples from a canned food matrix spiked with a mixture of equinumerous spores from the thermophiles, Geobacillus stearothermophilus and Geobacillus thermoglucosidans, and the mesophiles, Bacillus sporothermodurans, Bacillus cereus, and Bacillus subtilis, led to the detection of these spores with an average limit of 2 × 10(2) spores ml(-1). The data were normalized by setting the number of sequences resulting from DNA of an inactivated bacterial species, present in the matrix at the same concentration in all samples, to a fixed value for quantitative sample-to-sample comparisons. The 16S rRNA amplicon sequencing method was also employed to monitor population dynamics in a ready-to-eat rice meal, incubated over a period of 12 days at 7 °C. The most predominant outgrowth was observed by the genera Leuconostoc, Bacillus, and Paenibacillus. Analysis of meals pre-treated with weak acids showed inhibition of outgrowth of these three genera. The specificity of the amplicon synthesis was improved by the design of oligonucleotides that minimize the amplification of 16S rRNA genes from chloroplasts originating from plant-based material present in the food. This study shows that the composition of complex spoilage populations, including bacterial spores, can be monitored in complex food matrices by bar-coded amplicon sequencing in a quantitative manner. In order to allow sample

  4. Utility of coronal contrast-enhanced fat-suppressed FLAIR in the evaluation of optic neuropathy and atrophy

    Directory of Open Access Journals (Sweden)

    Kevin H. Boegel

    Full Text Available Background and purpose: Evaluating chronic sequelae of optic neuritis, such as optic neuropathy with or without optic nerve atrophy, can be challenging on whole brain MRI. This study evaluated the utility of dedicated coronal contrast-enhanced fat-suppressed FLAIR (CE-FS-FLAIR MR imaging to detect optic neuropathy and optic nerve atrophy. Materials and methods: Over 4.5 years, a 3 mm coronal CE-FS-FLAIR sequence at 1.5T was added to the routine brain MRIs of 124 consecutive patients, 102 of whom had suspected or known demyelinating disease. Retrospective record reviews confirmed that 28 of these 102 had documented onset of optic neuritis >4 weeks prior to the brain MRI. These 28 were compared to the other 22 (“controls” of the 124 patients who lacked a history of demyelinating disease or visual symptoms. Using coronal CE-FS-FLAIR, two neuroradiologists separately graded each optic nerve (n = 50 patients, 100 total nerves as either negative, equivocal, or positive for optic neuropathy or atrophy. The scoring was later repeated. Results: The mean time from acute optic neuritis onset to MRI was 4.1 ± 4.6 years (range 34 days-17.4 years. Per individual nerve grading, the range of sensitivity, specificity, and accuracy of coronal CE-FS-FLAIR in detecting optic neuropathy was 71.4–77.1%, 93.8–95.4%, and 85.5–89.0%, respectively, with strong interobserver (k = 0.667 − 0.678, p < 0.0001, and intraobserver (k = 0.706 − 0.763, p < 0.0001 agreement. For optic atrophy, interobserver agreement was moderate (k = 0.437 − 0.484, p < 0.0001, while intraobserver agreement was moderate-strong (k = 0.491 − 0.596, p < 0.0001. Conclusion: Coronal CE-FS-FLAIR is quite specific in detecting optic neuropathy years after the onset of acute optic neuritis, but is less useful in detecting optic nerve atrophy. Keywords: Optic

  5. Morphological features of MS lesions on FLAIR* at 7 T and their relation to patient characteristics

    NARCIS (Netherlands)

    Kilsdonk, I.D.; Lopez Soriano, A.; Kuijer, J.P.A.; de Graaf, W.L.; Castelijns, J.A.; Polman, C.H.; Luijten, P.R.; Geurts, J.J.G.; Barkhof, F.; Wattjes, M.P.

    2014-01-01

    Recently, a new MRI technique was developed at 3 Tesla (T), called fluid attenuated inversion recovery (FLAIR). In this study, we implemented FLAIR in an existing MS cohort at 7 T, to investigate whether we could corroborate results of previous 7 T studies that introduced specific MS lesion

  6. cDNA encoding a polypeptide including a hev ein sequence

    Energy Technology Data Exchange (ETDEWEB)

    Raikhel, Natasha V. (Okemos, MI); Broekaert, Willem F. (Dilbeek, BE); Chua, Nam-Hai (Scarsdale, NY); Kush, Anil (New York, NY)

    2000-07-04

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74-79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  7. Improved differentiation between MS and vascular brain lesions using FLAIR* at 7 Tesla

    Energy Technology Data Exchange (ETDEWEB)

    Kilsdonk, Iris D.; Wattjes, Mike P.; Lopez-Soriano, Alexandra; Jong, Marcus C. de; Graaf, Wolter L. de; Conijn, Mandy M.A.; Barkhof, Frederik [VU University Medical Center, Department of Radiology, De Boelelaan 1118, HZ, Amsterdam (Netherlands); Kuijer, Joost P.A. [VU University Medical Center, Department of Physics and Medical Technology, Amsterdam (Netherlands); Polman, Chris H. [VU University Medical Center, Department of Neurology, Amsterdam (Netherlands); Luijten, Peter R. [University Medical Center, Department of Radiology, Utrecht (Netherlands); Geurts, Jeroen J.G. [VU University, Department of Anatomy and Neurosciences, Amsterdam (Netherlands); Geerlings, Mirjam I. [University Medical Center, Julius Center for Health Sciences and Primary Care, Utrecht (Netherlands)

    2014-04-15

    To investigate whether a new magnetic resonance image (MRI) technique called T2*-weighted fluid attenuation inversion recovery (FLAIR*) can differentiate between multiple sclerosis (MS) and vascular brain lesions, at 7 Tesla (T). We examined 16 MS patients and 16 age-matched patients with (risk factors for) vascular disease. 3D-FLAIR and T2*-weighted images were combined into FLAIR* images. Lesion type and intensity, perivascular orientation and presence of a hypointense rim were analysed. In total, 433 cerebral lesions were detected in MS patients versus 86 lesions in vascular patients. Lesions in MS patients were significantly more often orientated in a perivascular manner: 74 % vs. 47 % (P < 0.001). Ten MS lesions (2.3 %) were surrounded by a hypointense rim on FLAIR*, and 24 MS lesions (5.5 %) were hypointense on T2*. No lesions in vascular patients showed any rim or hypointensity. Specificity of differentiating MS from vascular lesions on 7-T FLAIR* increased when the presence of a central vessel was taken into account (from 63 % to 88 %), most obviously for deep white matter lesions (from 69 % to 94 %). High sensitivity remained (81 %). 7-T FLAIR* improves differentiation between MS and vascular lesions based on lesion location, perivascular orientation and presence of hypointense (rims around) lesions. circle A new MRI technique T2*-weighted fluid attenuation inversion recovery (FLAIR*) was investigated. circle FLAIR* at 7-T MRI combines FLAIR and T2* images into a single image. circle FLAIR* at 7 T does not require enhancement with contrast agents. (orig.)

  8. The Optimization of Magnetic Resonance Imaging Pulse Sequences in Order to Better Detection of Multiple Sclerosis Plaques

    Directory of Open Access Journals (Sweden)

    Farshidfar Z.

    2017-09-01

    Full Text Available Background and objective: Magnetic resonance imaging (MRI is the most sensitive technique to detect multiple sclerosis (MS plaques in central nervous system. In some cases, the patients who were suspected to MS, Whereas MRI images are normal, but whether patients don’t have MS plaques or MRI images are not enough optimized enough in order to show MS plaques? The aim of the current study is evaluating the efficiency of different MRI sequences in order to better detection of MS plaques. Materials and methods: In this cross-sectional study which was performed at Shohada-E Tajrish in Tehran - Iran hospital between October, 2011 to April, 2012, included 20 patients who suspected to MS disease were selected by the method of random sampling and underwent routine brain Pulse sequences (Axial T2w, Axial T1w, Coronal T2w, Sagittal T1w, Axial FLAIR by Siemens, Avanto, 1.5 Tesla system. If any lesion which is suspected to the MS disease was observed, additional sequences such as: Sagittal FLAIR Fat Sat, Sagittal PDw-fat Sat, Sagittal PDw-water sat was also performed. Results: This study was performed in about 52 lesions and the results in more than 19 lesions showed that, for the Subcortical and Infratentorial areas, PDWw sequence with fat suppression is the best choice, And in nearly 33 plaques located in Periventricular area, FLAIR Fat Sat was the most effective sequence than both PDw fat and water suppression pulse sequences. Conclusion: Although large plaques may visible in all images, but important problem in patients with suspected MS is screening the tiny MS plaques. This study showed that for revealing the MS plaques located in the Subcortical and Infratentorial areas, PDw-fat sat is the most effective sequence, and for MS plaques in the periventricular area, FLAIR fat Sat is the best choice.

  9. The Optimization of Magnetic Resonance Imaging Pulse Sequences in Order to Better Detection of Multiple Sclerosis Plaques.

    Science.gov (United States)

    Farshidfar, Z; Faeghi, F; Haghighatkhah, H R; Abdolmohammadi, J

    2017-09-01

    Magnetic resonance imaging (MRI) is the most sensitive technique to detect multiple sclerosis (MS) plaques in central nervous system. In some cases, the patients who were suspected to MS, Whereas MRI images are normal, but whether patients don't have MS plaques or MRI images are not enough optimized enough in order to show MS plaques? The aim of the current study is evaluating the efficiency of different MRI sequences in order to better detection of MS plaques. In this cross-sectional study which was performed at Shohada-E Tajrish in Tehran - Iran hospital between October, 2011 to April, 2012, included 20 patients who suspected to MS disease were selected by the method of random sampling and underwent routine brain Pulse sequences (Axial T2w, Axial T1w, Coronal T2w, Sagittal T1w, Axial FLAIR) by Siemens, Avanto, 1.5 Tesla system. If any lesion which is suspected to the MS disease was observed, additional sequences such as: Sagittal FLAIR Fat Sat, Sagittal PDw-fat Sat, Sagittal PDw-water sat was also performed. This study was performed in about 52 lesions and the results in more than 19 lesions showed that, for the Subcortical and Infratentorial areas, PDWw sequence with fat suppression is the best choice, And in nearly 33 plaques located in Periventricular area, FLAIR Fat Sat was the most effective sequence than both PDw fat and water suppression pulse sequences. Although large plaques may visible in all images, but important problem in patients with suspected MS is screening the tiny MS plaques. This study showed that for revealing the MS plaques located in the Subcortical and Infratentorial areas, PDw-fat sat is the most effective sequence, and for MS plaques in the periventricular area, FLAIR fat Sat is the best choice.

  10. Including load sequence effects in the fatigue damage estimation of an offshore wind turbine substructure

    NARCIS (Netherlands)

    Dragt, R.C.; Maljaars, J.; Tuitman, J.T.; Salman, Y.; Otheguy, M.E.

    2016-01-01

    Retardation is a load sequence effect, which causes a reduced fatigue crack growth rate after an overload is encountered. Retardation can be cancelled when the overload is followed by an underload. The net effect is beneficial to the fatigue lifetime of Offshore Wind Turbines (OWTs). To be able to

  11. Voxel based morphometry of FLAIR MRI in children with intractable focal epilepsy: Implications for surgical intervention

    International Nuclear Information System (INIS)

    Riney, Catherine J.; Chong, William K.; Clark, Chris A.; Cross, J. Helen

    2012-01-01

    Purpose: Magnetic resonance imaging (MRI), in particular fluid-attenuated inversion-recovery (FLAIR), has transformed the delineation of structural brain pathology associated with focal epilepsy. However, to date there is no literature on voxel based morphometry (VBM) of FLAIR in children with epilepsy. The aim of this study was to explore the role of visual and VBM assessment of FLAIR in pre-operative investigation of children with intractable focal epilepsy. Methods: Children with intractable epilepsy due to focal cortical dysplasia (FCD) and children with intractable cryptogenic focal epilepsy (CFE) were investigated. FLAIR and T1-weighted MRI were acquired on a 1.5T MRI scanner (Siemens, Erlangen, Germany). VBM was performed using SPM5 (Wellcome Institute of Cognitive Neuroscience, London). Results: Eight children with FCD (M = 5, age 7.9–17.3 years) and 14 children with CFE (M = 8, 7.8–16.8 years) were enrolled. VBM of FLAIR detected 7/8 (88%) of FCD whilst VBM of T1-weighted MRI detected only 3/8 (38%) FCD. VBM of FLAIR detected abnormality in 4/14 children with CFE, in 2/14 (14%) the abnormality was concordant with other data on the epileptogenic zone and with visible abnormality on repeat visual inspection of MR data. VBM of T1-weighed MRI detected abnormality in 2/14 children with CFE, none of which correlated with visible abnormality. Discussion: This study highlights the important role that FLAIR imaging has in the pre-operative assessment of children with intractable epilepsy. VBM of FLAIR may provide important information allowing selection of children with intractable CFE who are likely to benefit from further neuroradiological or neurophysiological evaluation.

  12. Evaluation of Possible Prognostic Factors of Fulminant Acute Disseminated Encephalomyelitis (ADEM) on Magnetic Resonance Imaging with Fluid-Attenuated Inversion Recovery (FLAIR) and Diffusion-Weighted Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Donmez, F.Y.; Aslan, H.; Coskun, M. (Dept. of Radiology, Faculty of Medicine, Baskent Univ., Ankara (Turkey))

    2009-04-15

    Background: Acute disseminated encephalomyelitis (ADEM) may be a rapidly progressive disease with different clinical outcomes. Purpose: To investigate the radiological findings of fulminant ADEM on diffusion-weighted imaging (DWI) and fluid-attenuated inversion recovery (FLAIR) images, and to correlate these findings with clinical outcome. Material and Methods: Initial and follow-up magnetic resonance imaging (MRI) scans in eight patients were retrospectively evaluated for distribution of lesions on FLAIR images and presence of hemorrhage or contrast enhancement. DWI of the patients was evaluated as to cytotoxic versus vasogenic edema. The clinical records were analyzed, and MRI results and clinical outcome were correlated. Results: Four of the eight patients died, three had full recovery, and one had residual cortical blindness. The distribution of the hyperintense lesions on FLAIR sequence was as follows: frontal (37.5%), parietal (50%), temporal (37.5%), occipital (62.5%), basal ganglia (50%), pons (37.5%), mesencephalon (37.5%), and cerebellum (50%). Three of the patients who died had brainstem involvement. Two patients had a cytotoxic edema, one of whom died, and the other developed cortical blindness. Six patients had vasogenic edema: three of these patients had a rapid progression to coma and died; three of them recovered. Conclusion: DWI is not always helpful for evaluating the evolution or predicting the outcome of ADEM. However, extension of the lesions, particularly brainstem involvement, may have an influence on the prognosis.

  13. Evaluation of Possible Prognostic Factors of Fulminant Acute Disseminated Encephalomyelitis (ADEM) on Magnetic Resonance Imaging with Fluid-Attenuated Inversion Recovery (FLAIR) and Diffusion-Weighted Imaging

    International Nuclear Information System (INIS)

    Donmez, F.Y.; Aslan, H.; Coskun, M.

    2009-01-01

    Background: Acute disseminated encephalomyelitis (ADEM) may be a rapidly progressive disease with different clinical outcomes. Purpose: To investigate the radiological findings of fulminant ADEM on diffusion-weighted imaging (DWI) and fluid-attenuated inversion recovery (FLAIR) images, and to correlate these findings with clinical outcome. Material and Methods: Initial and follow-up magnetic resonance imaging (MRI) scans in eight patients were retrospectively evaluated for distribution of lesions on FLAIR images and presence of hemorrhage or contrast enhancement. DWI of the patients was evaluated as to cytotoxic versus vasogenic edema. The clinical records were analyzed, and MRI results and clinical outcome were correlated. Results: Four of the eight patients died, three had full recovery, and one had residual cortical blindness. The distribution of the hyperintense lesions on FLAIR sequence was as follows: frontal (37.5%), parietal (50%), temporal (37.5%), occipital (62.5%), basal ganglia (50%), pons (37.5%), mesencephalon (37.5%), and cerebellum (50%). Three of the patients who died had brainstem involvement. Two patients had a cytotoxic edema, one of whom died, and the other developed cortical blindness. Six patients had vasogenic edema: three of these patients had a rapid progression to coma and died; three of them recovered. Conclusion: DWI is not always helpful for evaluating the evolution or predicting the outcome of ADEM. However, extension of the lesions, particularly brainstem involvement, may have an influence on the prognosis

  14. Clinical value of 4-hour delayed gadolinium-Enhanced 3D FLAIR MR Images in Acute Vestibular Neuritis.

    Science.gov (United States)

    Byun, Hayoung; Chung, Jae Ho; Lee, Seung Hwan; Park, Chul Won; Park, Dong Woo; Kim, Tae Yoon

    2018-01-13

    To investigate the clinical significance of 4-hour delayed-enhanced 3.0 Tesla three-dimensional (3D) fluid-attenuated inversion recovery (FLAIR) magnetic resonance (MR) imaging in acute vestibular neuritis. A prospective observational study. Twenty-nine vestibular neuritis patients were enrolled between January 2017 and June 2017. Vestibular function tests, comprising the caloric and video head impulse tests and vestibular-evoked myogenic potential measurements, were performed. Precontrast, 10-minute, and 4-hour delayed-enhanced 3D-FLAIR MR images using double-dose IV gadolinium were obtained. After laterality and extent of inner ear enhancement were defined, the patients were divided into groups based on the patterns of enhancement, and clinical parameters were analyzed according to the groups. Twenty patients (20 of 29, 69.0%) had obviously asymmetric enhancement of the affected inner ear structures on 4-hour delayed images, whereas only three patients (10.3%) had marked enhancement on 10-minute delayed images. The duration of spontaneous nystagmus (DurSN) was significantly longer in the patients with enhancement, especially with enhancement of the whole inner ear, including the vestibule and semicircular canals (P vestibular function tests did not reveal any significant associations with MR enhancement. Contrast enhancement of the vestibular nerve and inner ear structures can be identified on 4-hour delayed-enhanced 3T 3D-FLAIR MR images in acute vestibular neuritis. The extent of inner ear enhancement may be associated with the DurSN. IV. Laryngoscope, 2017. © 2018 The American Laryngological, Rhinological and Otological Society, Inc.

  15. 3D-FLAIR MRI in facial nerve paralysis with and without audio-vestibular disorder.

    Science.gov (United States)

    Nakata, Seiichi; Mizuno, Terukazu; Naganawa, Shinji; Sugiura, Makoto; Yoshida, Tadao; Teranishi, Masaaki; Sone, Michihiko; Nakashima, Tsutomu

    2010-05-01

    Among patients with facial nerve paralysis, significant difference was observed on three-dimensional fluid-attenuated inversion recovery magnetic resonance imaging (3D-FLAIR MRI) between those with and without audio-vestibular disturbance. This MRI technique may contribute to elucidation of the pathology of Ramsay Hunt syndrome and Bell's palsy. To evaluate the 3D-FLAIR MRI findings in patients who have facial nerve paralysis with and without audio-vestibular disturbance. 3D-FLAIR MRI was performed with and without gadolinium enhancement in 15 patients (5 men and 10 women) with unilateral facial nerve paralysis: 3 patients with Ramsay Hunt syndrome, 3 patients having facial nerve paralysis with hearing loss or vertigo without vesicles, and 9 patients with Bell's palsy. Five of the six patients with audio-vestibular disturbance showed high signals in the inner ear on precontrast 3D-FLAIR. In comparison, among nine patients with Bell's palsy, only one patient showed high signals in the inner ear on precontrast 3D-FLAIR (p < 0.05).

  16. FLAIR lesion segmentation: Application in patients with brain tumors and acute ischemic stroke

    Energy Technology Data Exchange (ETDEWEB)

    Artzi, Moran, E-mail: artzimy@gmail.com [The Functional Brain Center, The Wohl Institute for Advanced Imaging, Tel Aviv Sourasky Medical Center, Tel Aviv (Israel); Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (Israel); Aizenstein, Orna, E-mail: ornaaize@gmail.com [The Functional Brain Center, The Wohl Institute for Advanced Imaging, Tel Aviv Sourasky Medical Center, Tel Aviv (Israel); Jonas-Kimchi, Tali, E-mail: talijk@tlvmc.gov.il [Radiology Department, Tel Aviv Sourasky Medical Center, Tel Aviv (Israel); Myers, Vicki, E-mail: vicki_myers@hotmail.com [The Functional Brain Center, The Wohl Institute for Advanced Imaging, Tel Aviv Sourasky Medical Center, Tel Aviv (Israel); Hallevi, Hen, E-mail: hen.hallevi@gmail.com [Neurology Department, Tel Aviv Sourasky Medical Center, Tel Aviv (Israel); Ben Bashat, Dafna, E-mail: dafnab@tlvmc.gov.il [The Functional Brain Center, The Wohl Institute for Advanced Imaging, Tel Aviv Sourasky Medical Center, Tel Aviv (Israel); Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (Israel)

    2013-09-15

    Background: Lesion size in fluid attenuation inversion recovery (FLAIR) images is an important clinical parameter for patient assessment and follow-up. Although manual delineation of lesion areas considered as ground truth, it is time-consuming, highly user-dependent and difficult to perform in areas of indistinct borders. In this study, an automatic methodology for FLAIR lesion segmentation is proposed, and its application in patients with brain tumors undergoing therapy; and in patients following stroke is demonstrated. Materials and methods: FLAIR lesion segmentation was performed in 57 magnetic resonance imaging (MRI) data sets obtained from 44 patients: 28 patients with primary brain tumors; 5 patients with recurrent-progressive glioblastoma (rGB) who were scanned longitudinally during anti-angiogenic therapy (18 MRI scans); and 11 patients following ischemic stroke. Results: FLAIR lesion segmentation was obtained in all patients. When compared to manual delineation, a high visual similarity was observed, with an absolute relative volume difference of 16.80% and 20.96% and a volumetric overlap error of 24.87% and 27.50% obtained for two raters: accepted values for automatic methods. Quantitative measurements of the segmented lesion volumes were in line with qualitative radiological assessment in four patients who received anti-anogiogenic drugs. In stroke patients the proposed methodology enabled identification of the ischemic lesion and differentiation from other FLAIR hyperintense areas, such as pre-existing disease. Conclusion: This study proposed a replicable methodology for FLAIR lesion detection and quantification and for discrimination between lesion of interest and pre-existing disease. Results from this study show the wide clinical applications of this methodology in research and clinical practice.

  17. FLAIR lesion segmentation: Application in patients with brain tumors and acute ischemic stroke

    International Nuclear Information System (INIS)

    Artzi, Moran; Aizenstein, Orna; Jonas-Kimchi, Tali; Myers, Vicki; Hallevi, Hen; Ben Bashat, Dafna

    2013-01-01

    Background: Lesion size in fluid attenuation inversion recovery (FLAIR) images is an important clinical parameter for patient assessment and follow-up. Although manual delineation of lesion areas considered as ground truth, it is time-consuming, highly user-dependent and difficult to perform in areas of indistinct borders. In this study, an automatic methodology for FLAIR lesion segmentation is proposed, and its application in patients with brain tumors undergoing therapy; and in patients following stroke is demonstrated. Materials and methods: FLAIR lesion segmentation was performed in 57 magnetic resonance imaging (MRI) data sets obtained from 44 patients: 28 patients with primary brain tumors; 5 patients with recurrent-progressive glioblastoma (rGB) who were scanned longitudinally during anti-angiogenic therapy (18 MRI scans); and 11 patients following ischemic stroke. Results: FLAIR lesion segmentation was obtained in all patients. When compared to manual delineation, a high visual similarity was observed, with an absolute relative volume difference of 16.80% and 20.96% and a volumetric overlap error of 24.87% and 27.50% obtained for two raters: accepted values for automatic methods. Quantitative measurements of the segmented lesion volumes were in line with qualitative radiological assessment in four patients who received anti-anogiogenic drugs. In stroke patients the proposed methodology enabled identification of the ischemic lesion and differentiation from other FLAIR hyperintense areas, such as pre-existing disease. Conclusion: This study proposed a replicable methodology for FLAIR lesion detection and quantification and for discrimination between lesion of interest and pre-existing disease. Results from this study show the wide clinical applications of this methodology in research and clinical practice

  18. Mitochondrial DNA sequence evolution and phylogeny of the Atlantic Alcidae, including the extinct great auk (Pinguinus impennis).

    Science.gov (United States)

    Moum, Truls; Arnason, Ulfur; Arnason, Einar

    2002-09-01

    The Atlantic auk assemblage includes four extant species, razorbill (Alca torda), dovekie (Alle alle), common murre (Uria aalge), and thick-billed murre (U. lomvia), and one recently extinct species, the flightless great auk (Pinguinus impennis). To determine the phylogenetic relationships among the species, a contiguous 4.2-kb region of the mitochondrial genome from the extant species was amplified using PCR. This region included one ribosomal RNA gene, four transfer RNA genes, two protein-coding genes, the control region, and intergenic spacers. Sets of PCR primers for amplifying the same region from great auk were designed from sequences of the extant species. The authenticity of the great auk sequence was ascertained by alternative amplifications, cloning, and separate analyses in an independent laboratory. Phylogenetic analyses of the entire assemblage, made possible by the great auk sequence, fully resolved the phylogenetic relationships and split it into two primary lineages, Uria versus Alle, Alca, and Pinguinus. A sister group relationship was identified between Alca and Pinguinus to the exclusion of ALLE: Phylogenetically, the flightless great auk originated late relative to other divergences within the assemblage. This suggests that three highly divergent species in terms of adaptive specializations, Alca, Alle, and Pinguinus, evolved from a single lineage in the Atlantic Ocean, in a process similar to the initial adaptive radiation of alcids in the Pacific Ocean.

  19. The genomic scrapheap challenge; extracting relevant data from unmapped whole genome sequencing reads, including strain specific genomic segments, in rats

    NARCIS (Netherlands)

    Van Der Weide, Robin H.; Simonis, Marieke; Hermsen, Roel; Toonen, Pim; Cuppen, Edwin; de Ligt, Joep

    2016-01-01

    Unmapped next-generation sequencing reads are typically ignored while they contain biologically relevant information. We systematically analyzed unmapped reads from whole genome sequencing of 33 inbred rat strains. High quality reads were selected and enriched for biologically relevant sequences;

  20. Improve Image Quality of Transversal Relaxation Time PROPELLER and FLAIR on Magnetic Resonance Imaging

    Science.gov (United States)

    Rauf, N.; Alam, D. Y.; Jamaluddin, M.; Samad, B. A.

    2018-03-01

    The Magnetic Resonance Imaging (MRI) is a medical imaging technique that uses the interaction between the magnetic field and the nuclear spins. MRI can be used to show disparity of pathology by transversal relaxation time (T2) weighted images. Some techniques for producing T2-weighted images are Periodically Rotated Overlapping Parallel Lines with Enhanced Reconstruction (PROPELLER) and Fluid Attenuated Inversion Recovery (FLAIR). A comparison of T2 PROPELLER and T2 FLAIR parameters in MRI image has been conducted. And improve Image Quality the image by using RadiAnt DICOM Viewer and ENVI software with method of image segmentation and Region of Interest (ROI). Brain images were randomly selected. The result of research showed that Time Repetition (TR) and Time Echo (TE) values in all types of images were not influenced by age. T2 FLAIR images had longer TR value (9000 ms), meanwhile T2 PROPELLER images had longer TE value (100.75 - 102.1 ms). Furthermore, areas with low and medium signal intensity appeared clearer by using T2 PROPELLER images (average coefficients of variation for low and medium signal intensity were 0.0431 and 0.0705, respectively). As for areas with high signal intensity appeared clearer by using T2 FLAIR images (average coefficient of variation was 0.0637).

  1. R179H mutation in ACTA2 expanding the phenotype to include prune-belly sequence and skin manifestations.

    Science.gov (United States)

    Richer, J; Milewicz, D M; Gow, R; de Nanassy, J; Maharajh, G; Miller, E; Oppenheimer, L; Weiler, G; O'Connor, M

    2012-03-01

    Mutations in ACTA2 (smooth muscle cell-specific isoform of α-actin) lead to a predisposition to thoracic aortic aneurysms and other vascular diseases. More recently, the ACTA2 R179H mutation has been described in individuals with global smooth muscle dysfunction. We report a patient heterozygous for the mutation in ACTA2 R179H who presented with megacystis at 13 weeks gestational age and, at birth, with prune-belly sequence. He also had deep skin dimples and creases on his palms and soles, a finding not previously described but possibly related to ACTA2. To our knowledge, this is the first report of the R179H mutation in ACTA2 in a child with prune-belly sequence. We think the R179H mutation in ACTA2 should be included in the differential diagnosis of individuals presenting with the sequence without an identified mechanical obstruction. Furthermore, as ACTA2 R179H has been reported in patients with severe vasculomyopathy and premature death, we recommend that molecular testing for this mutation be considered in fetuses presenting with fetal megacystis with a normal karyotype, particularly if the bladder diameter is 15 mm or more, to allow expectant parents to make an informed decision. Copyright © 2012 Wiley Periodicals, Inc.

  2. Sequence Variation in the Ribosomal Internal Transcribed Spacers, Including the 5.8S rDNA, of Naegleria spp.

    Science.gov (United States)

    De Jonckheere, J F

    1998-09-01

    The ribosomal internal transcribed spacer (ITS), including the 5.8S rDNA, from the majority of the 11 described species of the amoeboflagellate Naegleria and from Willaertia magna have a size between 300 and 450 bp. In N. jadini and N. minor these products are approximately 750 bp long. The products from strains of the pathogenic N. fowleri vary between 323 and 423 bp. These length variations in N. fowleri are due to insertions of short repeats in the ITS1, causing the elongation of one stem-loop in the putative secondary structure. In all other species the sizes were identical from strains of the same species. In N. jadini and N. minor there are long inserts in the ITS2. Naegleria italica, N. clarki and N. galeacystis have shorter inserts in the ITS2. These inserts cause the elongation of one stem-loop in the putative secondary structure proposed for the ITS2. Because of the small differences in sequence between N. fowleri and N. lovaniensis the ITS does not provide target sequences for specifically identifying the pathogenic N. fowleri. However, differences in ITS1 do allow to distinguish different N. fowleri isolates. The ITS and 5.8S rDNA sequences will be of additional help in describing new Naegleria spp., which becomes more based on molecular data because morphological differences are scarce in these organisms. Copyright © 1998 Elsevier GmbH. All rights reserved.

  3. Association between the perfusion/diffusion and diffusion/FLAIR mismatch: data from the AXIS2 trial.

    Science.gov (United States)

    Wouters, Anke; Dupont, Patrick; Ringelstein, Erich B; Norrving, Bo; Chamorro, Angel; Grond, Martin; Laage, Rico; Schneider, Armin; Wilms, Guido; Thomalla, Götz; Lemmens, Robin; Thijs, Vincent N

    2015-10-01

    The perfusion-/diffusion-weighted imaging (PWI/DWI) mismatch and the diffusion/fluid attenuated inversion recovery (DWI/FLAIR) mismatch are magnetic resonance imaging (MRI) markers of evolving brain ischemia. We examined whether the DWI/FLAIR mismatch was independently associated with the PWI/DWI mismatch. Furthermore, we determined whether the presence of the DWI/FLAIR mismatch in patients with the PWI/DWI mismatch would provide additional information regarding last seen normal time (LTM). We used data from the 'AX200 for ischemic stroke' trial (AXIS 2 study NCT00927836). We studied the association between the presence of the DWI/FLAIR and PWI/DWI mismatch, baseline National Institute of Health Stroke Scale (NIHSS), age, ischemic-core volume, gender, intravenous (IV) tissue plasminogen activator (tPA), and perfusion-mismatch volume in univariate analysis. Significant variables (Pmismatch. Patients with the double mismatch pattern had a shorter LTM than patients with the PWI/DWI mismatch alone (Median difference 90 minutes, Pmismatch patterns (odds ratio (OR) 2.6, 95% confidence interval (CI) 1.2 to 5.4). Our study implies that the DWI/FLAIR mismatch and PWI/DWI mismatch are strongly associated, independent from LTM. Furthermore, in the presence of the PWI/DWI mismatch, the DWI/FLAIR pattern indicates a shorter LTM. This could have implications in selecting patients for reperfusion therapy.

  4. An energy minimization method for MS lesion segmentation from T1-w and FLAIR images.

    Science.gov (United States)

    Zhao, Yue; Guo, Shuxu; Luo, Min; Liu, Yu; Bilello, Michel; Li, Chunming

    2017-06-01

    In this paper, we extend the multiplicative intrinsic component optimization (MICO) algorithm to multichannel MR image segmentation, with focus on segmentation of multiple sclerosis (MS) lesions. The MICO algorithm was originally proposed by Li et al. in Ref. [1] for normal brain tissue segmentation and intensity inhomogeneity correction of a single channel MR image, which exhibits desirable advantages over other methods for MR image segmentation and intensity inhomogeneity correction in terms of segmentation accuracy and robustness. In this paper, we extend the MICO algorithm to multi-channel MR image segmentation and enable the segmentation of MS lesions. We assign different weights for different channels to control the impact of each channel. The weighted channels allow the enhancement of the impact of the FLAIR image on the segmentation of MS lesions by assigning a larger weight to the FLAIR image channel than the other channels. With the inherent mechanism of estimation of the bias field, our method is able to deal with the intensity inhomogeneity in the input multi-channel MR images. In the application of our method, we only use T1-w and FLAIR images as the input two channel MR images. Experimental results show promising result of our method. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Lateralization of temporal lobe epilepsy using a novel uncertainty analysis of MR diffusion in hippocampus, cingulum, and fornix, and hippocampal volume and FLAIR intensity.

    Science.gov (United States)

    Nazem-Zadeh, Mohammad-Reza; Schwalb, Jason M; Elisevich, Kost V; Bagher-Ebadian, Hassan; Hamidian, Hajar; Akhondi-Asl, Ali-Reza; Jafari-Khouzani, Kourosh; Soltanian-Zadeh, Hamid

    2014-07-15

    To analyze the utility of a quantitative uncertainty analysis approach for evaluation and comparison of various MRI findings for the lateralization of epileptogenicity in mesial temporal lobe epilepsy (mTLE), including novel diffusion-based analyses. We estimated the hemispheric variation uncertainty (HVU) of hippocampal T1 volumetry and FLAIR (Fluid Attenuated Inversion Recovery) intensity. Using diffusion tensor images of 23 nonepileptic subjects, we estimated the HVU levels of mean diffusivity (MD) in the hippocampus, and fractional anisotropy (FA) in the posteroinferior cingulum and crus of fornix. Imaging from a retrospective cohort of 20 TLE patients who had undergone surgical resection with Engel class I outcomes was analyzed to determine whether asymmetry of preoperative volumetrics, FLAIR intensities, and MD values in hippocampi, as well as FA values in posteroinferior cingula and fornix crura correctly predicted laterality of seizure onset. Ten of the cohort had pathologically proven mesial temporal sclerosis (MTS). Seven of these patients had undergone extraoperative electrocorticography (ECoG) for lateralization or to rule out extra-temporal foci. HVU was estimated to be 3.1×10(-5) for hippocampal MD, 0.027 for FA in posteroinferior cingulum, 0.018 for FA in crus of fornix, 0.069 for hippocampal normalized volume, and 0.099 for hippocampal normalized FLAIR intensity. Using HVU analysis, a higher hippocampal MD value, lower FA within the posteroinferior cingulum and crus of fornix, shrinkage in hippocampal volume, and higher hippocampal FLAIR intensity were observed beyond uncertainty on the side ipsilateral to seizure onset for 10, 10, 9, 9, and 10 out of 10 pathology-proven MTS patients, respectively. Considering all 20 TLE patients, these numbers were 18, 15, 14, 13, and 16, respectively. However, consolidating the lateralization results of HVU analysis on these quantities by majority voting has detected the epileptogenic side for 19 out of 20 cases

  6. Anterior temporal lobe white matter abnormal signal (ATLAS) as an indicator of seizure focus laterality in temporal lobe epilepsy: comparison of double inversion recovery, FLAIR and T2W MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Morimoto, Emiko; Kanagaki, Mitsunori; Okada, Tomohisa; Yamamoto, Akira; Togashi, Kaori [Kyoto University Graduate School of Medicine, Department of Diagnostic Imaging and Nuclear Medicine, Kyoto (Japan); Mori, Nobuyuki [Tenri Hospital, Department of Radiology, Tenri, Nara (Japan); Matsumoto, Riki; Ikeda, Akio; Takahashi, Ryosuke [Kyoto University Graduate School of Medicine, Department of Neurology, Kyoto (Japan); Mikuni, Nobuhiro [Sapporo Medical University, Department of Neurosurgery, Sapporo, Hokkaido (Japan); Kunieda, Takeharu; Miyamoto, Susumu [Kyoto University Graduate School of Medicine, Department of Neurosurgery, Kyoto (Japan); Paul, Dominik [Siemens AG Healthcare Sector, Erlangen (Germany)

    2013-01-15

    To investigate the diagnostic capability of anterior temporal lobe white matter abnormal signal (ATLAS) for determining seizure focus laterality in temporal lobe epilepsy (TLE) by comparing different MR sequences. This prospective study was approved by the institutional review board and written informed consent was obtained. Three 3D sequences (double inversion recovery (DIR), fluid-attenuated inversion recovery (FLAIR) and T2-weighted imaging (T2WI)) and two 2D sequences (FLAIR and T2WI) were acquired at 3 T. Signal changes in the anterior temporal white matter of 21 normal volunteers were evaluated. ATLAS laterality was evaluated in 21 TLE patients. Agreement of independent evaluations by two neuroradiologists was assessed using {kappa} statistics. Differences in concordance between ATLAS laterality and clinically defined seizure focus laterality were analysed using McNemar's test with multiple comparisons. Pre-amygdala high signals (PAHS) were detected in all volunteers only on 3D-DIR. Inter-evaluator agreement was moderate to almost perfect for each sequence. Correct diagnosis of seizure laterality was significantly more frequent on 3D-DIR than on any other sequences (P {<=} 0.031 for each evaluator). The most sensitive sequence for detecting ATLAS laterality was 3D-DIR. ATLAS laterality on 3D-DIR can be a good indicator for determining seizure focus localization in TLE. (orig.)

  7. Anterior temporal lobe white matter abnormal signal (ATLAS) as an indicator of seizure focus laterality in temporal lobe epilepsy: comparison of double inversion recovery, FLAIR and T2W MR imaging

    International Nuclear Information System (INIS)

    Morimoto, Emiko; Kanagaki, Mitsunori; Okada, Tomohisa; Yamamoto, Akira; Togashi, Kaori; Mori, Nobuyuki; Matsumoto, Riki; Ikeda, Akio; Takahashi, Ryosuke; Mikuni, Nobuhiro; Kunieda, Takeharu; Miyamoto, Susumu; Paul, Dominik

    2013-01-01

    To investigate the diagnostic capability of anterior temporal lobe white matter abnormal signal (ATLAS) for determining seizure focus laterality in temporal lobe epilepsy (TLE) by comparing different MR sequences. This prospective study was approved by the institutional review board and written informed consent was obtained. Three 3D sequences (double inversion recovery (DIR), fluid-attenuated inversion recovery (FLAIR) and T2-weighted imaging (T2WI)) and two 2D sequences (FLAIR and T2WI) were acquired at 3 T. Signal changes in the anterior temporal white matter of 21 normal volunteers were evaluated. ATLAS laterality was evaluated in 21 TLE patients. Agreement of independent evaluations by two neuroradiologists was assessed using κ statistics. Differences in concordance between ATLAS laterality and clinically defined seizure focus laterality were analysed using McNemar's test with multiple comparisons. Pre-amygdala high signals (PAHS) were detected in all volunteers only on 3D-DIR. Inter-evaluator agreement was moderate to almost perfect for each sequence. Correct diagnosis of seizure laterality was significantly more frequent on 3D-DIR than on any other sequences (P ≤ 0.031 for each evaluator). The most sensitive sequence for detecting ATLAS laterality was 3D-DIR. ATLAS laterality on 3D-DIR can be a good indicator for determining seizure focus localization in TLE. (orig.)

  8. Value of fluid-attenuated inversion recovery sequences in early MRI of the brain in neonates with a perinatal hypoxic-ischemic encephalopathy

    Energy Technology Data Exchange (ETDEWEB)

    Sie, L.T.L.; Knaap, M.S. van der [Vrije Univ. Hospital, Amsterdam (Netherlands). Dept. of Neurology; Barkhof, F.; Valk, J. [Amsterdam Univ. (Netherlands). Dept. of Diagnostic Radiology, Pathology and Gastroenterology; Lafeber, H.N. [Univ. Hospital ' Vrije Universiteit' , Amsterdam (Netherlands). Dept. of Neonatology

    2000-10-01

    The aim of our study was to assess the usefulness of fluid-attenuated inversion recovery (FLAIR) sequences in comparison with conventional spin-echo and inversion MR imaging in neonates for evaluation of myelination and for detection of hypoxic-ischemic brain injury. We reviewed early MR scans of 18 neonates with suspected hypoxic-ischemic brain damage. Myelination could be evaluated with confidence using conventional MR imaging in all but 2 infants; however, the presence of myelin was very difficult to assess on FLAIR images. Overall, 53 lesions or groups of lesions were identified. The FLAIR technique was more sensitive in 11 of the lesions; especially (pre)cystic lesions could be identified much better and more cysts were found. Conventional MR imaging failed to identify 2 of the lesions and was more sensitive in 14 of the lesions; especially punctate hemorrhages and lesions in basal ganglia or thalami could be better determined. The FLAIR technique missed 3 of these lesions. In the remaining 28 lesions conventional MR and FLAIR images were equally diagnostic. The FLAIR technique and conventional MR imaging are complementary in detecting early sequelae of hypoxic-ischemic brain injury in neonates. The FLAIR technique is not suitable for assessing myelination of the neonatal brain; therefore, FLAIR cannot replace conventional MR imaging. (orig.)

  9. FLAIR* to visualize veins in white matter lesions: A new tool for the diagnosis of multiple sclerosis?

    International Nuclear Information System (INIS)

    Campion, T.; Turner, B.P.; Schmierer, K.; Smith, R.J.P.; Altmann, D.R.; Brito, G.C.; Evanson, J.; George, I.C.; Sati, P.; Reich, D.S.; Miquel, M.E.

    2017-01-01

    To explore the potential of a post-processing technique combining FLAIR and T 2 * (FLAIR*) to distinguish between lesions caused by multiple sclerosis (MS) from cerebral small vessel disease (SVD) in a clinical setting. FLAIR and T 2 * head datasets acquired at 3T of 25 people with relapsing MS (pwRMS) and ten with pwSVD were used. After post-processing, FLAIR* maps were used to determine the proportion of white matter lesions (WML) showing the 'vein in lesion' sign (VIL), a characteristic histopathological feature of MS plaques. Sensitivity and specificity of MS diagnosis were examined on the basis of >45% VIL + and >60% VIL + WML, and compared with current dissemination in space (DIS) MRI criteria. All pwRMS had >45% VIL + WML (range 58-100%) whilst in pwSVD the proportion of VIL + WML was significantly lower (0-64%; mean 32±20%). Sensitivity based on >45% VIL + was 100% and specificity 80% whilst with >60% VIL + as the criterion, sensitivity was 96% and specificity 90%. DIS criteria had 96% sensitivity and 40% specificity. FLAIR* enables VIL + WML detection in a clinical setting, facilitating differentiation of MS from SVD based on brain MRI. (orig.)

  10. FLAIR* to visualize veins in white matter lesions: A new tool for the diagnosis of multiple sclerosis?

    Energy Technology Data Exchange (ETDEWEB)

    Campion, T.; Turner, B.P.; Schmierer, K. [Queen Mary University of London, Blizard Institute (Neuroscience), London (United Kingdom); Barts Health NHS Trust, Emergency Care and Acute Medicine Clinical Academic Group Neuroscience, The Royal London Hospital, London (United Kingdom); Smith, R.J.P. [Queen Mary University of London, Blizard Institute (Neuroscience), London (United Kingdom); Gloucestershire Hospitals NHS Trust, Cheltenham (United Kingdom); Altmann, D.R. [London School of Hygiene and Tropical Medicine, Department of Medical Statistics, London (United Kingdom); Brito, G.C. [Queen Mary University of London, Blizard Institute (Neuroscience), London (United Kingdom); Evanson, J. [Barts Health NHS Trust, Emergency Care and Acute Medicine Clinical Academic Group Neuroscience, The Royal London Hospital, London (United Kingdom); George, I.C. [NIH, Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, Bethesda, MD (United States); Yale School of Medicine, Department of Neurology, New Haven, CT (United States); Sati, P.; Reich, D.S. [NIH, Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, Bethesda, MD (United States); Miquel, M.E. [Barts Health NHS Trust, Emergency Care and Acute Medicine Clinical Academic Group Neuroscience, The Royal London Hospital, London (United Kingdom); Queen Mary University of London, William Harvey Research Institute (Cardiovascular Biomedical Research Unit), London (United Kingdom)

    2017-10-15

    To explore the potential of a post-processing technique combining FLAIR and T{sub 2}* (FLAIR*) to distinguish between lesions caused by multiple sclerosis (MS) from cerebral small vessel disease (SVD) in a clinical setting. FLAIR and T{sub 2}* head datasets acquired at 3T of 25 people with relapsing MS (pwRMS) and ten with pwSVD were used. After post-processing, FLAIR* maps were used to determine the proportion of white matter lesions (WML) showing the 'vein in lesion' sign (VIL), a characteristic histopathological feature of MS plaques. Sensitivity and specificity of MS diagnosis were examined on the basis of >45% VIL{sup +} and >60% VIL{sup +} WML, and compared with current dissemination in space (DIS) MRI criteria. All pwRMS had >45% VIL{sup +} WML (range 58-100%) whilst in pwSVD the proportion of VIL{sup +} WML was significantly lower (0-64%; mean 32±20%). Sensitivity based on >45% VIL{sup +} was 100% and specificity 80% whilst with >60% VIL{sup +} as the criterion, sensitivity was 96% and specificity 90%. DIS criteria had 96% sensitivity and 40% specificity. FLAIR* enables VIL{sup +} WML detection in a clinical setting, facilitating differentiation of MS from SVD based on brain MRI. (orig.)

  11. Multimodal MEMPRAGE, FLAIR, and R2* Segmentation to Resolve Dura and Vessels from Cortical Gray Matter

    Directory of Open Access Journals (Sweden)

    Roberto Viviani

    2017-05-01

    Full Text Available While widely in use in automated segmentation approaches for the detection of group differences or of changes associated with continuous predictors in gray matter volume, T1-weighted images are known to represent dura and cortical vessels with signal intensities similar to those of gray matter. By considering multiple signal sources at once, multimodal segmentation approaches may be able to resolve these different tissue classes and address this potential confound. We explored here the simultaneous use of FLAIR and apparent transverse relaxation rates (a signal related to T2* relaxation maps and having similar contrast with T1-weighted images. Relative to T1-weighted images alone, multimodal segmentation had marked positive effects on 1. the separation of gray matter from dura, 2. the exclusion of vessels from the gray matter compartment, and 3. the contrast with extracerebral connective tissue. While obtainable together with the T1-weighted images without increasing scanning times, apparent transverse relaxation rates were less effective than added FLAIR images in providing the above mentioned advantages. FLAIR images also improved the detection of cortical matter in areas prone to susceptibility artifacts in standard MPRAGE T1-weighted images, while the addition of transverse relaxation maps exacerbated the effect of these artifacts on segmentation. Our results confirm that standard MPRAGE segmentation may overestimate gray matter volume by wrongly assigning vessels and dura to this compartment and show that multimodal approaches may greatly improve the specificity of cortical segmentation. Since multimodal segmentation is easily implemented, these benefits are immediately available to studies focusing on translational applications of structural imaging.

  12. Ulcerative colitis flair induced by mesalamine suppositories hypersensitivity.

    Science.gov (United States)

    Ding, Hao; Liu, Xiao-Chang; Mei, Qiao; Xu, Jian-Ming; Hu, Xiang-Yang; Hu, Jing

    2014-04-07

    Mesalamine suppositories have been used widely for the treatment of distal ulcerative colitis and considered to be safer than systemic administration for its limited systemic absorption. However, previous studies have shown that mesalamine suppository occasionally causes severe hypersensitivity reactions including fever, rashes, colitis exacerbation and acute eosinophilic pneumonia. Here we present a 25-year-old woman with ulcerative colitis with bloody diarrhea accompanied by abdominal pain and fever which were aggravated after introduction of mesalamine suppositories. In light of symptom exacerbation of ulcerative colitis, increased inflammatory injury of colon mucosa shown by colonoscopy and elevated peripheral eosinophil count after mesalamine suppositories administration, and the Naranjo algorithm score of 10, the possibility of hypersensitivity reaction to mesalamine suppositories should be considered, warning us to be aware of this potential reaction after administration of mesalamine formulations even if it is the suppositories.

  13. Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion.

    Science.gov (United States)

    Thomsen, Martin Christen Frølund; Nielsen, Morten

    2012-07-01

    Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active sites, etc. in biological sequences. Accurate generation of sequence logos is often compromised by sequence redundancy and low number of observations. Moreover, most methods available for sequence logo generation focus on displaying the position-specific enrichment of amino acids, discarding the equally valuable information related to amino acid depletion. Seq2logo aims at resolving these issues allowing the user to include sequence weighting to correct for data redundancy, pseudo counts to correct for low number of observations and different logotype representations each capturing different aspects related to amino acid enrichment and depletion. Besides allowing input in the format of peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing easy access for non-expert end-users to characterize and identify functionally conserved/variable amino acids in any given protein of interest. The output from the server is a sequence logo and a PSSM. Seq2Logo is available at http://www.cbs.dtu.dk/biotools/Seq2Logo (14 May 2012, date last accessed).

  14. The reduced mycorrhizal colonisation (rmc) mutation of tomato disrupts five gene sequences including the CYCLOPS/IPD3 homologue.

    Science.gov (United States)

    Larkan, Nicholas J; Ruzicka, Dan R; Edmonds-Tibbett, Tamara; Durkin, Jonathan M H; Jackson, Louise E; Smith, F Andrew; Schachtman, Daniel P; Smith, Sally E; Barker, Susan J

    2013-10-01

    Arbuscular mycorrhizal (AM) symbiosis in vascular plant roots is an ancient mutualistic interaction that evolved with land plants. More recently evolved root mutualisms have recruited components of the AM signalling pathway as identified with molecular approaches in model legume research. Earlier we reported that the reduced mycorrhizal colonisation (rmc) mutation of tomato mapped to chromosome 8. Here we report additional functional characterisation of the rmc mutation using genotype grafts and proteomic and transcriptomic analyses. Our results led to identification of the precise genome location of the Rmc locus from which we identified the mutation by sequencing. The rmc phenotype results from a deletion that disrupts five predicted gene sequences, one of which has close sequence match to the CYCLOPS/IPD3 gene identified in legumes as an essential intracellular regulator of both AM and rhizobial symbioses. Identification of two other genes not located at the rmc locus but with altered expression in the rmc genotype is also described. Possible roles of the other four disrupted genes in the deleted region are discussed. Our results support the identification of CYCLOPS/IPD3 in legumes and rice as a key gene required for AM symbiosis. The extensive characterisation of rmc in comparison with its 'parent' 76R, which has a normal mycorrhizal phenotype, has validated these lines as an important comparative model for glasshouse and field studies of AM and non-mycorrhizal plants with respect to plant competition and microbial interactions with vascular plant roots.

  15. Hot plays - prospects keeping the flair in the patch

    Energy Technology Data Exchange (ETDEWEB)

    Harrington, P.; Sword, M.

    1999-06-01

    Three different types of oil and natural gas plays in the Alberta oil patch, which are proving to become growth engines for a number explorers, are featured. One of these is the Musreau gas discovery by Chevron Canada Resources. The deep basin Wabamun formation is attracting a number of explorers, including junior producers willing to risk big dollars to drill high impact wells in hopes of finding hundreds of billions of cubic feet of gas. In oil plays, Tri Link Resources has been plugging away in southeastern Saskatchewan targeting the Ordovician formation north of the now famous Midale prospect. Some 100 million barrels of new reserves have been found to date, with more expected. Several junior producers are finding considerable success with shallow gas projects in northeastern Alberta drilling for Bluesky, Gething, Pekisko and Banff formations in the Haro/Boyer region. What makes this natural gas play particularly attractive are the low finding and development costs and long-life reserves. With the improving profitability of producing gas, the trend is now spreading to the northern reaches of Alberta and with technology and patience, a number of junior producers have initiated gas exploration programs in this area. Some oil discoveries have also been landed in the Haro/Boyer region.

  16. Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin.

    Directory of Open Access Journals (Sweden)

    Melissa K Boles

    2009-12-01

    Full Text Available An accurate and precisely annotated genome assembly is a fundamental requirement for functional genomic analysis. Here, the complete DNA sequence and gene annotation of mouse Chromosome 11 was used to test the efficacy of large-scale sequencing for mutation identification. We re-sequenced the 14,000 annotated exons and boundaries from over 900 genes in 41 recessive mutant mouse lines that were isolated in an N-ethyl-N-nitrosourea (ENU mutation screen targeted to mouse Chromosome 11. Fifty-nine sequence variants were identified in 55 genes from 31 mutant lines. 39% of the lesions lie in coding sequences and create primarily missense mutations. The other 61% lie in noncoding regions, many of them in highly conserved sequences. A lesion in the perinatal lethal line l11Jus13 alters a consensus splice site of nucleoredoxin (Nxn, inserting 10 amino acids into the resulting protein. We conclude that point mutations can be accurately and sensitively recovered by large-scale sequencing, and that conserved noncoding regions should be included for disease mutation identification. Only seven of the candidate genes we report have been previously targeted by mutation in mice or rats, showing that despite ongoing efforts to functionally annotate genes in the mammalian genome, an enormous gap remains between phenotype and function. Our data show that the classical positional mapping approach of disease mutation identification can be extended to large target regions using high-throughput sequencing.

  17. Decreased hyperintense vessels on FLAIR images after endovascular recanalization of symptomatic internal carotid artery occlusion

    International Nuclear Information System (INIS)

    Liu Wenhua; Yin Qin; Yao Lingling; Zhu Shuanggen; Xu Gelin; Zhang Renliang; Ke Kaifu; Liu Xinfeng

    2012-01-01

    Background and purpose: Hyperintense vessels (HV) on fluid-attenuated inversion recovery (FLAIR) images were assumed to be explained by slow antegrade or retrograde leptomeningeal collateral flow related to extracranial or intracranial artery steno-occlusion. The aim of this study was to investigate the effect of recanalization after endovascular therapy of symptomatic internal carotid artery (ICA) occlusion on the presence of HV. Methods: Eleven patients with symptomatic ICA occlusion were retrospectively enrolled. Changes in the HV on FLAIR images were examined in affected hemisphere of each patient after successful treatment with endovascular recanalization (angioplasty, n = 3; stent-assisted angioplasty, n = 8). The relationship between postoperative changes in the HV and Thrombolysis In Cerebral Ischemia (TICI) scale (I-III) was assessed. Results: After operation, HV of the 11 affected hemispheres were showed to be decreased (n = 3) or disappeared (n = 8) in treated side. The median interval between pre- and postoperative MRI examinations was 97.0 h (range, from 69. to 48.7 h). Of the 8 patients with disappeared HV, 7 achieved high TICI grade flow (III) and 1 had relatively low TICI grade flow (IIc) in treated side. However, all the 3 patients with decreased HV were found to be relatively low TICI grade flow (IIc). Conclusion: Our data indicate that endovascular recanalization of ICA occlusion was effective for decreasing HV. Postoperative decrease in HV can be considered as a marker for hemodynamic improvement.

  18. Sensitivity of different MRI sequences in the early detection of melanoma brain metastases

    Science.gov (United States)

    Breckwoldt, Michael O.; Schwarz, Daniel; Radbruch, Alexander; Enk, Alexander; Bendszus, Martin; Hassel, Jessica; Schlemmer, Heinz-Peter

    2018-01-01

    Background After the emergence of new MRI techniques such as susceptibility- and diffusion-weighted imaging (SWI and DWI) and because of specific imaging characteristics of melanoma brain metastases (MBM), it is unclear which MRI sequences are most beneficial for detection of MBM. This study was performed to investigate the sensitivity of six clinical MRI sequences in the early detection of MBM. Methods Medical records of all melanoma patients referred to our center between November 2005 and December 2016 were reviewed for presence of MBM. Analysis encompassed six MRI sequences at the time of initial diagnosis of first or new MBM, including non-enhanced T1-weighted (T1w), contrast-enhanced T1w (ceT1w), T2-weighted (T2w), T2w-FLAIR, susceptibility-weighted (SWI) and diffusion-weighted (DWI) MRI. Each lesion was rated with respect to its conspicuity (score from 0—not detectable to 3—clearly visible). Results Of 1210 patients, 217 with MBM were included in the analysis and up to 5 lesions per patient were evaluated. A total of 720 metastases were assessed and all six sequences were available for 425 MBM. Sensitivity (conspicuity ≥2) was 99.7% for ceT1w, 77.0% for FLAIR, 64.7% for SWI, 61.0% for T2w, 56.7% for T1w, and 48.4% for DWI. Thirty-one (7.3%) of 425 lesions were only detectable by ceT1w but no other sequence. Conclusions Contrast-enhanced T1-weighting is more sensitive than all other sequences for detection of MBM. Disruption of the blood-brain-barrier is consistently an earlier sign in MBM than perifocal edema, signal loss on SWI or diffusion restriction. PMID:29596475

  19. Learning Foreign Languages with ClipFlair: Using Captioning and Revoicing Activities to Increase Students' Motivation and Engagement

    Science.gov (United States)

    Baños, Rocío; Sokoli, Stavroula

    2015-01-01

    The purpose of this paper is to present the rationale and outcomes of ClipFlair, a European-funded project aimed at countering the factors that discourage Foreign Language Learning (FLL) by providing a motivating, easily accessible online platform to learn a foreign language through revoicing (e.g. dubbing) and captioning (e.g. subtitling). This…

  20. Hyperintense vessels on FLAIR: A useful non-invasive method for assessing intracerebral collaterals

    International Nuclear Information System (INIS)

    Liu Wenhua; Xu Gelin; Yue Xuanye; Wang Xiaoliang; Ma Minmin; Zhang Renliang; Wang Handong; Zhou Changsheng; Liu Xinfeng

    2011-01-01

    Objective: This study was aimed to evaluate relationship between hyperintense vessels (HV) on fluid-attenuated inversion recovery (FLAIR) and artery steno-occlusion related intracerebral collaterals. Materials and methods: A total of 233 patients with 260 atherosclerotic lesions in the M1 segment of the middle cerebral artery (MCA) were examined with FLAIR and digital subtraction angiography (DSA). HV were graded as 0, 1, 2 and 3 by its distributions in the MCA territory. Grade 0 indicated no HV; Grade 1 indicated the HV limited in Sylvian fissure; Grade 2 indicated the HV limited in Sylvian fissure and the temporal-occipital junction; Grade 3 indicated the HV extended to frontal-parietal lobes. Collateral blood flows were classified by DSA results. The relationship between HV grades and patterns of collateral flows was analyzed. Results: HV were observed in 76 out of 260 hemispheres. For patients with Grade 1 HV, most of their collateral flows (80.8%) were antegrade; for patients with Grade 2, the retrograde leptomeningeal flows were commonly manifested as anterior cerebral artery to MCA (75%); for patients with Grade 3 HV, most of the retrograde leptomeningeal flows were manifested as posterior cerebral artery to MCA (81.8%). As the grade HV increased, the frequency of retrograde leptomeningeal collateral from ACA to MCA decreased (100% to 75% and to 18.2%), and increased (0% to 25% and to 81.8%) for the retrograde leptomeningeal collateral via PCA to MCA (P < 0.001). Conclusions: The HV could assess non-invasively intracerebral collaterals in patients with steno-occlusive lesions of M1 segment of MCA.

  1. FLAIR vascular hyperintensities and 4D MR angiograms for the estimation of collateral blood flow in anterior cerebral artery ischemia.

    Directory of Open Access Journals (Sweden)

    Matthias Gawlitza

    Full Text Available To assess FLAIR vascular hyperintensities (FVH and dynamic (4D angiograms derived from perfusion raw data as proposed magnetic resonance (MR imaging markers of leptomeningeal collateral circulation in patients with ischemia in the territory of the anterior cerebral artery (ACA.Forty patients from two tertiary care university hospitals were included. Infarct volumes and perfusion deficits were manually measured on DWI images and TTP maps, respectively. FVH and collateral flow on 4D MR angiograms were assessed and graded as previously specified.Forty-one hemispheres were affected. Mean DWI lesion volume was 8.2 (± 13.9; range 0-76.9 ml, mean TTP lesion volume was 24.5 (± 17.2, range 0-76.7 ml. FVH were observed in 26/41 (63.4% hemispheres. Significant correlations were detected between FVH and TTP lesion volume (ρ = 0.4; P<0.01 absolute (ρ = 0.37; P<0.05 and relative mismatch volume (ρ = 0.35; P<0.05. The modified ASITN/SIR score correlated inversely with DWI lesion volume (ρ = -0.58; P<0.01 and positively with relative mismatch (ρ = 0.29; P< 0.05. ANOVA of the ASITN/SIR score revealed significant inter-group differences for DWI (P<0.001 and TTP lesion volumes (P<0.05. No correlation was observed between FVH scores and modified ASITH/SIR scores (ρ = -0.16; P = 0.32.FVH and flow patterns on 4D MR angiograms are markers of perfusion deficits and tissue at risk. As both methods did not show a correlation between each other, they seem to provide complimentary instead of redundant information. Previously shown evidence for the meaning of these specific MR signs in internal carotid and middle cerebral artery stroke seems to be transferrable to ischemic stroke in the ACA territory.

  2. Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

    DEFF Research Database (Denmark)

    Thomsen, Martin Christen Frølund; Nielsen, Morten

    2012-01-01

    valuable information related to amino acid depletion. Seq2logo aims at resolving these issues allowing the user to include sequence weighting to correct for data redundancy, pseudo counts to correct for low number of observations and different logotype representations each capturing different aspects...

  3. MR imaging with fluid attenuated inversion recovery sequence of childhood adrenoleukodystrophy : comparison with T2 weighted spin echo imaging

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Asiry; Seo, Jeong-Jin; Jeong, Gwang Woo; Chung, Tae Woong; Jeong, Yong Yeon; Kang, Heoung Keun; Kook, Hoon; Woo, Young Jong; Hwang, Tai Joo [Chonnam Univ. Medical School, Seoul (Korea, Republic of)

    1999-03-01

    The purpose of this study was to evaluate the usefulness of FLAIR(Fluid Attenuated Inversion Recovery) MR imaging in childhood adrenoleukodystrophy by comparing with those of T2-weighted FSE imaging, and to correlate MRI findings with clinical manifestations. Axial FLAIR images(TR/TE/TI=10004/123/2200) and T2-weighted FSE images(TR/TE=4000/104) of brain in six male patients(age range : 6-17 years, mean age : 10.2 years) with biochemically confirmed adrenoleukodystrophy were compared visually by two radiologists for detection, conspicuity, and the extent of lesion. Quantitatively, we compared lesion/CSF contrast, lesion/CSF contrast to noise ratio(CNR), lesion/white matter(WM) contrast, and lesion/WM CNR between FLAIR and T2 weighted image. We correlated MR findings with clinical manifestations of neurologic symptoms and evaluated whether MRI could detect white matter lesions in neurologically asymptomatic patients. Visual detection of lesions was better with FLAIR images in 2 of the 6 cases and it was equal in the remainders. Visual conspicuity and detection of the extent of lesion were superior on FLAIR images than T2-weighted images in all 6 cases. In the quantitative assessment of lesions, FLAIR was superior to T2-weighted image for lesion/CSF contrast and lesion/CSF CNR, but was inferior to T2 weighted image for lesion/WM contrast and lesion/WM CNR. In one case, FLAIR images distinguished the portion of encephalomalacic change from lesions. MR findings of adrenoleukodystrophy were correlated with clinical manifestations in symptomatic 4 cases, and also detected white matter lesions in asymptomatic 2 cases. MR imaging with FLAIR sequence provided images that were equal or superior to T2-weighted images in the evaluation of childhood adrenoleukodystrophy. MRI findings were well correlated with clinical manifestations and could detect white matter lesions in neurologically asymptomatic adrenoleukodystrophy patients.

  4. Comparison of different magnetic resonance cholangiography techniques in living liver donors including Gd-EOB-DTPA enhanced T1-weighted sequences.

    Directory of Open Access Journals (Sweden)

    Sonja Kinner

    Full Text Available 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.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.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 = 0.622-0.804.3D 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.

  5. Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller's organ, of the cattle tick, Rhipicephalus australis.

    Directory of Open Access Journals (Sweden)

    Sergio Munoz

    Full Text Available The cattle tick of Australia, Rhipicephalus australis, is a vector for microbial parasites that cause serious bovine diseases. The Haller's organ, located in the tick's forelegs, is crucial for host detection and mating. To facilitate the development of new technologies for better control of this agricultural pest, we aimed to sequence and annotate the transcriptome of the R. australis forelegs and associated tissues, including the Haller's organ. As G protein-coupled receptors (GPCRs are an important family of eukaryotic proteins studied as pharmaceutical targets in humans, we prioritized the identification and classification of the GPCRs expressed in the foreleg tissues. The two forelegs from adult R. australis were excised, RNA extracted, and pyrosequenced with 454 technology. Reads were assembled into unigenes and annotated by sequence similarity. Python scripts were written to find open reading frames (ORFs from each unigene. These ORFs were analyzed by different GPCR prediction approaches based on sequence alignments, support vector machines, hidden Markov models, and principal component analysis. GPCRs consistently predicted by multiple methods were further studied by phylogenetic analysis and 3D homology modeling. From 4,782 assembled unigenes, 40,907 possible ORFs were predicted. Using Blastp, Pfam, GPCRpred, TMHMM, and PCA-GPCR, a basic set of 46 GPCR candidates were compiled and a phylogenetic tree was constructed. With further screening of tertiary structures predicted by RaptorX, 6 likely GPCRs emerged and the strongest candidate was classified by PCA-GPCR to be a GABAB receptor.

  6. MRI sequences in head and neck radiology. State of the art

    International Nuclear Information System (INIS)

    Widmann, Gerlig; Henninger, Benjamin; Kremser, Christian; Jaschke, Werner

    2017-01-01

    Magnetic resonance imaging (MRI) has become an essential imaging modality for the evaluation of head and neck pathologies. However, the diagnostic power of MRI is strongly related to the appropriate selection and interpretation of imaging protocols and sequences. The aim of this article is to review state-of-the-art sequences for the clinical routine in head and neck MRI and to describe the evidence for which medical question these sequences and techniques are useful. Literature review of state-of-the-art sequences in head and neck MRI. Basic sequences (T1w, T2w, T1wC+) and fat suppression techniques (TIRM/STIR, Dixon, Spectral Fat sat) are important tools in the diagnostic workup of inflammation, congenital lesions and tumors including staging. Additional sequences (SSFP (CISS, FIESTA), SPACE, VISTA, 3D-FLAIR) are used for pathologies of the cranial nerves, labyrinth and evaluation of endolymphatic hydrops in Meniere's disease. Vessel and perfusion sequences (3D-TOF, TWIST/TRICKS angiography, DCE) are used in vascular contact syndromes, vascular malformations and analysis of microvascular parameters of tissue perfusion. Diffusion-weighted imaging (EPI-DWI, non-EPI-DWI, RESOLVE) is helpful in cholesteatoma imaging, estimation of malignancy, and evaluation of treatment response and posttreatment recurrence in head and neck cancer. Understanding of MRI sequences and close collaboration with referring physicians improves the diagnostic confidence of MRI in the daily routine and drives further research in this fascinating image modality.

  7. MRI sequences in head and neck radiology. State of the art

    Energy Technology Data Exchange (ETDEWEB)

    Widmann, Gerlig; Henninger, Benjamin; Kremser, Christian; Jaschke, Werner [Medical Univ. of Innsbruck (Austria). Dept. of Radiology

    2017-05-15

    Magnetic resonance imaging (MRI) has become an essential imaging modality for the evaluation of head and neck pathologies. However, the diagnostic power of MRI is strongly related to the appropriate selection and interpretation of imaging protocols and sequences. The aim of this article is to review state-of-the-art sequences for the clinical routine in head and neck MRI and to describe the evidence for which medical question these sequences and techniques are useful. Literature review of state-of-the-art sequences in head and neck MRI. Basic sequences (T1w, T2w, T1wC+) and fat suppression techniques (TIRM/STIR, Dixon, Spectral Fat sat) are important tools in the diagnostic workup of inflammation, congenital lesions and tumors including staging. Additional sequences (SSFP (CISS, FIESTA), SPACE, VISTA, 3D-FLAIR) are used for pathologies of the cranial nerves, labyrinth and evaluation of endolymphatic hydrops in Meniere's disease. Vessel and perfusion sequences (3D-TOF, TWIST/TRICKS angiography, DCE) are used in vascular contact syndromes, vascular malformations and analysis of microvascular parameters of tissue perfusion. Diffusion-weighted imaging (EPI-DWI, non-EPI-DWI, RESOLVE) is helpful in cholesteatoma imaging, estimation of malignancy, and evaluation of treatment response and posttreatment recurrence in head and neck cancer. Understanding of MRI sequences and close collaboration with referring physicians improves the diagnostic confidence of MRI in the daily routine and drives further research in this fascinating image modality.

  8. Single-shot echo-planar MR sequences in the diagnosis of intracranial infectious diseases

    International Nuclear Information System (INIS)

    Tsuchiya, Kazuhiro; Katase, Shichiro; Yoshino, Ayako; Yamakami, Norio; Hachiya, Junichi

    1998-01-01

    The purpose of this study was to present our preliminary experience in the application of echo-planar-imaging (EPI) MR sequences for the diagnosis of intracranial infectious diseases and to assess the value of these sequences. We reviewed single-shot EPI MR images obtained at 1.5 T in 17 patients and compared these images with conventional or fast spin-echo (SE) or fluid attenuated inversion-recovery (FLAIR) images. The clinical diagnoses for the 17 patients were meningitis (2 patients), encephalitis or meningoencephalitis (7 patients), brain abscess (5 patients), epidural empyema (2 patients) and Creutzfeldt-Jakob disease (1 patient). We obtained EPI-T 2 -weighted (T 2 W) images in 8 patients, EPI-FLAIR images in 13 patients and EPI-diffusion-weighted (DW) images in 14 patients. Among the 8 patients for whom EPI-T 2 W imaging was performed, EPI-T 2 W imaging yielded superior results compared with SE-T 2 W imaging in 3 patients as a consequence of patient motion and equal results compared with SE-T 2 W imaging in 5 patients. Among the 13 patients for whom EPI-FLAIR imaging was performed, the EPI-FLAIR images were superior to conventional FLAIR images in 3 unstable patients. In the remaining 10 patients for whom EPI-FLAIR imaging was performed, EPI-FLAIR images were equivalent or inferior to conventional FLAIR images. In 6 patients with encephalitis or meningoencephalitis, the encephalitic lesions showed hyperintensity in EPI-DW images to a greater extent than in images obtained with the other techniques. In 3 patients, EPI-DW images also demonstrated hyperintensity for the contents of abscesses or areas of empyema that was not seen with the other imaging techniques. The value of EPI-T 2 W and EPI-FLAIR imaging is limited in uncooperative patients. EPI-DW imaging was found to be of value for the evaluation of several intracranial infectious diseases. (author)

  9. Single-shot echo-planar MR sequences in the diagnosis of intracranial infectious diseases

    Energy Technology Data Exchange (ETDEWEB)

    Tsuchiya, Kazuhiro; Katase, Shichiro; Yoshino, Ayako; Yamakami, Norio; Hachiya, Junichi [Kyorin Univ., Mitaka, Tokyo (Japan). School of Medicine

    1998-06-01

    The purpose of this study was to present our preliminary experience in the application of echo-planar-imaging (EPI) MR sequences for the diagnosis of intracranial infectious diseases and to assess the value of these sequences. We reviewed single-shot EPI MR images obtained at 1.5 T in 17 patients and compared these images with conventional or fast spin-echo (SE) or fluid attenuated inversion-recovery (FLAIR) images. The clinical diagnoses for the 17 patients were meningitis (2 patients), encephalitis or meningoencephalitis (7 patients), brain abscess (5 patients), epidural empyema (2 patients) and Creutzfeldt-Jakob disease (1 patient). We obtained EPI-T{sub 2}-weighted (T{sub 2}W) images in 8 patients, EPI-FLAIR images in 13 patients and EPI-diffusion-weighted (DW) images in 14 patients. Among the 8 patients for whom EPI-T{sub 2}W imaging was performed, EPI-T{sub 2}W imaging yielded superior results compared with SE-T{sub 2}W imaging in 3 patients as a consequence of patient motion and equal results compared with SE-T{sub 2}W imaging in 5 patients. Among the 13 patients for whom EPI-FLAIR imaging was performed, the EPI-FLAIR images were superior to conventional FLAIR images in 3 unstable patients. In the remaining 10 patients for whom EPI-FLAIR imaging was performed, EPI-FLAIR images were equivalent or inferior to conventional FLAIR images. In 6 patients with encephalitis or meningoencephalitis, the encephalitic lesions showed hyperintensity in EPI-DW images to a greater extent than in images obtained with the other techniques. In 3 patients, EPI-DW images also demonstrated hyperintensity for the contents of abscesses or areas of empyema that was not seen with the other imaging techniques. The value of EPI-T{sub 2}W and EPI-FLAIR imaging is limited in uncooperative patients. EPI-DW imaging was found to be of value for the evaluation of several intracranial infectious diseases. (author)

  10. Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench.

    Science.gov (United States)

    Beckers, Matthew; Mohorianu, Irina; Stocks, Matthew; Applegate, Christopher; Dalmay, Tamas; Moulton, Vincent

    2017-06-01

    Recently, high-throughput sequencing (HTS) has revealed compelling details about the small RNA (sRNA) population in eukaryotes. These 20 to 25 nt noncoding RNAs can influence gene expression by acting as guides for the sequence-specific regulatory mechanism known as RNA silencing. The increase in sequencing depth and number of samples per project enables a better understanding of the role sRNAs play by facilitating the study of expression patterns. However, the intricacy of the biological hypotheses coupled with a lack of appropriate tools often leads to inadequate mining of the available data and thus, an incomplete description of the biological mechanisms involved. To enable a comprehensive study of differential expression in sRNA data sets, we present a new interactive pipeline that guides researchers through the various stages of data preprocessing and analysis. This includes various tools, some of which we specifically developed for sRNA analysis, for quality checking and normalization of sRNA samples as well as tools for the detection of differentially expressed sRNAs and identification of the resulting expression patterns. The pipeline is available within the UEA sRNA Workbench, a user-friendly software package for the processing of sRNA data sets. We demonstrate the use of the pipeline on a H. sapiens data set; additional examples on a B. terrestris data set and on an A. thaliana data set are described in the Supplemental Information A comparison with existing approaches is also included, which exemplifies some of the issues that need to be addressed for sRNA analysis and how the new pipeline may be used to do this. © 2017 Beckers et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  11. Morphology and SSU rDNA sequence analysis of two hypotrichous ciliates (Protozoa, Ciliophora, Hypotrichia) including the new species Metaurostylopsis parastruederkypkeae n. sp.

    Science.gov (United States)

    Lu, Borong; Wang, Chundi; Huang, Jie; Shi, Yuhong; Chen, Xiangrui

    2016-10-01

    The morphology and phylogeny of two hypotrichous ciliates, Metaurostylopsis parastruederkypkeae n. sp. and Neourostylopsis flavicana (Wang et al., 2011) Chen et al., 2013 were investigated based on morphology, infraciliature and the small subunit (SSU) ribosomal RNA gene (rRNA) sequence. The new species, M. parastruederkypkeae n. sp. was identified according to its characteristics: body shape ellipsoidal, size about (165-200) × (45-60) μm in vivo, cell color reddish; two types of cortical granules including wheat grain-like and yellow-greenish larger ones along the marginal cirri rows and dorsal kineties and dot-like and reddish smaller ones, grouped around marginal cirri on ventral side and arranged in short lines on dorsal side; 26-41 adoral membranelles; three frontal and one parabuccal, five to seven frontoterminal, one buccal, and three to six transverse cirri; seven to thirteen midventral pairs; five to nine unpaired ventral cirri, five to seven left and three to five right marginal rows; and three complete dorsal kineties. Phylogenetic analysis based on SSU rDNA sequences showed that both Metaurostylopsis and Neourostylopsis are monophyletic. As the internal relationship between and within both genera are not clear, further studies on the species in these two genera are necessary. The key characteristics of all known twelve Metaurostylopsis-Apourostylopsis-Neourostylopsis species complex were updated.

  12. Prevalence and sequence variations of the genes encoding the five antigens included in the novel 5CVMB vaccine covering group B meningococcal disease.

    Science.gov (United States)

    Jacobsson, Susanne; Hedberg, Sara Thulin; Mölling, Paula; Unemo, Magnus; Comanducci, Maurizio; Rappuoli, Rino; Olcén, Per

    2009-03-04

    During the recent years, projects are in progress for designing broad-range non-capsular-based meningococcal vaccines, covering also serogroup B isolates. We have examined three genes encoding antigens (NadA, GNA1030 and GNA2091) included in a novel vaccine, i.e. the 5 Component Vaccine against Meningococcus B (5CVMB), in terms of gene prevalence and sequence variations. These data were combined with the results from a similar study, examining the two additional antigens included in the 5CVMB (fHbp and GNA2132). nadA and fHbp v. 1 were present in 38% (n=36), respectively 71% (n=67) of the isolates, whereas gna2132, gna1030 and gna2091 were present in all the Neisseria meningitidis isolates tested (n=95). The level of amino acid conservation was relatively high in GNA1030 (93%), GNA2091 (92%), and within the main variants of NadA and fHbp. GNA2132 (54% of the amino acids conserved) appeared to be the most diversified antigen. Consequently, the theoretical coverage of the 5CVMB antigens and the feasibility to use these in a broad-range meningococcal vaccine is appealing.

  13. [A case of atypical type of Sturge-Weber syndrome demonstrated reversible change by MRI FLAIR method in ictus and in postictal state].

    Science.gov (United States)

    Sasaki, M; Igarashi, K; Suzuki, S; Saito, K

    1999-07-01

    We report a patient of atypical type of Sturge-Weber syndrome who demonstrated a reversible change by MRI FLAIR method in ictus and postictal state. A 5-year-old boy was admitted to our hospital because of severe headache, vomiting and loss of consciousness with his eyes conjugated to left for a few minutes. He had no facial nevus and other abnormal findings in physical examination. CT scan showed two small calcifications in the right occipital lobe. Postcontrast T 1-weighted image of MRI demonstrated a right parieto-occipital leptomeningeal enhancement. We diagnosed this case as an atypical type of Sturge-Weber syndrome. Although, on admission, FLAIR method showed the area of high signal intensity, after anticonvulsant therapy, those abnormal area disappeared. It is presumably detected by FLAIR method slight extravasation of plasma element in the surface of the brain due to regional hyperperfusion in ictus.

  14. Relationship between fluid-attenuated inversion-recovery (FLAIR) signal intensity and inflammatory mediator's levels in the hippocampus of patients with temporal lobe epilepsy and mesial temporal sclerosis.

    Science.gov (United States)

    Varella, Pedro Paulo Vasconcellos; Santiago, Joselita Ferreira Carvalho; Carrete, Henrique; Higa, Elisa Mieko Suemitsu; Yacubian, Elza Márcia Targas; Centeno, Ricardo Silva; Caboclo, Luís Otávio Sales Ferreira; Castro Neto, Eduardo Ferreira de; Canzian, Mauro; Amado, Débora; Cavalheiro, Esper Abrão; Naffah-Mazzacoratti, Maria da Graça

    2011-02-01

    We investigated a relationship between the FLAIR signal found in mesial temporal sclerosis (MTS) and inflammation. Twenty nine patients were selected through clinical and MRI analysis and submitted to cortico-amygdalo-hippocampectomy to seizure control. Glutamate, TNFα, IL1, nitric oxide (NO) levels and immunostaining against IL1β and CD45 was performed. Control tissues (n=10) were obtained after autopsy of patients without neurological disorders. The glutamate was decreased in the temporal lobe epilepsy (TLE) -MTS group (p<0.001), suggesting increased release of this neurotransmitter. The IL1β and TNFα were increased in the hippocampus (p<0.05) demonstrating an active inflammatory process. A positive linear correlation between FLAIR signal and NO and IL1β levels and a negative linear correlation between FLAIR signal and glutamate concentration was found. Lymphocytes infiltrates were present in hippocampi of TLE patients. These data showed an association between hippocampal signal alteration and increased inflammatory markers in TLE-MTS.

  15. Detection of Subarachnoid Hemorrhage at Acute and Subacute/Chronic Stages: Comparison of Four Magnetic Resonance Imaging Pulse Sequences and Computed Tomography

    Directory of Open Access Journals (Sweden)

    Mei-Kang Yuan

    2005-03-01

    Conclusion: FLAIR and GE T2* MRI pulse sequences, and CT scans, are all statistically significant indicators of acute SAH. GE T2*-weighted images are statistically significant indicators of subacute-to-chronic SAH, whereas other MRI pulse sequences, and CT scans, are not.

  16. L'uso del doppiaggio e del sottotitolaggio nell'insegnamento della L2: Il caso della piattaforma ClipFlair

    Directory of Open Access Journals (Sweden)

    Lupe Romero

    2016-01-01

    Full Text Available Abstract – The purpose of this paper is to present the Clipflair project, a web platform for foreign language learning (FLL through revoicing and captioning of clips. Using audiovisual material in the language classroom is a common resource for teachers since it introduces variety, provides exposure to nonverbal cultural elements and, most importantly, presents linguistic and cultural aspects of communication in their context. However, teachers using this resource face the difficulty of finding active tasks that will engage learners and discourage passive viewing. ClipFlair proposes working with AV material productively while also motivating learners by getting them to revoice or caption a clip. Revoicing is a term used to refer to (rerecording voice onto a clip, as in dubbing, free commentary, audio description and karaoke singing. The term captioning refers to adding written text to a clip, such as standard subtitles, annotations and intertitles. Clips can be short video or audio files, including documentaries, film scenes, news pieces, animations and songs. ClipFlair develops materials that enable foreign language learners to practice all four standard CEFR skills: writing, speaking, listening and reading. Within the project’s scope, more than 350 ready-made activities, which involve captioning and/or revoicing of clips, has been created. These activities has been created for more than 16 languages including English, Spanish and Italian, but focus is placed on less widely taught languages, namely Estonian, Greek, Romanian and Polish, as well as minority languages, i.e. Basque, Catalan and Irish. Non-European languages, namely Arabic, Chinese, Japanese, Russian and Ukrainian are also included. The platform has three different areas: The Gallery offers the materials and the activities; the Studio area, offers a captioning and revoicing tools, in order to create or practice and learn languages by using the activities; the Social Network area

  17. T2-FLAIR Mismatch, an Imaging Biomarker for IDH and 1p/19q Status in Lower-grade Gliomas: A TCGA/TCIA Project.

    Science.gov (United States)

    Patel, Sohil H; Poisson, Laila M; Brat, Daniel J; Zhou, Yueren; Cooper, Lee; Snuderl, Matija; Thomas, Cheddhi; Franceschi, Ana M; Griffith, Brent; Flanders, Adam E; Golfinos, John G; Chi, Andrew S; Jain, Rajan

    2017-10-15

    Purpose: Lower-grade gliomas (WHO grade II/III) have been classified into clinically relevant molecular subtypes based on IDH and 1p/19q mutation status. The purpose was to investigate whether T2/FLAIR MRI features could distinguish between lower-grade glioma molecular subtypes. Experimental Design: MRI scans from the TCGA/TCIA lower grade glioma database ( n = 125) were evaluated by two independent neuroradiologists to assess (i) presence/absence of homogenous signal on T2WI; (ii) presence/absence of "T2-FLAIR mismatch" sign; (iii) sharp or indistinct lesion margins; and (iv) presence/absence of peritumoral edema. Metrics with moderate-substantial agreement underwent consensus review and were correlated with glioma molecular subtypes. Somatic mutation, DNA copy number, DNA methylation, gene expression, and protein array data from the TCGA lower-grade glioma database were analyzed for molecular-radiographic associations. A separate institutional cohort ( n = 82) was analyzed to validate the T2-FLAIR mismatch sign. Results: Among TCGA/TCIA cases, interreader agreement was calculated for lesion homogeneity [ κ = 0.234 (0.111-0.358)], T2-FLAIR mismatch sign [ κ = 0.728 (0.538-0.918)], lesion margins [ κ = 0.292 (0.135-0.449)], and peritumoral edema [ κ = 0.173 (0.096-0.250)]. All 15 cases that were positive for the T2-FLAIR mismatch sign were IDH -mutant, 1p/19q non-codeleted tumors ( P mismatch sign [ κ = 0.747 (0.536-0.958)]; all 10 cases positive for the T2-FLAIR mismatch sign were IDH -mutant, 1p/19q non-codeleted tumors ( P mismatch sign represents a highly specific imaging biomarker for the IDH -mutant, 1p/19q non-codeleted molecular subtype. Clin Cancer Res; 23(20); 6078-85. ©2017 AACR . ©2017 American Association for Cancer Research.

  18. Comparison of Different 3.0 T Magnetic Resonance Sequences for Lumbosacral Plexus and Its Branches: Preliminary Study

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Hyuk Joon; Lee, Joon Woo; Lee, Jee Hye; Kang, Heung Sik [Dept. of Radiology, Seoul National University Bundang Hospital, Seongnam (Korea, Republic of)

    2013-01-15

    To prospectively evaluate four magnetic resonance sequences [ProSet, fluid attenuation inversion recovery (FLAIR), balanced turbo field echo (B-TFE), T2 Drive] for the lumbosacral plexus and its branches. Ten healthy volunteers who underwent four MRI sequences on lumbosacral area were evaluated for image quality (1 to 5; 1 = poor, 5 = excellent), the number of visualized bilateral spinal nerves from L2 to S1, the overlapping vessels obscuring the plexus (1 = many, 2 = some, 3 = few), and image quality defining spinal nerves (0 = nonvisualized, 1 = poor, 2 = moderate, 3 = good). The ProSet (mean = 4.2, range 3-5) and B-TFE (mean = 3.7, range 3-5) showed better image quality than others. The number of visualized spinal nerves was the largest on ProSet image (mean = 9.2, range 8-10). FLAIR (mean = 2.1, range 1-3) and T2 Drive sequences (mean = 2.1, range 1-3) discriminated the nerves well from the vessels. The main branches of the lumbosacral plexus were well visualized on both ProSet (mean = 2.9, range 2-3) and FLAIR images (mean = 2.6, range 1-3). All of these were statistically significant. ProSet is the best sequence in the evaluation of the lumbosacral plexus and its major branches while FLAIR can be a complementary sequence for the evaluation of nerves overlapping vascular structures.

  19. High-throughput sequencing reveals microbial communities in drinking water treatment sludge from six geographically distributed plants, including potentially toxic cyanobacteria and pathogens.

    Science.gov (United States)

    Xu, Hangzhou; Pei, Haiyan; Jin, Yan; Ma, Chunxia; Wang, Yuting; Sun, Jiongming; Li, Hongmin

    2018-04-10

    The microbial community structures of drinking water treatment sludge (DWTS) generated for raw water (RW) from different locations and with different source types - including river water, lake water and reservoir water -were investigated using high-throughput sequencing. Because the unit operations in the six DWTPs were similar, community composition in fresh sludge may be determined by microbial community in the corresponding RW. Although Proteobacteria, Cyanobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Planctomycetes were the dominant phyla among the six DWTS samples, no single phylum exhibited similar abundance across all the samples, owing to differences in total phosphorus, chemical oxygen demand, Al, Fe, and chloride in RW. Three genera of potentially toxic cyanobacteria (Planktothrix, Microcystis and Cylindrospermopsis), and four potential pathogens (Escherichia coli, Bacteroides ovatus, Prevotella copri and Rickettsia) were found in sludge samples. Because proliferation of potentially toxic cyanobacteria and Rickettsia in RW was mainly affected by nutrients, while growth of Escherichia coli, Bacteroides ovatus and Prevotella copri in RW may be influenced by Fe, control of nutrients and Fe in RW is essential to decrease toxic cyanobacteria and pathogens in DWTS. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Identification and characterization of intervening sequences within 23S rRNA genes from more than 200 Campylobacter isolates from seven species including atypical campylobacters

    Directory of Open Access Journals (Sweden)

    Millar Beverley C

    2009-12-01

    Full Text Available Abstract Background Identification and characterization of intervening sequences (IVSs within 23S rRNA genes from Campylobacter organisms including atypical campylobacters were carried out using two PCR primer pairs, designed to generate helix 25 and 45 regions. Results Only C. sputorum biovar sputorum LMG7975 and fecalis LMG8531, LMG8534 and LMG6728 of a total of 204 Campylobacter isolates (n = 56 C. jejuni; n = 11 C. coli; n = 33 C. fetus; n = 43 C. upsaliensis; n = 30 C. hyointestinalis; n = 4 C. sputorum biovar sputorum; n = 5 C. sputorum biovar fecalis; n = 5 C. sputorum biovar paraureolyticus; n = 10 C. concisus; n = 7 C. curvus were shown to carry IVSs in helix 25 region. C. sputorum biovar fecalis LMG8531 and LMG8534, interestingly, carried two different kinds of the 23S rRNA genes with and without the IVS, respectively. Consequently, in a total of 265 isolates of 269, including 65 C. lari isolates examined previously, the absence of IVSs was identified in the helix 25 region. In the helix 45 region, all the C. hyointestinalis, C. sputorum and C. concisus isolates were shown not to carry any IVSs. However, the 30 of 56 C. jejuni isolates (54%, 5 of 11 C. coli (45%, 25 of 33 C. fetus (76%, 30 of 43 C. upsaliensis (70% and 6 of 7 C. curvus (90% were shown to carry IVSs. In C. jejuni and C. upsaliensis isolates, two different kinds of the 23S rRNA genes were also identified to occur with and without IVSs in the helix 45 region, respectively. Conclusions Secondary structure models were also constructed with all the IVSs identified in the present study. In the purified RNA fractions from the isolates which carried the 16S or 23S rRNA genes with the IVSs, no 16S or 23S rRNA was evident, respectively.

  1. Development and analytical validation of a 25-gene next generation sequencing panel that includes the BRCA1 and BRCA2 genes to assess hereditary cancer risk.

    Science.gov (United States)

    Judkins, Thaddeus; Leclair, Benoît; Bowles, Karla; Gutin, Natalia; Trost, Jeff; McCulloch, James; Bhatnagar, Satish; Murray, Adam; Craft, Jonathan; Wardell, Bryan; Bastian, Mark; Mitchell, Jeffrey; Chen, Jian; Tran, Thanh; Williams, Deborah; Potter, Jennifer; Jammulapati, Srikanth; Perry, Michael; Morris, Brian; Roa, Benjamin; Timms, Kirsten

    2015-04-02

    Germline DNA mutations that increase the susceptibility of a patient to certain cancers have been identified in various genes, and patients can be screened for mutations in these genes to assess their level of risk for developing cancer. Traditional methods using Sanger sequencing focus on small groups of genes and therefore are unable to screen for numerous genes from several patients simultaneously. The goal of the present study was to validate a 25-gene panel to assess genetic risk for cancer in 8 different tissues using next generation sequencing (NGS) techniques. Twenty-five genes associated with hereditary cancer syndromes were selected for development of a panel to screen for risk of these cancers using NGS. In an initial technical assessment, NGS results for BRCA1 and BRCA2 were compared with Sanger sequencing in 1864 anonymized DNA samples from patients who had undergone previous clinical testing. Next, the entire gene panel was validated using parallel NGS and Sanger sequencing in 100 anonymized DNA samples. Large rearrangement analysis was validated using NGS, microarray comparative genomic hybridization (CGH), and multiplex ligation-dependent probe amplification analyses (MLPA). NGS identified 15,877 sequence variants, while Sanger sequencing identified 15,878 in the BRCA1 and BRCA2 comparison study of the same regions. Based on these results, the NGS process was refined prior to the validation of the full gene panel. In the validation study, NGS and Sanger sequencing were 100% concordant for the 3,923 collective variants across all genes for an analytical sensitivity of the NGS assay of >99.92% (lower limit of 95% confidence interval). NGS, microarray CGH and MLPA correctly identified all expected positive and negative large rearrangement results for the 25-gene panel. This study provides a thorough validation of the 25-gene NGS panel and indicates that this analysis tool can be used to collect clinically significant information related to risk of

  2. Clinical value of periventricular low-intensity areas detected by fluid attenuated inversion recovery (FLAIR). Relationships between perinatal vital parameter and neonatal MRI

    Energy Technology Data Exchange (ETDEWEB)

    Kadowaki, Sachiko; Iwata, Osuke; Tamura, Masanori [Nagano Children' s Hospital, Toyoshina (Japan)] (and others)

    2002-01-01

    A follow-up study was performed to assess the correlation among the incidence of periventricular low intensities (PVLI) on MRI (magnetic resonance imaging) FLAIR (fluid attenuated inversion recovery) imaging, clinical evidence of perinatal insults that may cause white matter damage, and the outcome of the infants. We evaluated periventricular white matter lesions of 329 neonates whose MRI were obtained before two months corrected age. The detective rate of periventricular abnormalities on FLAIR imaging was significantly higher than that of T1-T2 weighted imaging. The most typical lesion detected on FLAIR imaging was periventricular low intensities (PVLI), frequently observed in the neonates with a history of preterm labour, very low birth weight, birth asphyxia and severe respiratory failure. Although we could not characterize the risk factors of PVLI, the incidence of PVLI had a strong correlation with the scores of motor and developmental tests at 12 and 36-months corrected age. In conclusion, FLAIR imaging, detecting the border zone damage of white matter, would be a strong tool to pick out neonates at high risk of neurological disturbances from those without clinical evidence of neurological insults in the neonatal period. (author)

  3. A prospective comparison study of fast T1 weighted fluid attenuation inversion recovery and T1 weighted turbo spin echo sequence at 3 T in degenerative disease of the cervical spine.

    Science.gov (United States)

    Ganesan, K; Bydder, G M

    2014-09-01

    This study compared T1 fluid attenuation inversion recovery (FLAIR) and T1 turbo spin echo (TSE) sequences for evaluation of cervical spine degenerative disease at 3 T. 72 patients (44 males and 28 females; mean age of 39 years; age range, 27-75 years) with suspected cervical spine degenerative disease were prospectively evaluated. Sagittal images of the spine were obtained using T1 FLAIR and T1 TSE sequences. Two experienced neuroradiologists compared the sequences qualitatively and quantitatively. On qualitative evaluation, cerebrospinal fluid (CSF) nulling and contrast at cord-CSF, disc-CSF and disc-cord interfaces were significantly higher on fast T1 FLAIR images than on T1 TSE images (p degenerative disease, owing to higher cord-CSF, disc-cord and disc-CSF contrast. However, intrinsic cord contrast is low on T1 FLAIR images. T1 FLAIR is more promising and sensitive than T1 TSE for evaluation of degenerative spondyloarthropathy and may provide a foundation for development of MR protocols for early detection of degenerative and neoplastic diseases.

  4. MRI of the brain stem using fluid attenuated inversion recivery pulse sequences

    International Nuclear Information System (INIS)

    De Coene, B.; Hajnal, J.V.; Pennock, J.M.; Bydder, G.M.

    1993-01-01

    Heavily T2-weighted fluid-attenuated inversion recovery (FLAIR) sequences with inversion times of 2000-2500 ms and echo times of 130-200 ms were used to image the brain stem of a normal adult and five patients. These sequences produce high signal from many white matter tracts and display high lesion contrast. The corticospinal and parietopontine tracts, lateral and medial lemnisci, superior and inferior cerebellar peduncles, medial longitudinal fasciculi, thalamo-olivary tracts the cuneate and gracile fasiculi gave high signal and were directly visualised. The oculomotor and trigeminal nerves were demonstrated within the brain stem. Lesions not seen with conventional T2-weighted spin echo sequences were seen with high contrast in patients with infarction, multiple sclerosis, sarcoidosis, chunt obstruction and metastatic tumour. The anatomical detail and high lesion contrast given by the FLAIR pulse sequence appear likely to be of value in diagnosis of disease in the brain stem. (orig.)

  5. Automated segmentation of MS lesions in FLAIR, DIR and T2-w MR images via an information theoretic approach

    Science.gov (United States)

    Hill, Jason E.; Matlock, Kevin; Pal, Ranadip; Nutter, Brian; Mitra, Sunanda

    2016-03-01

    Magnetic Resonance Imaging (MRI) is a vital tool in the diagnosis and characterization of multiple sclerosis (MS). MS lesions can be imaged with relatively high contrast using either Fluid Attenuated Inversion Recovery (FLAIR) or Double Inversion Recovery (DIR). Automated segmentation and accurate tracking of MS lesions from MRI remains a challenging problem. Here, an information theoretic approach to cluster the voxels in pseudo-colorized multispectral MR data (FLAIR, DIR, T2-weighted) is utilized to automatically segment MS lesions of various sizes and noise levels. The Improved Jump Method (IJM) clustering, assisted by edge suppression, is applied to the segmentation of white matter (WM), gray matter (GM), cerebrospinal fluid (CSF) and MS lesions, if present, into a subset of slices determined to be the best MS lesion candidates via Otsu's method. From this preliminary clustering, the modal data values for the tissues can be determined. A Euclidean distance is then used to estimate the fuzzy memberships of each brain voxel for all tissue types and their 50/50 partial volumes. From these estimates, binary discrete and fuzzy MS lesion masks are constructed. Validation is provided by using three synthetic MS lesions brains (mild, moderate and severe) with labeled ground truths. The MS lesions of mild, moderate and severe designations were detected with a sensitivity of 83.2%, and 88.5%, and 94.5%, and with the corresponding Dice similarity coefficient (DSC) of 0.7098, 0.8739, and 0.8266, respectively. The effect of MRI noise is also examined by simulated noise and the application of a bilateral filter in preprocessing.

  6. Experimental acute intracerebral hemorrhage: Value of MR sequences for a safe diagnosis at 1.5 and 0.5 T

    International Nuclear Information System (INIS)

    Kueker, W.; Thron, A.; Thiex, R.; Rohde, I.; Rohde, V.

    2000-01-01

    To determine the detectability of intracerebral hematomas with MR imaging at 1.5 T and 0.5 T with fluid attenuated inversion recovery turbo spin-echo (FLAIR) and gradient-echo sequences. Material and Methods: Twenty-seven intracerebral hematomas were created in 25 piglets by injection of venous blood into the brain through a burr hole. All were imaged with T2*-weighted gradient echo sequences (fast field echo, FFE), T2-weighted fluid attenuated inversion recovery turbo spin-echo sequences (FLAIR), T2-weighted turbo spin-echo (TSE) and T1-weighted spin-echo sequences. Follow-up was performed on the 2nd, 4th and 10th postoperative days. Ten animals were additionally investigated with similar sequences at 0.5 T. Histologic correlation was obtained in all cases. Results: T2* FFE sequences detected all acute intracerebral hematomas and demonstrated the size correctly at 1.5 T and 0.5 T. The conspicuity was better at 1.5 T. FLAIR sequences were unreliable in the hyperacute phase at 1.5 T. However, subarachnoid and intraventricular extension was best appreciated with FLAIR images. T2 TSE images were incapable of detecting para ventricular and subarachnoid hemorrhages, but clearly demonstrated intracerebral blood in other locations. T1-weighted images were insensitive to hemorrhage in the acute state but very useful in subacute and chronic hematomas. Conclusion: The safe and reliable diagnosis of intracerebral hemorrhage is probably possible with MR imaging at 1.5 T and 0.5 T even of hematomas less than 90 min old, but requires the application of at least FLAIR, T2* FFE and T1 sequences and is therefore time consuming

  7. Catalogue of generic plant states leading to core melt in PWRs: includes appendix 1: detailed description of sequences leading to core melt

    International Nuclear Information System (INIS)

    1996-11-01

    The Task Group on thermal-hydraulic system behaviour was given a mandate from PWG 2 on Coolant System-Behaviour with the approval of CSNI to deal with the topic of Accident Management. A writing group was set up to identify generic plant states leading to core melt for pressurized water reactors (PWR) and find 'possible approaches to accident management measures' (AM-Measures) for dealing with them. From a matrix of 15 initiating events and 12 system failures (i.e. from 180 possibilities), 32 event sequences have been identified as leading to core melt. Each sequence has been divided into characteristic plant state intervals according to safety function challenges. For each of the 141 defined characteristic plant state intervals, the members of the Writing Group made proposals for AM-Measures

  8. Evaluation of multimodal segmentation based on 3D T1-, T2- and FLAIR-weighted images - the difficulty of choosing.

    Science.gov (United States)

    Lindig, Tobias; Kotikalapudi, Raviteja; Schweikardt, Daniel; Martin, Pascal; Bender, Friedemann; Klose, Uwe; Ernemann, Ulrike; Focke, Niels K; Bender, Benjamin

    2018-04-15

    Voxel-based morphometry is still mainly based on T1-weighted MRI scans. Misclassification of vessels and dura mater as gray matter has been previously reported. Goal of the present work was to evaluate the effect of multimodal segmentation methods available in SPM12, and their influence on identification of age related atrophy and lesion detection in epilepsy patients. 3D T1-, T2- and FLAIR-images of 77 healthy adults (mean age 35.8 years, 19-66 years, 45 females), 7 patients with malformation of cortical development (MCD) (mean age 28.1 years,19-40 years, 3 females), and 5 patients with left hippocampal sclerosis (LHS) (mean age 49.0 years, 25-67 years, 3 females) from a 3T scanner were evaluated. Segmentation based on T1-only, T1+T2, T1+FLAIR, T2+FLAIR, and T1+T2+FLAIR were compared in the healthy subjects. Clinical VBM results based on the different segmentation approaches for MCD and for LHS were compared. T1-only segmentation overestimated total intracranial volume by about 80ml compared to the other segmentation methods. This was due to misclassification of dura mater and vessels as GM and CSF. Significant differences were found for several anatomical regions: the occipital lobe, the basal ganglia/thalamus, the pre- and postcentral gyrus, the cerebellum, and the brainstem. None of the segmentation methods yielded completely satisfying results for the basal ganglia/thalamus and the brainstem. The best correlation with age could be found for the multimodal T1+T2+FLAIR segmentation. Highest T-scores for identification of LHS were found for T1+T2 segmentation, while highest T-scores for MCD were dependent on lesion and anatomical location. Multimodal segmentation is superior to T1-only segmentation and reduces the misclassification of dura mater and vessels as GM and CSF. Depending on the anatomical region and the pathology of interest (atrophy, lesion detection, etc.), different combinations of T1, T2 and FLAIR yield optimal results. Copyright © 2017 Elsevier

  9. MR features of the developing perianterior horn structure including subcallosal fasciculus in infants and children

    Energy Technology Data Exchange (ETDEWEB)

    Utsunomiya, Hidetsuna [Fukuoka University School of Medicine, Department of Diagnostic Radiology, Nanakuma, Jonan-ku, Fukuoka (Japan); Nakamura, Yasuhiro [St. Mary' s Hospital, Department of Pathology, Kurume (Japan)

    2007-11-15

    To describe the changes in the magnetic resonance (MR) signal of the perianterior horn structure (PAS) with increasing age, we studied 69 infants and children aged between 3 days and 9.4 years (average: 2.8 years) without any neurological deficits. T1- and T2-weighted images and FLAIR (fluid attenuation inversion recovery) images were obtained in the axial plane. Based on a comparison of the intensity of the PAS with that of the cortex in each sequence (T1-WI/FLAIR/T2-WI), we classified the signal-intensity patterns into four types: I, low/low/high; II, low/high/high; III, iso/high/high; IV, high/low/low. Signal-intensity types I, II, III and IV were seen in 22, 8, 17, and 22 subjects, respectively, with younger subjects showing type I or II intensity patterns and older subjects showing type III or IV. In addition, T1-weighted and FLAIR images of subjects with a type I intensity pattern showed a rim of an isointensity component around the PAS that histologically coincided with migrating glial cells. The low-intensity area on FLAIR and T2-WI images of subjects with a type IV intensity pattern may represent myelinated fibers of the subcallosal fasciculus (ScF). The intensity of the MR signals of the PAS changes with increasing age, and this change may reflect histological features. A better understanding of these characteristics may help us to clarify myelination abnormalities, particularly those related to the ScF in the frontal lobe in infants and children. (orig.)

  10. A 1-minute full brain MR exam using a multicontrast EPI sequence.

    Science.gov (United States)

    Skare, Stefan; Sprenger, Tim; Norbeck, Ola; Rydén, Henric; Blomberg, Lars; Avventi, Enrico; Engström, Mathias

    2018-06-01

    A new multicontrast echo-planar imaging (EPI)-based sequence is proposed for brain MRI, which can directly generate six MR contrasts (T 1 -FLAIR, T 2 -w, diffusion-weighted (DWI), apparent diffusion coefficient (ADC), T2*-w, T 2 -FLAIR) in 1 min with full brain coverage. This could enable clinical MR clinical screening in similar time as a conventional CT exam but with more soft-tissue information. Eleven sequence modules were created as dynamic building blocks for the sequence. Two EPI readout modules were reused throughout the sequence and were prepended by other modules to form the desired MR contrasts. Two scan protocols were optimized with scan times of 55-75 s. Motion experiments were carried out on two volunteers to investigate the robustness against head motion. Scans on patients were carried out and compared to conventional clinical images. The pulse sequence is found to be robust against motion given its single-shot nature of each contrast. For excessive out-of-plane head motion, the T 1 -FLAIR and T 2 -FLAIR contrasts suffer from incomplete inversion. Despite lower signal-to-noise ratio (SNR) and resolution, the 1-min multicontrast EPI data show promising correspondence with conventional diagnostic scans on patients. A 1 min multicontrast brain MRI scan based on EPI readouts has been presented in this feasibility study. Preliminary data show potential for clinical brain MRI use with minimal bore time for the patient. Such short examination time could be useful (e.g., for screening and acute stroke). The sequence may also help planning conventional brain MRI scans if run at the beginning of an examination. Magn Reson Med 79:3045-3054, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  11. Whole Genome Sequencing and Comparisons of Different Chinese Rabies Virus Lineages Including the First Complete Genome of an Arctic-like Strain in China.

    Science.gov (United States)

    Li, Hao; Guo, Zhen Yang; Zhang, Jian; Tao, Xiao Yan; Zhu, Wu Yang; Tang, Qing; Liu, Hong Tu

    2016-05-01

    To learn the rabies genome molecular characteristics and compare the difference of China rabies lineages. The complete genomes of 12 strains from different China rabies lineages were amplified and sequenced, and all the China street strain genomes (total 43), Arctic and Arctic-like genomes were aligned using ClustalX2, the genome homologies were analyzed using MegAlign software, and the phylogenetic trees were constructed by MEGA 5. First Arctic-like rabies genome in China (CQH1202D) was reported, and we supplemented the rabies genome data of China, ensuring at least one genome was available in each China lineage. The genome size of China V (11908nt) is obviously shorter than other lineages' (11923-11925nt) for the difference of N-P non-coding regions. Among different lineages, the genome homologies are almost under 90%. CQH1202D (China IV lineage) has close relationship with strains from South Korea and they share about 95% genome similarities. The molecular characteristics of 6 different China rabies lineages were compared and analyzed from genome level, which benefits for continued comprehensive rabies surveillance, rabies prevention and control in China. Copyright © 2016 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  12. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene.

    Science.gov (United States)

    Oka, Tomoichiro; Saif, Linda J; Marthaler, Douglas; Esseili, Malak A; Meulia, Tea; Lin, Chun-Ming; Vlasova, Anastasia N; Jung, Kwonil; Zhang, Yan; Wang, Qiuhong

    2014-10-10

    The highly contagious and deadly porcine epidemic diarrhea virus (PEDV) first appeared in the US in April 2013. Since then the virus has spread rapidly nationwide and to Canada and Mexico causing high mortality among nursing piglets and significant economic losses. Currently there are no efficacious preventive measures or therapeutic tools to control PEDV in the US. The isolation of PEDV in cell culture is the first step toward the development of an attenuated vaccine, to study the biology of PEDV and to develop in vitro PEDV immunoassays, inactivation assays and screen for PEDV antivirals. In this study, nine of 88 US PEDV strains were isolated successfully on Vero cells with supplemental trypsin and subjected to genomic sequence analysis. They differed genetically mainly in the N-terminal S protein region as follows: (1) strains (n=7) similar to the highly virulent US PEDV strains; (2) one similar to the reportedly US S INDEL PEDV strain; and (3) one novel strain most closely related to highly virulent US PEDV strains, but with a large (197aa) deletion in the S protein. Representative strains of these three genetic groups were passaged serially and grew to titers of ∼5-6log10 plaque forming units/mL. To our knowledge, this is the first report of the isolation in cell culture of an S INDEL PEDV strain and a PEDV strain with a large (197aa) deletion in the S protein. We also designed primer sets to detect these genetically diverse US PEDV strains. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Relationship between fluid-attenuated inversion-recovery (FLAIR signal intensity and inflammatory mediator's levels in the hippocampus of patients with temporal lobe epilepsy and mesial temporal sclerosis

    Directory of Open Access Journals (Sweden)

    Pedro Paulo Vasconcellos Varella

    2011-02-01

    Full Text Available We investigated a relationship between the FLAIR signal found in mesial temporal sclerosis (MTS and inflammation. Twenty nine patients were selected through clinical and MRI analysis and submitted to cortico-amygdalo-hippocampectomy to seizure control. Glutamate, TNFα, IL1, nitric oxide (NO levels and immunostaining against IL1β and CD45 was performed. Control tissues (n=10 were obtained after autopsy of patients without neurological disorders. The glutamate was decreased in the temporal lobe epilepsy (TLE -MTS group (p<0.001, suggesting increased release of this neurotransmitter. The IL1β and TNFα were increased in the hippocampus (p<0.05 demonstrating an active inflammatory process. A positive linear correlation between FLAIR signal and NO and IL1β levels and a negative linear correlation between FLAIR signal and glutamate concentration was found. Lymphocytes infiltrates were present in hippocampi of TLE patients. These data showed an association between hippocampal signal alteration and increased inflammatory markers in TLE-MTS.

  14. MRI Sequences in Head & Neck Radiology - State of the Art.

    Science.gov (United States)

    Widmann, Gerlig; Henninger, Benjamin; Kremser, Christian; Jaschke, Werner

    2017-05-01

    Background  Magnetic resonance imaging (MRI) has become an essential imaging modality for the evaluation of head & neck pathologies. However, the diagnostic power of MRI is strongly related to the appropriate selection and interpretation of imaging protocols and sequences. The aim of this article is to review state-of-the-art sequences for the clinical routine in head & neck MRI and to describe the evidence for which medical question these sequences and techniques are useful. Method  Literature review of state-of-the-art sequences in head & neck MRI. Results and Conclusion  Basic sequences (T1w, T2w, T1wC+) and fat suppression techniques (TIRM/STIR, Dixon, Spectral Fat sat) are important tools in the diagnostic workup of inflammation, congenital lesions and tumors including staging. Additional sequences (SSFP (CISS, FIESTA), SPACE, VISTA, 3D-FLAIR) are used for pathologies of the cranial nerves, labyrinth and evaluation of endolymphatic hydrops in Menière's disease. Vessel and perfusion sequences (3D-TOF, TWIST/TRICKS angiography, DCE) are used in vascular contact syndromes, vascular malformations and analysis of microvascular parameters of tissue perfusion. Diffusion-weighted imaging (EPI-DWI, non-EPI-DWI, RESOLVE) is helpful in cholesteatoma imaging, estimation of malignancy, and evaluation of treatment response and posttreatment recurrence in head & neck cancer. Understanding of MRI sequences and close collaboration with referring physicians improves the diagnostic confidence of MRI in the daily routine and drives further research in this fascinating image modality. Key Points:   · Understanding of MRI sequences is essential for the correct and reliable interpretation of MRI findings.. · MRI protocols have to be carefully selected based on relevant clinical information.. · Close collaboration with referring physicians improves the output obtained from the diagnostic possibilities of MRI.. Citation Format · Widmann G, Henninger B, Kremser C et

  15. FLAIR-hyperintense vessel sign, diffusion-perfusion mismatch and infarct growth in acute ischemic stroke without vascular recanalisation therapy.

    Science.gov (United States)

    Gawlitza, Matthias; Gragert, Jasmin; Quäschling, Ulf; Hoffmann, Karl Titus

    2014-10-01

    To investigate the relation between DWI-PWI mismatch and FLAIR-hyperintense vessel (FHV) sign and their influence on the prediction of the infarct growth in stroke patients without vessel recanalising therapy. Thirty-three patients with non-lacunar acute stroke and not eligible for recanalisation therapy received cerebral MRI at the day of admission and after 7±1 days. DWI and PWI lesion volumes, DWI-PWI mismatch volumes, infarct growth, relative mismatch and relative infarct growth were assessed. FHV sign was subdivided into (i) proximal or (ii) distal, the latter graded as either (i) prominent or (ii) subtle. FHV sign did not predict absolute or relative infarct growth. Significantly larger DWI lesions, PWI lesions and mismatch volumes were observed in FHV-positive infarcts. There were significant correlations between the degree of FHV sign and PWI lesion volume (r=0.52; Pmismatch volume (r=0.49; Pmismatch and relative infarct growth (r=0.91; Pmismatch volumes and infarct growth was evident (r=0.18, P=0.35). The FHV sign is associated with larger PWI lesion volumes and DWI-to-PWI mismatch volumes in acute stroke and thus seems to be an indicator of collateral flow. However, it is unsuitable to predict infarct growth. The latter occurred when DWI-to-PWI mismatches were present with bigger relative mismatch volumes making subsequent infarct growth more likely. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  16. Automatic iterative segmentation of multiple sclerosis lesions using Student's t mixture models and probabilistic anatomical atlases in FLAIR images.

    Science.gov (United States)

    Freire, Paulo G L; Ferrari, Ricardo J

    2016-06-01

    Multiple sclerosis (MS) is a demyelinating autoimmune disease that attacks the central nervous system (CNS) and affects more than 2 million people worldwide. The segmentation of MS lesions in magnetic resonance imaging (MRI) is a very important task to assess how a patient is responding to treatment and how the disease is progressing. Computational approaches have been proposed over the years to segment MS lesions and reduce the amount of time spent on manual delineation and inter- and intra-rater variability and bias. However, fully-automatic segmentation of MS lesions still remains an open problem. In this work, we propose an iterative approach using Student's t mixture models and probabilistic anatomical atlases to automatically segment MS lesions in Fluid Attenuated Inversion Recovery (FLAIR) images. Our technique resembles a refinement approach by iteratively segmenting brain tissues into smaller classes until MS lesions are grouped as the most hyperintense one. To validate our technique we used 21 clinical images from the 2015 Longitudinal Multiple Sclerosis Lesion Segmentation Challenge dataset. Evaluation using Dice Similarity Coefficient (DSC), True Positive Ratio (TPR), False Positive Ratio (FPR), Volume Difference (VD) and Pearson's r coefficient shows that our technique has a good spatial and volumetric agreement with raters' manual delineations. Also, a comparison between our proposal and the state-of-the-art shows that our technique is comparable and, in some cases, better than some approaches, thus being a viable alternative for automatic MS lesion segmentation in MRI. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Comparison of two fat-suppressed magnetic resonance imaging pulse sequences to standard t2-weighted images for brain parenchymal contrast and lesion detection in dogs with inflammatory intracranial disease.

    Science.gov (United States)

    Young, Benjamin D; Mankin, Joseph M; Griffin, John F; Fosgate, Geoffrey T; Fowler, Jennifer L; Levine, Jonathan M

    2015-01-01

    T2-weighted (T2w) sequences are commonly relied upon in magnetic resonance imaging protocols for the detection of brain lesions in dogs. Previously, the effect of fluid suppression via fluid-attenuated inversion recovery (FLAIR) has been compared to T2-weighting with mixed results. Short tau inversion recovery (STIR) has been reported to increase the detection of some CNS lesions in people. The purpose of the current study was to evaluate the effect of fat suppression on brain parenchymal contrast resolution and lesion detection in dogs. We compared three sequences: T2w images, STIR, and T2w FLAIR with chemical fat suppression (T2-FLAIR-FS) in dogs with meningoencephalitis. Dogs with meningoencephalitis and dogs with idiopathic epilepsy were retrospectively identified and anonymized. Evaluators recorded the presence or absence of lesions within 12 predetermined brain regions on randomized sequences, viewing and scoring each sequence individually. Additionally, signal-to-noise ratios, contrast-to-noise ratios, and relative contrast (RC) were measured in a reference population. Short tau inversion recovery sequences had the highest RC between gray and white matter. While descriptively more lesions were identified by evaluators on T2-FLAIR-FS images, there was no statistical difference in the relative sensitivity of lesion detection between the sequences. Nor was there a statistical difference in false lesion detection within our reference population. Short tau inversion recovery may be favored for enhanced anatomic contrast depiction in brain imaging. No benefit of the inclusion of a fat-suppressed T2-FLAIR sequence was found. © 2014 American College of Veterinary Radiology.

  18. Comparative analysis of MR sequences to detect structural brain lesions in tuberous sclerosis

    Energy Technology Data Exchange (ETDEWEB)

    Pinto Gama, Hugo Pereira; Campos Meirelles, Rogerio Goncalves de; Mendonca do Rego, Jose Iram [Santa Casa de Misericordia de Sao Paulo, Section of Radiology, Sao Paulo (Brazil); Rocha, Antonio Jose da; Silva, Carlos Jorge da [Santa Casa de Misericordia de Sao Paulo, Section of Radiology, Centro de Medicina Diagnostica Fleury, Sao Paulo (Brazil); Braga, Flavio Tulio [Federal University of Sao Paulo, Escola Paulista de Medicina, Section of Radiology, Centro de Medicina Diagnostica Fleury, Santa Casa de Misericordia de Sao Paulo, Department of Diagnostic Imaging, Sao Paulo (Brazil); Martins Maia, Antonio Carlos [Federal University of Sao Paulo, Escola Paulista de Medicina, Section of Radiology, Centro de Medicina Diagnostica Fleury, Department of Neurology, Sao Paulo (Brazil); Lederman, Henrique Manoel [Federal University of Sao Paulo, Escola Paulista de Medicina, Division of Diagnostic Imaging in Pediatrics, Department of Diagnostic Imaging, Sao Paulo (Brazil)

    2006-02-01

    Tuberous sclerosis (TS) is a neurocutaneous genetically inherited disease with variable penetrance characterized by dysplasias and hamartomas affecting multiple organs. MR is the imaging method of choice to demonstrate structural brain lesions in TS. To compare MR sequences and determine which is most useful for the demonstration of each type of brain lesion in TS patients. We reviewed MR scans of 18 TS patients for the presence of cortical tubers, white matter lesions (radial bands), subependymal nodules, and subependymal giant cell astrocytoma (SGCA) on the following sequences: (1) T1-weighted spin-echo (T1 SE) images before and after gadolinium (Gd) injection; (2) nonenhanced T1 SE sequence with an additional magnetization transfer contrast medium pulse on resonance (T1 SE/MTC); and (3) fluid-attenuated inversion recovery (FLAIR) sequence. Cortical tubers were found in significantly (P<0.05) larger numbers and more conspicuously in FLAIR and T1 SE/MTC sequences. The T1 SE/MTC sequence was far superior to other methods in detecting white matter lesions (P<0.01). There was no significant difference between the T1 SE/MTC and T1 SE (before and after Gd injection) sequences in the detection of subependymal nodules; FLAIR sequence showed less sensitivity than the others in identifying the nodules. T1 SE sequences after Gd injection demonstrated better the limits of the SGCA. We demonstrated the importance of appropriate MRI sequences for diagnosis of the most frequent brain lesions in TS. Our study reinforces the fact that each sequence has a particular application according to the type of TS lesion. Gd injection might be useful in detecting SGCA; however, the parameters of size and location are also important for a presumptive diagnosis of these tumors. (orig.)

  19. FLAIR vascular hyperintensities and dynamic 4D angiograms for the estimation of collateral blood flow in posterior circulation occlusion

    International Nuclear Information System (INIS)

    Foerster, Alex; Wenz, Holger; Kerl, Hans Ulrich; Al-Zghloul, Mansour; Habich, Sonia; Groden, Christoph

    2014-01-01

    The objectives of this paper are to assess collateral blood flow in posterior circulation occlusion by MRI-based approaches (fluid-attenuated inversion recovery (FLAIR) vascular hyperintensities (FVHs), collateralization on dynamic 4D angiograms) and investigate its relation to ischemic lesion size and growth. In 28 patients with posterior cerebral artery (PCA) and 10 patients with basilar artery (BA) occlusion, MRI findings were analyzed, with emphasis on distal FVH and collateralization on dynamic 4D angiograms. In PCA occlusion, distal FVH was observed in 18/29 (62.1 %), in BA occlusion, in 8/10 (80 %) cases. Collateralization on dynamic 4D angiograms was graded 1 in 8 (27.6 %) patients, 2 in 1 (3.4 %) patient, 3 in 12 (41.4 %) patients, and 4 in 8 (27.6 %) patients with PCA occlusion and 0 in 1 (10 %) patient, 2 in 3 (30 %) patients, 3 in 1 (10 %) patient, and 4 in 5 (50 %) patients with BA occlusion. FVH grade showed neither correlation with initial or follow-up diffusion-weighted image (DWI) lesion size nor DWI-perfusion-weighted imaging (PWI) mismatch ratio. Collateralization on dynamic 4D angiograms correlated inversely with initial DWI lesion size and moderately with the DWI-(PWI) mismatch ratio. The combination of distal FVH and collateralization grade on dynamic 4D angiograms correlated inversely with initial as well as follow-up DWI lesion size and highly with the DWI-PWI mismatch ratio. In posterior circulation occlusion, FVH is a frequent finding, but its prognostic value is limited. Dynamic 4D angiograms are advantageous to examine and graduate collateral blood flow. The combination of both parameters results in an improved characterization of collateral blood flow and might have prognostic relevance. (orig.)

  20. Fast spine echo and fast fluid attenuated inversion recovery sequences in multiple sclerosis

    International Nuclear Information System (INIS)

    Paolillo, Andrea; Giugni, Elisabetta; Bozzao, Alessandro; Bastianello, Stefano

    1997-01-01

    Fast spin echo (FSE) and fast fluid attenuated inversion recovery (fast-FLAIR) sequences, were compared with conventional spin echo (CSE) in quantitating multiple sclerosis (MS) lesion burden. For each sequence, the total number and volume of MS lesions were calculated in 38 remitting multiple sclerosis patients using a semiautomated lesion detection program. Conventional spin echo, fast spin echo, and fast fluid attenuated inversion recovery image were reported on randomly and at different times by two expert observers. Interobserver differences, the time needed to quantitative multiple sclerosis lesions and lesion signal intensity (contrast-to-noise ratio and overall contrast) were considered. The lesions were classified by site into infratentorial, white matter and cortical/subcortical. A total of 2970 lesions with a volume of 961.7 cm 3 was calculated on conventional spin echo images. Fast spin echo images depicted fewer (16.6%; p < .005) and smaller (24.9%; p < .0001) lesions and the differences were statistically significant. Despite an overall nonsignificant reduction for fast-FLAIR images (-5% and 4.8% for lesion number and volume, respectively), significantly lower values (lesion number: p < 0.1; volume: p < .04)were observed for infratentorial lesions, while significantly higher values were seen for cortical/subcortical lesions (lesion number: p < .01; volume: p < .02). A higher lesion/white matter contrast (p < .002), a significant time saving for lesion burden quantitation (p < .05) and very low interobserver variability were found in favor of fast-FLAIR. Our data suggest that, despite the limitations regarding infratentorial lesions, fast-FLAIR sequences are indicated in R studies because of their good identification of cortical/subcortical lesions, almost complete interobserver agreement, higher contrast-to-noise ratio and limited time needed for semiautomated quantitation

  1. Hyperintense acute reperfusion marker on FLAIR is not associated with early haemorrhagic transformation in the elderly

    International Nuclear Information System (INIS)

    Rozanski, Michal; Ebinger, Martin; Schmidt, Wolf U.; Hotter, Benjamin; Pittl, Sandra; Heuschmann, Peter U.; Jungehuelsing, Jan G.; Fiebach, Jochen B.

    2010-01-01

    The hyperintense acute reperfusion marker (HARM) has been described as a predictor for haemorrhagic transformation (HT) in acute ischaemic stroke. We hypothesised that this phenomenon is not present in the elderly. It was possible to assess 47/84 consecutive patients aged 80 and over with diagnosed ischaemic stroke or transient ischaemic attack (TIA). MRI was performed within 24 h of onset of symptoms with follow-up MRI within a further 48 h. Of 47 included patients, 19 showed HARM; it was only seen on follow-up examination. Ten of the 47 patients underwent thrombolysis with recombinant tissue plasminogen activator (rt-PA); 4 of them showed HARM, and 1 of those showed HT. HARM was found in three out of eight patients with haemorrhagic transformation on baseline and/or follow-up MRI. We did not observe an association between HARM and early HT either in the whole group or in the patients who received thrombolysis. HARM was not associated with HT in the elderly after ischaemic stroke, independent of treatment. While it may indicate dysfunction of the blood-brain barrier (BBB), it does not necessarily amount to HT. (orig.)

  2. Prognostic Value of Labyrinthine 3D-FLAIR Abnormalities in Idiopathic Sudden Sensorineural Hearing Loss.

    Science.gov (United States)

    Lee, J I; Yoon, R G; Lee, J H; Park, J W; Yoo, M H; Ahn, J H; Chung, J W; Park, H J

    2016-12-01

    According to recent research, modern MR imaging can detect the presense of abnormalities on labyrinthine. Our aim was to report the patterns and prognostic role of abnormal findings on labyrinthine imaging in patients with sudden sensorineural hearing loss. This study comprised 113 patients who were diagnosed with unilateral sudden sensorineural hearing loss and underwent 3T MR imaging, including pre-/postcontrast 3D fluid-attenuated inversion recovery and T1-weighted imaging. We analyzed abnormalities on MR imaging and correlated them with audiometric results. Thirty-one (27%) patients showed abnormal findings on labyrinthine MR imaging in the affected ear. The initial/final hearing levels of the MRI+ group (91 ± 25/73 ± 27 dB hearing loss) were significantly worse than those of the MRI- group (69 ± 30/48 ± 24 dB hearing loss). The incidence of abnormalities on labyrinthine MR imaging was significantly lower (3 of 40, 8%) in 40 patients with initial mild-to-moderate hearing loss than in those with profound hearing loss (16 of 34, 47%). Considering hearing improvement by the Siegel criteria, the rate of complete or partial recovery was significantly higher in the MRI- group (34%) than in the MRI+ group (10%). In patients with initial severe or profound hearing loss, the MRI- group showed greater hearing improvement (38 ± 21 dB) than the MRI+ group (23 ± 22 dB). Abnormalities on labyrinthine MR imaging were found in 27% of patients with sudden sensorineural hearing loss. The initial hearing loss was worse in the MRI+ group than in the MRI- group. In patients with initial severe and profound hearing loss, the presence of abnormalities on labyrinthine MR imaging indicated a poor prognosis. © 2016 by American Journal of Neuroradiology.

  3. A de novo 1.58 Mb deletion, including MAP2K6 and mapping 1.28 Mb upstream to SOX9, identified in a patient with Pierre Robin sequence and osteopenia with multiple fractures.

    Science.gov (United States)

    Smyk, Marta; Roeder, Elizabeth; Cheung, Sau Wai; Szafranski, Przemyslaw; Stankiewicz, Paweł

    2015-08-01

    Defects of long-range regulatory elements of dosage-sensitive genes represent an under-recognized mechanism underlying genetic diseases. Haploinsufficiency of SOX9, the gene essential for development of testes and differentiation of chondrocytes, results in campomelic dysplasia, a skeletal malformation syndrome often associated with sex reversal. Chromosomal rearrangements with breakpoints mapping up to 1.6 Mb up- and downstream to SOX9, and disrupting its distant cis-regulatory elements, have been described in patients with milder forms of campomelic dysplasia, Pierre Robin sequence, and sex reversal. We present an ∼1.58 Mb deletion mapping ∼1.28 Mb upstream to SOX9 that encompasses its putative long-range cis-regulatory element(s) and MAP2K6 in a patient with Pierre Robin sequence and osteopenia with multiple fractures. Low bone mass panel testing using massively parallel sequencing of 23 nuclear genes, including COL1A1 and COL1A2 was negative. Based on the previous mouse model of Map2k6, suggesting that Sox9 is likely a downstream target of the p38 MAPK pathway, and our previous chromosome conformation capture-on-chip (4C) data showing potential interactions between SOX9 promoter and MAP2K6, we hypothesize that deletion of MAP2K6 might have affected SOX9 expression and contributed to our patient's phenotype. © 2015 Wiley Periodicals, Inc.

  4. Chairs with Flair

    Science.gov (United States)

    White, Carla Sabatino

    2005-01-01

    In the art lesson described in this article, students explore the arts of architecture, design, painting, and sculpture within four time periods: early colonial (1500-1700), late colonial (1700-1776), the quest for independence (1776-1860), and industrialization and growth (1860-1900). Through class discussion, readings, and slide presentations,…

  5. Blood-Labyrinth Barrier Permeability in Menière Disease and Idiopathic Sudden Sensorineural Hearing Loss: Findings on Delayed Postcontrast 3D-FLAIR MRI.

    Science.gov (United States)

    Pakdaman, M N; Ishiyama, G; Ishiyama, A; Peng, K A; Kim, H J; Pope, W B; Sepahdari, A R

    2016-06-02

    Menière disease and idiopathic sudden sensorineural hearing loss can have overlapping clinical presentation and may have similar pathophysiology. Prior studies using postcontrast 3D-FLAIR MR imaging suggest abnormal blood-labyrinth barrier permeability in both conditions, but the 2 diseases have not been directly compared by using the same imaging techniques. We hypothesized that delayed postcontrast 3D-FLAIR MR imaging would show differences in blood-labyrinth barrier permeability between Menière disease and idiopathic sudden sensorineural hearing loss. Patients with unilateral Menière disease (n = 32) and unilateral idiopathic sudden sensorineural hearing loss (n = 11) imaged with delayed postcontrast 3D-FLAIR MR imaging were retrospectively studied. Signal intensities of the medulla and perilymph of the cochlear basal turns of both ears in each patient were measured in a blinded fashion. Cochlea/medulla ratios were calculated for each ear as a surrogate for blood-labyrinth barrier permeability. The ears were segregated by clinical diagnosis. Cochlea/medulla ratio was higher in symptomatic ears of patients with Menière disease (12.6 ± 7.4) than in patients with idiopathic sudden sensorineural hearing loss (5.7 ± 2.0) and asymptomatic ears of patients with Menière disease (8.0 ± 3.1), indicating increased blood-labyrinth barrier permeability in Menière disease ears. The differences in cochlea/medulla ratio between symptomatic and asymptomatic ears were significantly higher in Menière disease than in idiopathic sudden sensorineural hearing loss. Asymptomatic ears in patients with Menière disease showed higher cochlea/medulla ratio than symptomatic and asymptomatic ears in patients with idiopathic sudden sensorineural hearing loss. Increased cochlea/medulla ratio indicates increased blood-labyrinth barrier permeability in Menière disease compared with idiopathic sudden sensorineural hearing loss. Increased cochlea/medulla ratio in asymptomatic ears of

  6. Complete nucleotide sequences and construction of full-length infectious cDNA clones of cucumber green mottle mosaic virus (CGMMV) in a versatile newly developed binary vector including both 35S and T7 promoters.

    Science.gov (United States)

    Park, Chan-Hwan; Ju, Hye-Kyoung; Han, Jae-Yeong; Park, Jong-Seo; Kim, Ik-Hyun; Seo, Eun-Young; Kim, Jung-Kyu; Hammond, John; Lim, Hyoun-Sub

    2017-04-01

    Seed-transmitted viruses have caused significant damage to watermelon crops in Korea in recent years, with cucumber green mottle mosaic virus (CGMMV) infection widespread as a result of infected seed lots. To determine the likely origin of CGMMV infection, we collected CGMMV isolates from watermelon and melon fields and generated full-length infectious cDNA clones. The full-length cDNAs were cloned into newly constructed binary vector pJY, which includes both the 35S and T7 promoters for versatile usage (agroinfiltration and in vitro RNA transcription) and a modified hepatitis delta virus ribozyme sequence to precisely cleave RNA transcripts at the 3' end of the tobamovirus genome. Three CGMMV isolates (OMpj, Wpj, and Mpj) were separately evaluated for infectivity in Nicotiana benthamiana, demonstrated by either Agroinfiltration or inoculation with in vitro RNA transcripts. CGMMV nucleotide identities to other tobamoviruses were calculated from pairwise alignments using DNAMAN. CGMMV identities were 49.89% to tobacco mosaic virus; 49.85% to pepper mild mottle virus; 50.47% to tomato mosaic virus; 60.9% to zucchini green mottle mosaic virus; and 60.96% to kyuri green mottle mosaic virus, confirming that CGMMV is a distinct species most similar to other cucurbit-infecting tobamoviruses. We further performed phylogenetic analysis to determine relationships of our new Korean CGMMV isolates to previously characterized isolates from Canada, China, India, Israel, Japan, Korea, Russia, Spain, and Taiwan available from NCBI. Analysis of CGMMV amino acid sequences showed three major clades, broadly typified as 'Russian,' 'Israeli,' and 'Asian' groups. All of our new Korean isolates fell within the 'Asian' clade. Neither the 128 nor 186 kDa RdRps of the three new isolates showed any detectable gene silencing suppressor function.

  7. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  8. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  9. Variability in a three-generation family with Pierre Robin sequence, acampomelic campomelic dysplasia, and intellectual disability due to a novel ∼1 Mb deletion upstream of SOX9, and including KCNJ2 and KCNJ16.

    Science.gov (United States)

    Castori, Marco; Bottillo, Irene; Morlino, Silvia; Barone, Chiara; Cascone, Piero; Grammatico, Paola; Laino, Luigi

    2016-01-01

    Campomelic dysplasia and acampomelic campomelic dysplasia (ACD) are allelic disorders due to heterozygous mutations in or around SOX9. Translocations and deletions involving the SOX9 5' regulatory region are rare causes of these disorders, as well as Pierre Robin sequence (PRS) and 46,XY gonadal dysgenesis. Genotype-phenotype correlations are not straightforward due to the complex epigenetic regulation of SOX9 expression during development. We report a three-generation pedigree with a novel ∼1 Mb deletion upstream of SOX9 and including KCNJ2 and KCNJ16, and ascertained for dominant transmission of PRS. Further characterization of the family identified subtle appendicular anomalies and a variable constellation of axial skeletal features evocative of ACD in several members. Affected males showed learning disability. The identified deletion was smaller than all other chromosome rearrangements associated with ACD. Comparison with other reported translocations and deletions involving this region allowed further refining of genotype-phenotype correlations and an update of the smallest regions of overlap associated with the different phenotypes. Intrafamilial variability in this pedigree suggests a phenotypic continuity between ACD and PRS in patients carrying mutations in the SOX9 5' regulatory region. © 2015 Wiley Periodicals, Inc.

  10. Amino-terminal domain of the v-fms oncogene product includes a functional signal peptide that directs synthesis of a transforming glycoprotein in the absence of feline leukemia virus gag sequences

    International Nuclear Information System (INIS)

    Wheeler, E.F.; Roussel, M.F.; Hampe, A.; Walker, M.H.; Fried, V.A.; Look, A.T.; Rettenmier, C.W.; Sherr, C.J.

    1986-01-01

    The nucleotide sequence of a 5' segment of the human genomic c-fms proto-oncogene suggested that recombination between feline leukemia virus and feline c-fms sequences might have occurred in a region encoding the 5' untranslated portion of c-fms mRNA. The polyprotein precursor gP180/sup gag-fms/ encoded by the McDonough strain of feline sarcoma virus was therefore predicted to contain 34 v-fms-coded amino acids derived from sequences of the c-fms gene that are not ordinarily translated from the proto-oncogene mRNA. The (gP180/sup gag-fms/) polyprotein was cotranslationally cleaved near the gag-fms junction to remove its gag gene-coded portion. Determination of the amino-terminal sequence of the resulting v-fms-coded glycoprotein, gp120/sup v-fms/, showed that the site of proteolysis corresponded to a predicted signal peptidase cleavage site within the c-fms gene product. Together, these analyses suggested that the linked gag sequences may not be necessary for expression of a biologically active v-fms gene product. The gag-fms sequences of feline sarcoma virus strain McDonough and the v-fms sequences alone were inserted into a murine retroviral vector containing a neomycin resistance gene. The authors conclude that a cryptic hydrophobic signal peptide sequence in v-fms was unmasked by gag deletion, thereby allowing the correct orientation and transport of the v-fms was unmasked by gag deletion, thereby allowing the correct orientation and transport of the v-fms gene product within membranous organelles. It seems likely that the proteolytic cleavage of gP180/gag-fms/ is mediated by signal peptidase and that the amino termini of gp140/sup v-fms/ and the c-fms gene product are identical

  11. MRI assessment of relapsed glioblastoma during treatment with bevacizumab: Volumetric measurement of enhanced and FLAIR lesions for evaluation of response and progression—A pilot study

    Energy Technology Data Exchange (ETDEWEB)

    Pichler, Josef, E-mail: josef.pichler@gespag.at [Wagner Jauregg Weg 15, 4020 Linz, Landesnervenklinik Linz (Austria); Pachinger, Corinna, E-mail: pachingercorinna@gmx.at [Wagner Jauregg Weg 15, 4020 Linz, Landesnervenklinik Linz (Austria); Pelz, Manuela, E-mail: mauela.pelz@gespag.at [Wagner Jauregg Weg 15, 4020 Linz, Landesnervenklinik Linz (Austria); Kleiser, Raimund, E-mail: raimund.kleiser@gespag.at [Wagner Jauregg Weg 15, 4020 Linz, Landesnervenklinik Linz (Austria)

    2013-05-15

    Purpose: To develop a magnetic resonance imaging (MRI) metric that is useful for therapy monitoring in patients with relapsed glioblastoma (GBM) during treatment with the antiangiogenic monoclonal antibody bevacizumab (Bev). We evaluated the feasibility of tumour volume measurement with our software tool in clinical routine and tried to establish reproducible and quantitative parameters for surveillance of patients on treatment with antiangiogenic drugs. Materials and methods: In this retrospective institutional pilot study, 18 patients (11 men, 7 women; mean age 53.5) with recurrent GBM received bevacizumab and irinotecan every two weeks as second line therapy. Follow up scans were assessed every two to four months. Data were collected on a 1.5 T MR System (Siemens, Symphony) with the standard head coil using our standardized tumour protocol. Volumetric measurement was performed with a commercial available software stroketool in FLAIR and T1-c imaging with following procedure: Pre-processing involved cutting noise and electing a Gaussian of 3 × 3 to smooth images, selecting a ROI (region of interest) in healthy brain area of the contra lateral side with quantifying the intensity value, adding 20% to this value to define the threshold level. Only values above this threshold are left corresponding to the tumour lesion. For the volumetric measurement the detected tumour area was circuited in all slices and finally summing up all values and multiplied by slice thickness to get the whole volume. Results: With McDonalds criteria progression was indicated in 14 out of 18 patients. In contrast, volumetric measurement showed an increase of contrast enhancement of >25%, defined as threshold for progression, in 11 patients (78%) and in 12 patients (85%) in FLAIR volume, respectively. 6 patients revealed that volumes in MRI increased earlier than the last scan, which was primarily defined as the date of progression with McDonald criteria, changing PFS after re-evaluation of

  12. Bilateral mesial temporal sclerosis: MRI with high-resolution fast spin-echo and fluid-attenuated inversion-recovery sequences

    International Nuclear Information System (INIS)

    Oppenheim, C.; Dormont, D.; Lehericy, S.; Marsault, C.; Hasboun, D.; Bazin, B.; Samson, S.; Baulac, M.

    1999-01-01

    We report a retrospective analysis of MRI in 206 patients with intractable seizures and describe the findings in bilateral mesial temporal sclerosis (MTS) on fast spin-echo (FSE) and fast fluid-attenuated inversion-recovery (fFLAIR) sequences. Criteria for MTS were atrophy, signal change and loss of the digitations of the head of the hippocampus. In patients with bilateral MRI signs of MTS, correlation with clinical electro, volumetric MRI data and neuropsychological tests, when available, was performed. Bilateral MTS was observed in seven patients. Bilateral loss of the digitations and signal change of fFLAIR was seen in all seven. In three, bilateral atrophy was obvious. In two patients, mild bilateral atrophy was observed and in two others, the hippocampi were: asymmetrical, with obvious atrophy on only one side. Volumetric data confirmed bilateral symmetrical atrophy in five patients, and volumes were at the lowest of the normal range in other two. The EEG showed temporal abnormalities in all patients, unilateral in five and bilateral in two. All patients had memory impairment and neuropsychological data confirmed visual and verbal memory deficits; two patients failed the Wada test on both sides. High-resolution T2-weighted FSE and fFLAIR sequences allow diagnosis of bilateral MTS, which has important therapeutic and prognostic implications. (orig.)

  13. Whole-genome sequence of Pseudomonas fluorescens EK007-RG4, a promising biocontrol agent against a broad range of bacteria, including the fire blight bacterium Erwinia amylovora

    DEFF Research Database (Denmark)

    Habibi, Roghayeh; Tarighi, Saeed; Behravan, Javad

    2017-01-01

    Here, we report the first draft whole-genome sequence of Pseudomonas fluorescens strain EK007-RG4, which was isolated from the phylloplane of a pear tree. P. fluorescens EK007-RG4 displays strong antagonism against Erwinia amylovora, the causal agent for fire blight disease, in addition to several...

  14. Deep sequencing of HIV-1 near full-length proviral genomes identifies high rates of BF1 recombinants including two novel circulating recombinant forms (CRF) 70_BF1 and a disseminating 71_BF1 among blood donors in Pernambuco, Brazil.

    Science.gov (United States)

    Pessôa, Rodrigo; Watanabe, Jaqueline Tomoko; Calabria, Paula; Felix, Alvina Clara; Loureiro, Paula; Sabino, Ester C; Busch, Michael P; Sanabani, Sabri S

    2014-01-01

    The findings of frequent circulation of HIV-1 subclade F1 viruses and the scarcity of BF1 recombinant viruses based on pol subgenomic fragment sequencing among blood donors in Pernambuco (PE), Northeast of Brazil, were reported recently. Here, we aimed to determine whether the classification of these strains (n = 26) extends to the whole genome sequences. Five overlapping amplicons spanning the HIV near full-length genomes (NFLGs) were PCR amplified from peripheral blood mononuclear cells (PBMCs) of 26 blood donors. The amplicons were molecularly bar-coded, pooled, and sequenced by Illumina paired-end protocol. The prevalence of viral variants containing drug resistant mutations (DRMs) was compared between plasma and PBMCs. Of the 26 samples studied, 20 NFLGs and 4 partial fragments were de novo assembled into contiguous sequences and successfully subtyped. Two distinct BF1 recombinant profiles designated CRF70_BF1 and CRF71_BF1, with 4 samples in profile I and 11 in profile II were detected and thus constitute two novel recombinant forms circulating in PE. Evidence of dual infections was detected in four patients co-infected with distinct HIV-1 subtypes. According to our estimate, the new CRF71_BF1 accounts for 10% of the HIV-1 circulating strains among blood donors in PE. Discordant data between the plasma and PBMCs-virus were found in 15 of 24 donors. Six of these strains displayed major DRMs only in PBMCs and four of which had detectable DRMs changes at prevalence between 1-20% of the sequenced population. The high percentage of the new RF71_BF1 and other BF1 recombinants found among blood donors in Pernambuco, coupled with high rates of transmitted DRMs and dual infections confirm the need for effective surveillance to monitor the prevalence and distribution of HIV variants in a variety of settings in Brazil.

  15. Group-specific amplification of HLA-DQA1 revealed a number of genomic full-length sequences including the novel HLA alleles DQA1*01:10 and DQA1*01:11.

    Science.gov (United States)

    Witter, K; Halliwell, J A; Mautner, J; Jolesch, A; von Welser, G; Rampp, I; Spannagl, M; Kauke, T; Dick, A

    2014-01-01

    In this article, we describe a subgroup-specific amplification assay for HLA-DQA1 that encompasses the whole coding region and allows us to sequence full-length HLA-DQA1 genes. We introduce the novel alleles HLA-DQA1*01:10 and HLA-DQA1*01:11. Moreover, we were able to confirm the full-length genomic sequence data of the alleles HLA-DQA1*01:07, HLA-DQA1*03:01:01, HLA-DQA1*03:02, HLA-DQA1*04:01:02, HLA-DQA1*04:02, HLA-DQA1*05:03, HLA-DQA1*05:05:01:02 and HLA-DQA1*06:01:01. A complete genomic overview of all six HLA-DQA1 allele groups is now available from the submission of our data to the IMGT/HLA database. Because our approach facilitates the analysis of all HLA-DQA1 allele sequences, HLA-DQA1 may become the first HLA locus from which all subgroup members will be known in detail in the near future. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. Identification of a Novel Heterozygous De Novo 7-bp Frameshift Deletion in PBX1 by Whole-Exome Sequencing Causing a Multi-Organ Syndrome Including Bilateral Dysplastic Kidneys and Hypoplastic Clavicles

    Directory of Open Access Journals (Sweden)

    Korbinian Maria Riedhammer

    2017-11-01

    Full Text Available IntroductionCongenital anomalies of the kidney and urinary tract (CAKUT represent the primary cause of chronic kidney disease in children. Many genes have been attributed to the genesis of this disorder. Recently, haploinsufficiency of PBX1 caused by microdeletions has been shown to result in bilateral renal hypoplasia and other organ malformations.Materials and methodsHere, we report on a 14-year-old male patient with congenital bilateral dysplastic kidneys, cryptorchidism, hypoplastic clavicles, developmental delay, impaired intelligence, and minor dysmorphic features. Presuming a syndromic origin, we performed SNP array analysis to scan for large copy number variations (CNVs followed by whole-exome sequencing (WES. Sanger sequencing was done to confirm the variant’s de novo status.ResultsSNP array analysis did not reveal any microdeletions or -duplications larger than 50 or 100 kb, respectively. WES identified a novel heterozygous 7-bp frameshift deletion in PBX1 (c.413_419del, p.Gly138Valfs*40 resulting in a loss-of-function. The de novo status could be confirmed by Sanger sequencing.DiscussionBy WES, we identified a novel heterozygous de novo 7-bp frameshift deletion in PBX1. Our findings expand the spectrum of causative variants in PBX1-related CAKUT. In this case, WES proved to be the apt technique to detect the variant responsible for the patient’s phenotype, as single gene testing is not feasible given the multitude of genes involved in CAKUT and SNP array analysis misses rare single-nucleotide variants and small Indels.

  17. DWI-ASPECTS (Diffusion-Weighted Imaging-Alberta Stroke Program Early Computed Tomography Scores) and DWI-FLAIR (Diffusion-Weighted Imaging-Fluid Attenuated Inversion Recovery) Mismatch in Thrombectomy Candidates: An Intrarater and Interrater Agreement Study.

    Science.gov (United States)

    Fahed, Robert; Lecler, Augustin; Sabben, Candice; Khoury, Naim; Ducroux, Célina; Chalumeau, Vanessa; Botta, Daniele; Kalsoum, Erwah; Boisseau, William; Duron, Loïc; Cabral, Dominique; Koskas, Patricia; Benaïssa, Azzedine; Koulakian, Hasmik; Obadia, Michael; Maïer, Benjamin; Weisenburger-Lile, David; Lapergue, Bertrand; Wang, Adrien; Redjem, Hocine; Ciccio, Gabriele; Smajda, Stanislas; Desilles, Jean-Philippe; Mazighi, Mikaël; Ben Maacha, Malek; Akkari, Inès; Zuber, Kevin; Blanc, Raphaël; Raymond, Jean; Piotin, Michel

    2018-01-01

    We aimed to study the intrarater and interrater agreement of clinicians attributing DWI-ASPECTS (Diffusion-Weighted Imaging-Alberta Stroke Program Early Computed Tomography Scores) and DWI-FLAIR (Diffusion-Weighted Imaging-Fluid Attenuated Inversion Recovery) mismatch in patients with acute ischemic stroke referred for mechanical thrombectomy. Eighteen raters independently scored anonymized magnetic resonance imaging scans of 30 participants from a multicentre thrombectomy trial, in 2 different reading sessions. Agreement was measured using Fleiss κ and Cohen κ statistics. Interrater agreement for DWI-ASPECTS was slight (κ=0.17 [0.14-0.21]). Four raters (22.2%) had a substantial (or higher) intrarater agreement. Dichotomization of the DWI-ASPECTS (0-5 versus 6-10 or 0-6 versus 7-10) increased the interrater agreement to a substantial level (κ=0.62 [0.48-0.75] and 0.68 [0.55-0.79], respectively) and more raters reached a substantial (or higher) intrarater agreement (17/18 raters [94.4%]). Interrater agreement for DWI-FLAIR mismatch was moderate (κ=0.43 [0.33-0.57]); 11 raters (61.1%) reached a substantial (or higher) intrarater agreement. Agreement between clinicians assessing DWI-ASPECTS and DWI-FLAIR mismatch may not be sufficient to make repeatable clinical decisions in mechanical thrombectomy. The dichotomization of the DWI-ASPECTS (0-5 versus 0-6 or 0-6 versus 7-10) improved interrater and intrarater agreement, however, its relevance for patients selection for mechanical thrombectomy needs to be validated in a randomized trial. © 2017 American Heart Association, Inc.

  18. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  19. Statistical approach of measurement of signal to noise ratio in according to change pulse sequence on brain MRI meningioma and cyst images

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Eul Kyu [Inje Paik University Hospital Jeo-dong, Seoul (Korea, Republic of); Choi, Kwan Woo [Asan Medical Center, Seoul (Korea, Republic of); Jeong, Hoi Woun [The Baekseok Culture University, Cheonan (Korea, Republic of); Jang, Seo Goo [The Soonchunhyang University, Asan (Korea, Republic of); Kim, Ki Won [Kyung Hee University Hospital at Gang-dong, Seoul (Korea, Republic of); Son, Soon Yong [The Wonkwang Health Science University, Iksan (Korea, Republic of); Min, Jung Whan; Son, Jin Hyun [The Shingu University, Sungnam (Korea, Republic of)

    2016-09-15

    The purpose of this study was to needed basis of measure MRI CAD development for signal to noise ratio (SNR) by pulse sequence analysis from region of interest (ROI) in brain magnetic resonance imaging (MRI) contrast. We examined images of brain MRI contrast enhancement of 117 patients, from January 2005 to December 2015 in a University-affiliated hospital, Seoul, Korea. Diagnosed as one of two brain diseases such as meningioma and cysts SNR for each patient's image of brain MRI were calculated by using Image J. Differences of SNR among two brain diseases were tested by SPSS Statistics21 ANOVA test for there was statistical significance (p < 0.05). We have analysis socio-demographical variables, SNR according to sequence disease, 95% confidence according to SNR of sequence and difference in a mean of SNR. Meningioma results, with the quality of distributions in the order of T1CE, T2 and T1, FLAIR. Cysts results, with the quality of distributions in the order of T2 and T1, T1CE and FLAIR. SNR of MRI sequences of the brain would be useful to classify disease. Therefore, this study will contribute to evaluate brain diseases, and be a fundamental to enhancing the accuracy of CAD development.

  20. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  1. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...... on transcriptional evidence. Analysis of repetitive sequences suggests that they are underrepresented in the reference assembly, reflecting an enrichment of gene-rich regions in the current assembly. Characterization of Lotus natural variation by resequencing of L. japonicus accessions and diploid Lotus species...... is currently ongoing, facilitated by the MG20 reference sequence...

  2. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene......This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis...

  3. Evolution of DNA sequencing.

    Science.gov (United States)

    Tipu, Hamid Nawaz; Shabbir, Ambreen

    2015-03-01

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted in it. Detection of terminated sequences was done radiographically on Polyacrylamide Gel Electrophoresis (PAGE). Improvements that have evolved over time in original Sanger sequencing include replacement of radiography with fluorescence, use of separate fluorescent markers for each nucleotide, use of capillary electrophoresis instead of polyacrylamide gel electrophoresis and then introduction of capillary array electrophoresis. However, this technique suffered from few inherent limitations like decreased sensitivity for low level mutant alleles, complexities in analyzing highly polymorphic regions like Major Histocompatibility Complex (MHC) and high DNA concentrations required. Several Next Generation Sequencing (NGS) technologies have been introduced by Roche, Illumina and other commercial manufacturers that tend to overcome Sanger sequencing limitations and have been reviewed. Introduction of NGS in clinical research and medical diagnostics is expected to change entire diagnostic approach. These include study of cancer variants, detection of minimal residual disease, exome sequencing, detection of Single Nucleotide Polymorphisms (SNPs) and their disease association, epigenetic regulation of gene expression and sequencing of microorganisms genome.

  4. Pump apparatus including deconsolidator

    Energy Technology Data Exchange (ETDEWEB)

    Sonwane, Chandrashekhar; Saunders, Timothy; Fitzsimmons, Mark Andrew

    2014-10-07

    A pump apparatus includes a particulate pump that defines a passage that extends from an inlet to an outlet. A duct is in flow communication with the outlet. The duct includes a deconsolidator configured to fragment particle agglomerates received from the passage.

  5. The Colliding Beams Sequencer

    International Nuclear Information System (INIS)

    Johnson, D.E.; Johnson, R.P.

    1989-01-01

    The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

  6. Optical modulator including grapene

    Science.gov (United States)

    Liu, Ming; Yin, Xiaobo; Zhang, Xiang

    2016-06-07

    The present invention provides for a one or more layer graphene optical modulator. In a first exemplary embodiment the optical modulator includes an optical waveguide, a nanoscale oxide spacer adjacent to a working region of the waveguide, and a monolayer graphene sheet adjacent to the spacer. In a second exemplary embodiment, the optical modulator includes at least one pair of active media, where the pair includes an oxide spacer, a first monolayer graphene sheet adjacent to a first side of the spacer, and a second monolayer graphene sheet adjacent to a second side of the spacer, and at least one optical waveguide adjacent to the pair.

  7. Temporal pole signal abnormality on MR imaging in temporal lobe epilepsy with hippocampal sclerosis: a fluid-attenuated inversion-recovery study; Anormalidade de sinal na imagem por RM do polo temporal na epilepsia do lobo temporal com esclerose hipocampal: um estudo pela sequencia inversao recuperacao com supressao da agua livre (FLAIR)

    Energy Technology Data Exchange (ETDEWEB)

    Carrete Junior, Henrique; Abdala, Nitamar; Szjenfeld, Jacob; Nogueira, Roberto Gomes [Universidade Federal de Sao Paulo (UNIFESP-EPM), Sao Paulo, SP (Brazil). Dept. de Diagnostico por Imagem; Lin, Katia; Caboclo, Luis Otavio; Centeno, Ricardo Silva; Sakamoto, Americo Ceiki; Yacubian, Elza Marcia Targas [Universidade Federal de Sao Paulo (UNIFESP-EPM), Sao Paulo, SP (Brazil). Dept. de Neurologia e Neurocirurgia

    2007-09-15

    Objective: To determine the frequency and regional involvement of temporal pole signal abnormality (TPA) in patients with hippocampal sclerosis (HS) using fluid-attenuated inversion-recovery (FLAIR) MR imaging, and to correlate this feature with history. Method: Coronal FLAIR images of the temporal pole were assessed in 120 patients with HS and in 30 normal subjects, to evaluate gray-white matter demarcation. Results: Ninety (75%) of 120 patients had associated TPA. The HS side made difference regarding the presence of TPA, with a left side prevalence (p=0.04, {chi}{sup 2} test). The anteromedial zone of temporal pole was affected in 27 (30%) out of 90 patients. In 63 (70%) patients the lateral zone were also affected. Patients with TPA were younger at seizure onset (p=0.018), but without association with duration of epilepsy. Conclusion: Our FLAIR study show temporal pole signal abnormality in 3/4 of patients with HS, mainly seen on the anteromedial region, with a larger prevalence when the left hippocampus was involved. (author)

  8. Sequence Handling by Sequence Analysis Toolbox v1.0

    DEFF Research Database (Denmark)

    Ingrell, Christian Ravnsborg; Matthiesen, Rune; Jensen, Ole Nørregaard

    2006-01-01

    analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl......The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence...... inositol-anchored proteins....

  9. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  10. SNMR pulse sequence phase cycling

    Science.gov (United States)

    Walsh, David O; Grunewald, Elliot D

    2013-11-12

    Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

  11. Moebius sequence

    DEFF Research Database (Denmark)

    Pedersen, Line Kjeldgaard; Maimburg, Rikke Damkjær; Hertz, Jens Michael

    2017-01-01

    and photographical evaluation. Five patients maintained the diagnosis of MS according to the diagnostic criteria. RESULTS: All five patients had bilateral facial and abducens paralysis confirmed by ophthalmological examination. Three of five had normal brain MR imaging. Two had missing facial nerves and one had......BACKGROUND: Moebius Sequence (MS) is a rare disorder defined by bilateral congenital paralysis of the abducens and facial nerves in combination with various odontological, craniofacial, ophthalmological and orthopaedic conditions. The aetiology is still unknown; but both genetic (de novo mutations...

  12. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    Science.gov (United States)

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; Akiyama, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin; Hazama, Makoto; Nishine, Tsutomu; Harada, Akira; Yamamoto, Rintaro; Matsumoto, Hiroyuki; Sakaguchi, Sumito; Ikegami, Takashi; Kashiwagi, Katsuya; Fujiwake, Syuji; Inoue, Kouji; Togawa, Yoshiyuki; Izawa, Masaki; Ohara, Eiji; Watahiki, Masanori; Yoneda, Yuko; Ishikawa, Tomokazu; Ozawa, Kaori; Tanaka, Takumi; Matsuura, Shuji; Kawai, Jun; Okazaki, Yasushi; Muramatsu, Masami; Inoue, Yorinao; Kira, Akira; Hayashizaki, Yoshihide

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3′ end and 5′ end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can

  13. RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.

    Science.gov (United States)

    Shibata, K; Itoh, M; Aizawa, K; Nagaoka, S; Sasaki, N; Carninci, P; Konno, H; Akiyama, J; Nishi, K; Kitsunai, T; Tashiro, H; Itoh, M; Sumi, N; Ishii, Y; Nakamura, S; Hazama, M; Nishine, T; Harada, A; Yamamoto, R; Matsumoto, H; Sakaguchi, S; Ikegami, T; Kashiwagi, K; Fujiwake, S; Inoue, K; Togawa, Y

    2000-11-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3' end and 5' end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be

  14. Reduction of MRI acoustic noise achieved by manipulation of scan parameters – A study using veterinary MR sequences

    International Nuclear Information System (INIS)

    Baker, Martin A.

    2013-01-01

    Sound pressure levels were measured within an MR scan room for a range of sequences employed in veterinary brain scanning, using a test phantom in an extremity coil. Variation of TR and TE, and use of a quieter gradient mode (‘whisper’ mode) were evaluated to determine their effect on sound pressure levels (SPLs). Use of a human head coil and a human brain sequence was also evaluated. Significant differences in SPL were achieved for T2, T1, T2* gradient echo and VIBE sequences by varying TR or TE, or by selecting the ‘whisper’ gradient mode. An appreciable reduction was achieved for the FLAIR sequence. Noise levels were not affected when a head coil was used in place of an extremity coil. Due to sequence parameters employed, veterinary patients and anaesthetists may be exposed to higher sound levels than those experienced in human MR examinations. The techniques described are particularly valuable in small animal MR scanning where ear protection is not routinely provided for the patient.

  15. Graphene nanodevices for DNA sequencing

    NARCIS (Netherlands)

    Heerema, S.J.; Dekker, C.

    2016-01-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with

  16. Graphene nanodevices for DNA sequencing

    Science.gov (United States)

    Heerema, Stephanie J.; Dekker, Cees

    2016-02-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  17. Temporal pole signal abnormality on MR imaging in temporal lobe epilepsy with hippocampal sclerosis: a fluid-attenuated inversion-recovery study Anormalidade de sinal na imagem por RM do pólo temporal na epilepsia do lobo temporal com esclerose hipocampal: um estudo pela seqüência inversão recuperação com supressão da água livre (FLAIR

    Directory of Open Access Journals (Sweden)

    Henrique Carrete Junior

    2007-09-01

    Full Text Available OBJECTIVE: To determine the frequency and regional involvement of temporal pole signal abnormality (TPA in patients with hippocampal sclerosis (HS using fluid-attenuated inversion-recovery (FLAIR MR imaging, and to correlate this feature with history. METHOD: Coronal FLAIR images of the temporal pole were assessed in 120 patients with HS and in 30 normal subjects, to evaluate gray-white matter demarcation. RESULTS: Ninety (75% of 120 patients had associated TPA. The HS side made difference regarding the presence of TPA, with a left side prevalence (p=0.04, chi2 test. The anteromedial zone of temporal pole was affected in 27 (30% out of 90 patients. In 63 (70% patients the lateral zone were also affected. Patients with TPA were younger at seizure onset (p=0.018, but without association with duration of epilepsy. CONCLUSION: Our FLAIR study show temporal pole signal abnormality in 3/4 of patients with HS, mainly seen on the anteromedial region, with a larger prevalence when the left hippocampus was involved.OBJETIVO: Determinar a freqüência e o envolvimento regional da anormalidade de sinal do pólo temporal (APT em pacientes com esclerose hipocampal (EH utilizando seqüência inversão recuperação com supressão da água (FLAIR por RM, e correlacioná-la com a história. MÉTODO: Foram analisadas as imagens coronais FLAIR dos pólos temporais de 120 pacientes com EH e de 30 indivíduos normais, para avaliar a demarcação entre substâncias branca e cinzenta. RESULTADOS: Noventa (75% dos 120 pacientes tinham APT associada. Houve prevalência do lado esquerdo (p=0.04, chi2 teste na relação entre APT e o lado da EH. A zona ântero-medial estava acometida em 27 (30% destes pacientes. Em 63 (70% pacientes também a zona lateral estava acometida. Pacientes com APT apresentaram início da epilepsia quando mais jovens (p=0.018, porém sem associação com a sua duração. CONCLUSÃO: A seqüência FLAIR mostra haver ATP em 3/4 dos pacientes com EH

  18. Microdeletion del(22(q12.2 encompassing the facial development-associated gene, MN1 (meningioma 1 in a child with Pierre-Robin sequence (including cleft palate and neurofibromatosis 2 (NF2: a case report and review of the literature

    Directory of Open Access Journals (Sweden)

    Davidson Tom B

    2012-03-01

    Full Text Available Abstract Background Pierre-Robin sequence (PRS is defined by micro- and/or retrognathia, glossoptosis and cleft soft palate, either caused by deformational defect or part of a malformation syndrome. Neurofibromatosis type 2 (NF2 is an autosomal dominant syndrome caused by mutations in the NF2 gene on chromosome 22q12.2. NF2 is characterized by bilateral vestibular schwannomas, spinal cord schwannomas, meningiomas and ependymomas, and juvenile cataracts. To date, NF2 and PRS have not been described together in the same patient. Case presentation We report a female with PRS (micrognathia, cleft palate, microcephaly, ocular hypertelorism, mental retardation and bilateral hearing loss, who at age 15 was also diagnosed with severe NF2 (bilateral cerebellopontine schwannomas and multiple extramedullary/intradural spine tumors. This is the first published report of an individual with both diagnosed PRS and NF2. High resolution karyotype revealed 46, XX, del(22(q12.1q12.3, FISH confirmed a deletion encompassing NF2, and chromosomal microarray identified a 3,693 kb deletion encompassing multiple genes including NF2 and MN1 (meningioma 1. Five additional patients with craniofacial dysmorphism and deletion in chromosome 22-adjacent-to or containing NF2 were identified in PubMed and the DECIPHER clinical chromosomal database. Their shared chromosomal deletion encompassed MN1, PITPNB and TTC28. MN1, initially cloned from a patient with meningioma, is an oncogene in murine hematopoiesis and participates as a fusion gene (TEL/MN1 in human myeloid leukemias. Interestingly, Mn1-haploinsufficient mice have abnormal skull development and secondary cleft palate. Additionally, Mn1 regulates maturation and function of calvarial osteoblasts and is an upstream regulator of Tbx22, a gene associated with murine and human cleft palate. This suggests that deletion of MN1 in the six patients we describe may be causally linked to their cleft palates and/or craniofacial

  19. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  20. The sequence of sequencers: The history of sequencing DNA

    Science.gov (United States)

    Heather, James M.; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

  1. "First generation" automated DNA sequencing technology.

    Science.gov (United States)

    Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

    2011-10-01

    Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

  2. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  3. Nanogrid rolling circle DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Church, George M.; Porreca, Gregory J.; Shendure, Jay; Rosenbaum, Abraham Meir

    2017-04-18

    The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.

  4. Chip-based sequencing nucleic acids

    Science.gov (United States)

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  5. DNA Sequencing apparatus

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1992-01-01

    An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

  6. Modelling passive margin sequence stratigraphy

    Science.gov (United States)

    Steckler, M.S.; Reynolds, D.; Coakley, B.; Swift, B.A.; Jarrard, R.D.

    1993-01-01

    We have modelled stratigraphic sequences to aid in deciphering the sedimentary response to sea-level change. Sequence geometry is found to be most sensitive to sea level, but other factors, including subsidence rate and sediment supply, can produce similar changes. Sediment loading and compaction also play a major role in generating accommodation, a factor often neglected in sequence-stratigraphic models. All of these parameters can control whether a type 1 or type 2 sequence boundary is produced. The models indicate that variations in margin characteristics produce systematic shifts in sequence boundary timing and systems tract distribution. The timing of the sequence boundary formation and systems tracts may differ by up to one-half of a sea-level cycle. Thus correlative sequence boundaries will not be synchronous. While rates of sea-level change may exceed the rate of thermal subsidence, isostasy and compaction may amplify the rate of total subsidence to several times greater than the thermal subsidence. Thus, total subsidence does not vary uniformly across the margin since it is modified by the sediment load. The amplitude of sea-level changes cannot be determined accurately without accounting for the major processes that affect sediment accumulation. Backstripping of a seismic line on the New Jersey margin is used to reconstruct continental margin geometry. The reconstructions show that the pre-existing ramp-margin geometry, rather than sea level, controls clinoform heights and slopes and sedimentary bypass. Backstripping also reveals progressive deformation of sequences due to compaction. Further work is still needed to understand quantitatively the role of sea level and the tectonic and sedimentary processes controlling sequence formation and influencing sequence architecture.

  7. Poisson process approximation for sequence repeats, and sequencing by hybridization.

    Science.gov (United States)

    Arratia, R; Martin, D; Reinert, G; Waterman, M S

    1996-01-01

    Sequencing by hybridization is a tool to determine a DNA sequence from the unordered list of all l-tuples contained in this sequence; typical numbers for l are l = 8, 10, 12. For theoretical purposes we assume that the multiset of all l-tuples is known. This multiset determines the DNA sequence uniquely if none of the so-called Ukkonen transformations are possible. These transformations require repeats of (l-1)-tuples in the sequence, with these repeats occurring in certain spatial patterns. We model DNA as an i.i.d. sequence. We first prove Poisson process approximations for the process of indicators of all leftmost long repeats allowing self-overlap and for the process of indicators of all left-most long repeats without self-overlap. Using the Chen-Stein method, we get bounds on the error of these approximations. As a corollary, we approximate the distribution of longest repeats. In the second step we analyze the spatial patterns of the repeats. Finally we combine these two steps to prove an approximation for the probability that a random sequence is uniquely recoverable from its list of l-tuples. For all our results we give some numerical examples including error bounds.

  8. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  9. Memory and learning with rapid audiovisual sequences

    Science.gov (United States)

    Keller, Arielle S.; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

  10. Memory and learning with rapid audiovisual sequences.

    Science.gov (United States)

    Keller, Arielle S; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed.

  11. Revisiting the relationship of three-dimensional fluid attenuation inversion recovery imaging and hearing outcomes in adults with idiopathic unilateral sudden sensorineural hearing loss

    Energy Technology Data Exchange (ETDEWEB)

    Liao, Wen-Huei [School of Medicine, National Yang Ming University, Taipei, 11221, Taiwan (China); Department of Otolaryngology, Taipei Veterans General Hospital, Taipei, 11217, Taiwan (China); Wu, Hsiu-Mei [School of Medicine, National Yang Ming University, Taipei, 11221, Taiwan (China); Department of Radiology, Taipei Veterans General Hospital, Taipei, 11217, Taiwan (China); Wu, Hung-Yi [Department of Radiology, Taipei Veterans General Hospital, Taipei, 11217, Taiwan (China); Tu, Tzong-Yang; Shiao, An-Suey [School of Medicine, National Yang Ming University, Taipei, 11221, Taiwan (China); Department of Otolaryngology, Taipei Veterans General Hospital, Taipei, 11217, Taiwan (China); Castillo, Mauricio [Department of Radiology, University of North Carolina, Chapel Hill, NC, 27599-7510 (United States); Hung, Sheng-Che, E-mail: hsz829@gmail.com [School of Medicine, National Yang Ming University, Taipei, 11221, Taiwan (China); Department of Radiology, Taipei Veterans General Hospital, Taipei, 11217, Taiwan (China); Department of Biomedical Imaging and Radiological Sciences, National Yang Ming University, Taipei, 11221, Taiwan (China)

    2016-12-15

    Background and purpose: Three-dimensional fluid attenuation inversion recovery (3D FLAIR) may demonstrate high signal in the inner ears of patients with idiopathic sudden sensorineural hearing loss (ISSNHL), but the correlations of this finding with outcomes are still controversial. Here we compared 4 3D MRI sequences with the outcomes of patients with ISSNHL. Materials and methods: 77 adult patients with ISSNHL underwent MRI with pre contrast FLAIR, fast imaging employing steady-state acquisition images (FIESTA-C), post contrast T1WI and post contrast FLAIR. The extent and degree of high signal in both cochleas were evaluated in all patients, and asymmetry ratios between the affected ears and the normal ones were calculated. The relationships among MRI findings, including extent and asymmetry of abnormal cochlear high signals, degree of FLAIR enhancement, and clinical information, including age, vestibular symptoms, baseline hearing loss, and final hearing outcomes were analyzed. Results: 54 patients (28 men; age, 52.1 ± 15.5 years) were included in our study. Asymmetric cochlear signal intensities were more frequently observed in pre contrast and post contrast FLAIR (79.6% and 68.5%) than in FIESTA-C (61.1%) and T1WI (51.9%) (p < 0.001). Age, baseline hearing loss, extent of high signal and asymmetry ratios of pre contrast and post contrast FLAIR were all correlated with final hearing outcomes. In multivariate analysis, age and the extent of high signals were the most significant predictors of final hearing outcomes. Conclusion: 3D FLAIR provides a higher sensitivity in detecting the asymmetric cochlear signal abnormality. The more asymmetric FLAIR signals and presence of high signals beyond cochlea indicated a poorer prognosis.

  12. Massively parallel signature sequencing.

    Science.gov (United States)

    Zhou, Daixing; Rao, Mahendra S; Walker, Roger; Khrebtukova, Irina; Haudenschild, Christian D; Miura, Takumi; Decola, Shannon; Vermaas, Eric; Moon, Keith; Vasicek, Thomas J

    2006-01-01

    Massively parallel signature sequencing is an ultra-high throughput sequencing technology. It can simultaneously sequence millions of sequence tags, and, therefore, is ideal for whole genome analysis. When applied to expression profiling, it reveals almost every transcript in the sample and provides its accurate expression level. This chapter describes the technology and its application in establishing stem cell transcriptome databases.

  13. Goldbach Partitions and Sequences

    Indian Academy of Sciences (India)

    IAS Admin

    as a sum of two primes (for even numbers) and three primes (for odd numbers). We call this the Goldbach sequence g(n), which may be converted into a binary sequence b(n) by mapping each even number to 0 and each odd number to 1. The resulting binary sequences may be used as pseudorandom sequences in ...

  14. Image analysis for DNA sequencing

    International Nuclear Information System (INIS)

    Palaniappan, K.; Huang, T.S.

    1991-01-01

    This paper reports that there is a great deal of interest in automating the process of DNA (deoxyribonucleic acid) sequencing to support the analysis of genomic DNA such as the Human and Mouse Genome projects. In one class of gel-based sequencing protocols autoradiograph images are generated in the final step and usually require manual interpretation to reconstruct the DNA sequence represented by the image. The need to handle a large volume of sequence information necessitates automation of the manual autoradiograph reading step through image analysis in order to reduce the length of time required to obtain sequence data and reduce transcription errors. Various adaptive image enhancement, segmentation and alignment methods were applied to autoradiograph images. The methods are adaptive to the local characteristics of the image such as noise, background signal, or presence of edges. Once the two-dimensional data is converted to a set of aligned one-dimensional profiles waveform analysis is used to determine the location of each band which represents one nucleotide in the sequence. Different classification strategies including a rule-based approach are investigated to map the profile signals, augmented with the original two-dimensional image data as necessary, to textual DNA sequence information

  15. Integrated sequence analysis. Final report

    International Nuclear Information System (INIS)

    Andersson, K.; Pyy, P.

    1998-02-01

    The NKS/RAK subprojet 3 'integrated sequence analysis' (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term 'methodology' denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  16. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  17. Platyrrhine dental eruption sequences.

    Science.gov (United States)

    Henderson, Emily

    2007-10-01

    To determine dental eruption sequences of extant platyrrhines, 367 mandibles and maxillae of informative juvenile specimens from all 16 genera were scored for presence of permanent teeth including three intermediate eruption stages following Harvati (Am J Phys Anthropol 112 (2000) 69-85). The timing of molar eruption relative to that of the anterior dentition is variable in platyrrhines. Aotus is precocious, with all molars erupting in succession before replacement of any deciduous teeth, while Cebus is delayed in M2-3 eruption relative to I1-2. Callitrichines have a distinct tendency toward delayed canine and premolar development. Platyrrhine eruption sequences presented here show some evidence of conformity to Schultz's Rule, with relatively early replacement of deciduous dentition in "slower"-growing animals. The relationship of dental eruption sequences to degree of folivory, body mass, brain mass, and dietary quality is also examined. The early eruption of molars relative to anterior teeth in Pithecia, Chiropotes, and Cacajao, in comparison to genera such as Ateles, Lagothrix, and Alouatta, showing relatively later eruption of the molars, appears to be consistent with current phylogenetic hypotheses. Schultz (Am J Phys Anthropol 19 (1935) 489-581) postulated early relative molar eruption as the primitive dental eruption schedule for primates. The extremely early molar eruption of Aotus versus Callicebus (where both incisors erupt before M2 and M3, with M3 usually last) may lend support to the status of Aotus as a basal taxon. The early relative molar eruption of the fossil platyrrhine species Branisella boliviana is also consistent with this hypothesis (Takai et al.: Am J Phys Anthropol 111 (2000) 263-281). (c) 2007 Wiley-Liss, Inc.

  18. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  19. CORRELATION BETWEEN INTERESTS, FLAIRS AND VOCATIONAL PREFERENCES WITH THE PROFESSIONAL CAREER ELECTION WHEN GRADUATED FROM THE TECHNOLOGIC AGRICULTURE COLLEGE, MEXICO / LA CORRELACIÓN ENTRE LOS INTERESES, APTITUDES Y PREFERENCIAS VOCACIONALES CON LA CARRERA QUE ELIGEN AL EGRESAR LOS ALUMNOS DEL CENTRO DE BACHILLERATO TECNOLÓGICO AGROPECUARIO, MÉXICO

    Directory of Open Access Journals (Sweden)

    Teresa De León Mendoza

    2012-05-01

    Full Text Available An activity required in the educational field is the vocational counseling, which is considered fundamental because of the importance on the future of the students. Nevertheless there are only a few researches that meassure the correlation between the dominant areas identified by the career adviser and with the professional career election taken by the student at the end of high scholl degree.The methodology used in this research allow the vocational counseling or career adviser to provide the student with information of the specific area attached to their interests and flairs. The results of this research work, demonstrate that there is a correlation between the interests, skills and specific areas identified in the student, with the race which elects the graduation of his high school.

  20. Finding Common Sequence and Structure Motifs in a set of RNA sequences

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Heyer, Laurie J.; Stormo, Gary D.

    1997-01-01

    We present a computational scheme to search for the most common motif, composed of a combination of sequence and structure constraints, among a collection of RNA sequences. The method uses a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences......, and comparisons with other approaches, are provided. The solutions include finding consensus structure identical to published ones....

  1. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  2. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  3. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  4. Protein sequence databases.

    Science.gov (United States)

    Apweiler, Rolf; Bairoch, Amos; Wu, Cathy H

    2004-02-01

    A variety of protein sequence databases exist, ranging from simple sequence repositories, which store data with little or no manual intervention in the creation of the records, to expertly curated universal databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each sequence record. As the focus of researchers moves from the genome to the proteins encoded by it, these databases will play an even more important role as central comprehensive resources of protein information. Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium.

  5. (including travel dates) Proposed itinerary

    Indian Academy of Sciences (India)

    Ashok

    31 July to 22 August 2012 (including travel dates). Proposed itinerary: Arrival in Bangalore on 1 August. 1-5 August: Bangalore, Karnataka. Suggested institutions: Indian Institute of Science, Bangalore. St Johns Medical College & Hospital, Bangalore. Jawaharlal Nehru Centre, Bangalore. 6-8 August: Chennai, TN.

  6. Malignant lymphomas (including myeloproliferative disorders)

    International Nuclear Information System (INIS)

    Todd, I.D.H.

    1985-01-01

    This chapter deals with the radiotherapy and cytotoxic chemotherapy of the malignant lymphomas. Included within this group are Hodgkin's disease, non-Hodgkin's lymphoma, mycosis fungoides, and chronic lymphatic leukaemia. A further section deals with the myeloproliferative disorders, including granulocytic leukaemia, polycythaemia vera, and primary thrombocythaemia. Excluded are myeloma and reticulum cell sarcoma of bone and acute leukaemia. With regard to Hodgkin's disease, the past 25 years have seen general recognition of the curative potential of radiotherapy, at least in the local stages, and, more recently, awareness of the ability to achieve long-term survival after combination chemotherapy in generalised or in recurrent disease. At the same time the importance of staging has become appreciated and the introduction of procedures such as lymphography, staging laparotomy, and computer tomography (CT) has enormously increased its reliability. Advances have not been so dramatic in the complex group of non-Hodgkins's lymphomas, but are still very real

  7. Sequences, groups, and number theory

    CERN Document Server

    Rigo, Michel

    2018-01-01

    This collaborative book presents recent trends on the study of sequences, including combinatorics on words and symbolic dynamics, and new interdisciplinary links to group theory and number theory. Other chapters branch out from those areas into subfields of theoretical computer science, such as complexity theory and theory of automata. The book is built around four general themes: number theory and sequences, word combinatorics, normal numbers, and group theory. Those topics are rounded out by investigations into automatic and regular sequences, tilings and theory of computation, discrete dynamical systems, ergodic theory, numeration systems, automaton semigroups, and amenable groups.  This volume is intended for use by graduate students or research mathematicians, as well as computer scientists who are working in automata theory and formal language theory. With its organization around unified themes, it would also be appropriate as a supplemental text for graduate level courses.

  8. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  9. Device including a contact detector

    DEFF Research Database (Denmark)

    2011-01-01

    The present invention relates to a probe for determining an electrical property of an area of a surface of a test sample, the probe is intended to be in a specific orientation relative to the test sample. The probe may comprise a supporting body defining a first surface. A plurality of cantilever...... of cantilever arms (12) contacting the surface of the test sample when performing the movement....... arms (12) may extend from the supporting body in co-planar relationship with the first surface. The plurality of cantilever arms (12) may extend substantially parallel to each other and each of the plurality of cantilever arms (12) may include an electrical conductive tip for contacting the area...

  10. Epigenomics: sequencing the methylome.

    Science.gov (United States)

    Hirst, Martin

    2013-01-01

    DNA methylation patterns are increasingly surveyed through methods that utilize massively parallel sequencing. Sequence-based assays developed to detect DNA methylation can be broadly divided into those that depend on affinity enrichment, chemical conversion, or enzymatic restriction. The DNA fragments resulting from these methods are uniformly subjected to library construction and massively parallel sequencing. The sequence reads are subsequently aligned to a reference genome and subjected to specialized analytical tools to extract the underlying methylation signature. This chapter will outline these emerging techniques.

  11. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    the feasibility of predicting the fetal KEL1 phenotype using next-generation sequencing (NGS) technology. STUDY DESIGN AND METHODS: The KEL1/2 single-nucleotide polymorphism was polymerase chain reaction (PCR) amplified with one adjoining base, and the PCR product was sequenced using a genome analyzer (GAIIx......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

  12. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  13. Delayed Sequence Intubation

    DEFF Research Database (Denmark)

    Weingart, Scott D; Trueger, N Seth; Wong, Nelson

    2015-01-01

    assessed. RESULTS: A total of 62 patients were enrolled: 19 patients required delayed sequence intubation to allow nonrebreather mask, 39 patients required it to allow NIPPV, and 4 patients required it for nasogastric tube placement. Saturations increased from a mean of 89.9% before delayed sequence...

  14. Cosmetology: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  15. Sequences for Student Investigation

    Science.gov (United States)

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  16. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  17. What Advances Are Being Made in DNA Sequencing?

    Science.gov (United States)

    ... diagnosis in the future. For more information about DNA sequencing technologies and their use: Genetics Home Reference discusses ... illustration of the decline in the cost of DNA sequencing , including that caused by the introduction of new ...

  18. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  19. Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores

    NARCIS (Netherlands)

    Boer, de P.; Caspers, M.; Sanders, J.W.; Kemperman, R.; Wijman, J.; Lommerse, G.; Roeselers, G.; Montijn, R.; Abee, T.; Kort, R.

    2015-01-01

    Background
    Spoilage of food products is frequently caused by bacterial spores and lactic acid bacteria. Identification of these organisms by classic cultivation methods is limited by their ability to form colonies on nutrient agar plates. In this study, we adapted and optimized 16S rRNA amplicon

  20. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  1. Repetitive sequence environment distinguishes housekeeping genes.

    Science.gov (United States)

    Eller, C Daniel; Regelson, Moira; Merriman, Barry; Nelson, Stan; Horvath, Steve; Marahrens, York

    2007-04-01

    Housekeeping genes are expressed across a wide variety of tissues. Since repetitive sequences have been reported to influence the expression of individual genes, we employed a novel approach to determine whether housekeeping genes can be distinguished from tissue-specific genes by their repetitive sequence context. We show that Alu elements are more highly concentrated around housekeeping genes while various longer (>400-bp) repetitive sequences ("repeats"), including Long Interspersed Nuclear Element-1 (LINE-1) elements, are excluded from these regions. We further show that isochore membership does not distinguish housekeeping genes from tissue-specific genes and that repetitive sequence environment distinguishes housekeeping genes from tissue-specific genes in every isochore. The distinct repetitive sequence environment, in combination with other previously published sequence properties of housekeeping genes, was used to develop a method of predicting housekeeping genes on the basis of DNA sequence alone. Using expression across tissue types as a measure of success, we demonstrate that repetitive sequence environment is by far the most important sequence feature identified to date for distinguishing housekeeping genes.

  2. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  3. General LTE Sequence

    OpenAIRE

    Billal, Masum

    2015-01-01

    In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

  4. [Sequence learning in major depressive disorder].

    Science.gov (United States)

    Borbély-Ipkovich, Emöke; Németh, Dezsö; Janacsek, Karolina; Gonda, Xénia

    2014-01-01

    Major Depressive Disorder (MDD) is one of the most common psychiatric diagnoses, accompanied by several psychological, behavioural and emotional symptoms, and in addition to the symptoms affecting the quality of life, it can lead to severe consequences, including suicide. Sequence learning plays a key role in adapting to the environment, neural plasticity, first language acquisition, social learning and skills, at the same time it defines the behaviour of the patient and also therapeutic possibilities. The aim of this paper is to review sequence learning and its consolidation in MDD. We know little about the effects of mood disorders on sequence learning; the results are contradictory, therefore, further studies are needed to test the effects of MDD on sequence learning and on the consolidation of implicitly acquired sequence knowledge.

  5. Nanopore sequencing detects structural variants in cancer.

    Science.gov (United States)

    Norris, Alexis L; Workman, Rachael E; Fan, Yunfan; Eshleman, James R; Timp, Winston

    2016-01-01

    Despite advances in sequencing, structural variants (SVs) remain difficult to reliably detect due to the short read length (nanopore sequencing on the MinION. Nanopore sequencing relies on a similar concept to a Coulter counter, reading the DNA sequence from the change in electrical current resulting from a DNA strand being forced through a nanometer-sized pore embedded in a membrane. Though nanopore sequencing currently has a relatively high mismatch rate that precludes base substitution and small frameshift mutation detection, its accuracy is sufficient for SV detection because of its long reads. In fact, long reads in some cases may improve SV detection efficiency. We have tested nanopore sequencing to detect a series of well-characterized SVs, including large deletions, inversions, and translocations that inactivate the CDKN2A/p16 and SMAD4/DPC4 tumor suppressor genes in pancreatic cancer. Using PCR amplicon mixes, we have demonstrated that nanopore sequencing can detect large deletions, translocations and inversions at dilutions as low as 1:100, with as few as 500 reads per sample. Given the speed, small footprint, and low capital cost, nanopore sequencing could become the ideal tool for the low-level detection of cancer-associated SVs needed for molecular relapse, early detection, or therapeutic monitoring.

  6. Short RNA indicator sequences are not completely degraded by autoclaving

    Science.gov (United States)

    Unnithan, Veena V.; Unc, Adrian; Joe, Valerisa; Smith, Geoffrey B.

    2014-01-01

    Short indicator RNA sequences (autoclaving and are recovered intact by molecular amplification. Primers targeting longer sequences are most likely to produce false positives due to amplification errors easily verified by melting curves analyses. If short indicator RNA sequences are used for virus identification and quantification then post autoclave RNA degradation methodology should be employed, which may include further autoclaving. PMID:24518856

  7. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  8. Computer simulation of replacement sequences in copper

    International Nuclear Information System (INIS)

    Schiffgens, J.O.; Schwartz, D.W.; Ariyasu, R.G.; Cascadden, S.E.

    1978-01-01

    Results of computer simulations of , , and replacement sequences in copper are presented, including displacement thresholds, focusing energies, energy losses per replacement, and replacement sequence lengths. These parameters are tabulated for six interatomic potentials and shown to vary in a systematic way with potential stiffness and range. Comparisons of results from calculations made with ADDES, a quasi-dynamical code, and COMENT, a dynamical code, show excellent agreement, demonstrating that the former can be calibrated and used satisfactorily in the analysis of low energy displacement cascades. Upper limits on , , and replacement sequences were found to be approximately 10, approximately 30, and approximately 14 replacements, respectively. (author)

  9. Nanopore-CMOS Interfaces for DNA Sequencing.

    Science.gov (United States)

    Magierowski, Sebastian; Huang, Yiyun; Wang, Chengjie; Ghafar-Zadeh, Ebrahim

    2016-08-06

    DNA sequencers based on nanopore sensors present an opportunity for a significant break from the template-based incumbents of the last forty years. Key advantages ushered by nanopore technology include a simplified chemistry and the ability to interface to CMOS technology. The latter opportunity offers substantial promise for improvement in sequencing speed, size and cost. This paper reviews existing and emerging means of interfacing nanopores to CMOS technology with an emphasis on massively-arrayed structures. It presents this in the context of incumbent DNA sequencing techniques, reviews and quantifies nanopore characteristics and models and presents CMOS circuit methods for the amplification of low-current nanopore signals in such interfaces.

  10. Abnormal hyperintensity within the subarachnoid space evaluated by fluid-attenuated inversion-recovery MR imaging: a spectrum of central nervous system diseases

    International Nuclear Information System (INIS)

    Maeda, M.; Sakuma, H.; Takeda, K.; Yagishita, A.; Yamamoto, T.

    2003-01-01

    A variety of central nervous system (CNS) diseases are associated with abnormal hyperintensity within the subarachnoid space (SAS) by fluid-attenuated inversion-recovery (FLAIR) MR imaging. Careful attention to the SAS can provide additional useful information that may not be available with conventional MR sequences. The purpose of this article is to provide a pictorial essay about CNS diseases and FLAIR images with abnormal hyperintensity within the SAS. We present several CNS diseases including subarachnoid hemorrhage, meningitis, leptomeningeal metastases, acute infarction, and severe arterial occlusive diseases such as moya-moya disease. We also review miscellaneous diseases or normal conditions that may exhibit cerebrospinal fluid hyperintensity on FLAIR images. Although the detection of abnormal hyperintensity suggests the underlying CNS diseases and narrows differential diagnoses, FLAIR imaging sometimes presents artifactual hyperintensity within the SAS that can cause the misinterpretation of normal SAS as pathologic conditions; therefore, radiologists should be familiar with such artifactual conditions as well as pathologic conditions shown as hyperintensity by FLAIR images. This knowledge is helpful in establishing the correct diagnosis. (orig.)

  11. Analysis of Neuronal Sequences Using Pairwise Biases

    Science.gov (United States)

    2015-08-27

    semantic memory (knowledge of facts) and implicit memory (e.g., how to ride a bike ). Evidence for the participation of the hippocampus in the formation of...very different from each other in many ways including duration and number of spikes. Still, these sequences share a similar trend in the general order...1 and 2 precede all other spikes in both s and s�). Many other sequences share this property with s and s�; in fact, we can completely characterize

  12. Palindromic sequence impedes sequencing-by-ligation mechanism.

    Science.gov (United States)

    Huang, Yu-Feng; Chen, Sheng-Chung; Chiang, Yih-Shien; Chen, Tzu-Han; Chiu, Kuo-Ping

    2012-01-01

    Current next-generation sequencing (NGS) platforms adopt two types of sequencing mechanisms: by synthesis or by ligation. The former is employed by 454 and Solexa systems, while the latter by SOLiD system. Although the pros and cons for each sequencing mechanism have more or less been discussed in a number of occasions, the potential obstacle imposed by palindromic sequences has not yet been addressed. To test the effect of the palindromic region on sequencing efficacy, we clonally amplified a paired-end ditag sequence composed of a 24-bp palindromic sequence flanked by a pair of tags from the E. coli genome. We used the near homogeneous fragments produced from MmeI digestion of the amplified clone to generate a sequencing library for SOLiD 5500xl sequencer. Results showed that, traditional ABI sequencers, which adopt sequencing-by-synthesis mechanism, were able to read through the palindromic region. However, SOLiD 5500xl was unable to do so. Instead, the palindromic region was read as miscellaneous random sequences. Moreover, readable tag sequence turned obscure ~2 bp prior to the palindromic region. Taken together, we demonstrate that SOLiD machines, which employ sequencing-by-ligation mechanism, are unable to read through the palindromic region. On the other hand, sequencing-by-synthesis sequencers had no difficulty in doing so.

  13. Goldbach Partitions and Sequences

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 11. Goldbach Partitions and Sequences. Subhash Kak. General Article Volume 19 Issue 11 November 2014 pp 1028-1037. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/019/11/1028-1037 ...

  14. THE RHIC SEQUENCER

    International Nuclear Information System (INIS)

    VAN ZEIJTS, J.; DOTTAVIO, T.; FRAK, B.; MICHNOFF, R.

    2001-01-01

    The Relativistic Heavy Ion Collider (RHIC) has a high level asynchronous time-line driven by a controlling program called the ''Sequencer''. Most high-level magnet and beam related issues are orchestrated by this system. The system also plays an important task in coordinated data acquisition and saving. We present the program, operator interface, operational impact and experience

  15. Goldbach Partitions and Sequences

    Indian Academy of Sciences (India)

    IAS Admin

    Properties of Goldbach partitions of numbers, as sums of primes, are presented and their potential applications to cryptography are described. The sequence of the number of partitions has excel- lent randomness properties. Goldbach partitions can be used to create ellipses and circles on the number line and they can also ...

  16. Generating Exome Enriched Sequencing Libraries from Formalin-Fixed, Paraffin-Embedded Tissue DNA for Next Generation Sequencing

    Science.gov (United States)

    Marosy, Beth A.; Craig, Brian D.; Hetrick, Kurt N.; Witmer, P. Dane; Ling, Hua; Griffith, Sean M.; Myers, Ben; Ostrander, Elaine A.; Stanford, Janet L.; Brody, Lawrence C.; Doheny, Kimberly F.

    2016-01-01

    This unit describes a protocol for generating exome enriched sequencing libraries using DNA extracted from Formalin Fixed Paraffin Embedded (FFPE) samples. Utilizing commercially available kits, we present a low input FFPE workflow starting with 50ng of DNA. This procedure includes a repair step to address damage caused by FFPE preservation that improves sequence quality. Subsequently, libraries undergo an in-solution targeted selection for exons, followed by sequencing using the Illumina next generation short read sequencing platform. PMID:28075488

  17. Metric representation of DNA sequences.

    Science.gov (United States)

    Wu, Z B

    2000-07-01

    A metric representation of DNA sequences is borrowed from symbolic dynamics. In view of this method, the pattern seen in the chaos game representation of DNA sequences is explained as the suppression of certain nucleotide strings in the DNA sequences. Frequencies of short nucleotide strings and suppression of the shortest ones in the DNA sequences can be determined by using the metric representation.

  18. On site DNA barcoding by nanopore sequencing.

    Directory of Open Access Journals (Sweden)

    Michele Menegon

    Full Text Available Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full exploitation of this approach is hampered by the high sequencing costs and the absence of equipped facilities in biodiversity-rich countries. In the present work, we developed a portable sequencing laboratory based on the portable DNA sequencer from Oxford Nanopore Technologies, the MinION. Complementary laboratory equipment and reagents were selected to be used in remote and tough environmental conditions. The performance of the MinION sequencer and the portable laboratory was tested for DNA barcoding in a mimicking tropical environment, as well as in a remote rainforest of Tanzania lacking electricity. Despite the relatively high sequencing error-rate of the MinION, the development of a suitable pipeline for data analysis allowed the accurate identification of different species of vertebrates including amphibians, reptiles and mammals. In situ sequencing of a wild frog allowed us to rapidly identify the species captured, thus confirming that effective DNA barcoding in the field is possible. These results open new perspectives for real-time-on-site DNA sequencing thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.

  19. Exploration of noncoding sequences in metagenomes.

    Directory of Open Access Journals (Sweden)

    Fabián Tobar-Tosse

    Full Text Available Environment-dependent genomic features have been defined for different metagenomes, whose genes and their associated processes are related to specific environments. Identification of ORFs and their functional categories are the most common methods for association between functional and environmental features. However, this analysis based on finding ORFs misses noncoding sequences and, therefore, some metagenome regulatory or structural information could be discarded. In this work we analyzed 23 whole metagenomes, including coding and noncoding sequences using the following sequence patterns: (G+C content, Codon Usage (Cd, Trinucleotide Usage (Tn, and functional assignments for ORF prediction. Herein, we present evidence of a high proportion of noncoding sequences discarded in common similarity-based methods in metagenomics, and the kind of relevant information present in those. We found a high density of trinucleotide repeat sequences (TRS in noncoding sequences, with a regulatory and adaptive function for metagenome communities. We present associations between trinucleotide values and gene function, where metagenome clustering correlate with microorganism adaptations and kinds of metagenomes. We propose here that noncoding sequences have relevant information to describe metagenomes that could be considered in a whole metagenome analysis in order to improve their organization, classification protocols, and their relation with the environment.

  20. CATEGORIZATION OF EVENT SEQUENCES FOR LICENSE APPLICATION

    Energy Technology Data Exchange (ETDEWEB)

    G.E. Ragan; P. Mecheret; D. Dexheimer

    2005-04-14

    The purposes of this analysis are: (1) Categorize (as Category 1, Category 2, or Beyond Category 2) internal event sequences that may occur before permanent closure of the repository at Yucca Mountain. (2) Categorize external event sequences that may occur before permanent closure of the repository at Yucca Mountain. This includes examining DBGM-1 seismic classifications and upgrading to DBGM-2, if appropriate, to ensure Beyond Category 2 categorization. (3) State the design and operational requirements that are invoked to make the categorization assignments valid. (4) Indicate the amount of material put at risk by Category 1 and Category 2 event sequences. (5) Estimate frequencies of Category 1 event sequences at the maximum capacity and receipt rate of the repository. (6) Distinguish occurrences associated with normal operations from event sequences. It is beyond the scope of the analysis to propose design requirements that may be required to control radiological exposure associated with normal operations. (7) Provide a convenient compilation of the results of the analysis in tabular form. The results of this analysis are used as inputs to the consequence analyses in an iterative design process that is depicted in Figure 1. Categorization of event sequences for permanent retrieval of waste from the repository is beyond the scope of this analysis. Cleanup activities that take place after an event sequence and other responses to abnormal events are also beyond the scope of the analysis.

  1. HPMV: human protein mutation viewer - relating sequence mutations to protein sequence architecture and function changes.

    Science.gov (United States)

    Sherman, Westley Arthur; Kuchibhatla, Durga Bhavani; Limviphuvadh, Vachiranee; Maurer-Stroh, Sebastian; Eisenhaber, Birgit; Eisenhaber, Frank

    2015-10-01

    Next-generation sequencing advances are rapidly expanding the number of human mutations to be analyzed for causative roles in genetic disorders. Our Human Protein Mutation Viewer (HPMV) is intended to explore the biomolecular mechanistic significance of non-synonymous human mutations in protein-coding genomic regions. The tool helps to assess whether protein mutations affect the occurrence of sequence-architectural features (globular domains, targeting signals, post-translational modification sites, etc.). As input, HPMV accepts protein mutations - as UniProt accessions with mutations (e.g. HGVS nomenclature), genome coordinates, or FASTA sequences. As output, HPMV provides an interactive cartoon showing the mutations in relation to elements of the sequence architecture. A large variety of protein sequence architectural features were selected for their particular relevance to mutation interpretation. Clicking a sequence feature in the cartoon expands a tree view of additional information including multiple sequence alignments of conserved domains and a simple 3D viewer mapping the mutation to known PDB structures, if available. The cartoon is also correlated with a multiple sequence alignment of similar sequences from other organisms. In cases where a mutation is likely to have a straightforward interpretation (e.g. a point mutation disrupting a well-understood targeting signal), this interpretation is suggested. The interactive cartoon can be downloaded as standalone viewer in Java jar format to be saved and viewed later with only a standard Java runtime environment. The HPMV website is: http://hpmv.bii.a-star.edu.sg/ .

  2. PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.

    Science.gov (United States)

    Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J

    2011-03-07

    Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

  3. PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

    Directory of Open Access Journals (Sweden)

    Baldwin Stephen A

    2011-03-01

    Full Text Available Abstract Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

  4. 7th International Workshop on the Identification of Transcribed Sequences. Beyond the Identification of Transcribed Sequences

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, Kathleen

    1997-11-19

    The Seventh Annual Human Genome Conference: Beyond the Identification of Transcribed Sequences (BITS) was held November 16-19, 1997 at the Asilomar Conference Center in Monterey, California. The format for the meeting was a combination of oral presentations, group discussions and poster sessions. The original workshop was held to discuss methodologies for the identification of transcribed sequences in mammalian genomes. Over the years, the focus of the workshops has gradually shifted towards functional analysis, with the most dramatic change in emphasis at this meeting, as reflected in the modest change in the workshop title. Topics presented and discussed included: (1) large scale expression and mutational analysis in yeast, C. elegans, Drosophila and zebrafish, (2) comparative mapping of zebrafish, chicken and Fugu; (3) functional analysis in mouse using promoter traps, mutational analysis of biochemical pathways, and Cre/lox constructs; (4) construction of 5 foot end and complete cDNA libraries; (5) expression analysis in mammalian organisms by array screening and differential display; (6) genome organization as determined by detailed transcriptional mapping and genomic sequence analysis; (7) analysis of genomic sequence, including gene and regulatory sequence predictions, annotation of genomic sequence, development of expression databases and verification of sequence analysis predictions; and (8) structural/functional relationships as determined by RNA secondary structure analysis and evolutionary conservation of non-coding sequences.

  5. Comparison of metagenomic samples using sequence signatures

    Directory of Open Access Journals (Sweden)

    Jiang Bai

    2012-12-01

    Full Text Available Abstract Background Sequence signatures, as defined by the frequencies of k-tuples (or k-mers, k-grams, have been used extensively to compare genomic sequences of individual organisms, to identify cis-regulatory modules, and to study the evolution of regulatory sequences. Recently many next-generation sequencing (NGS read data sets of metagenomic samples from a variety of different environments have been generated. The assembly of these reads can be difficult and analysis methods based on mapping reads to genes or pathways are also restricted by the availability and completeness of existing databases. Sequence-signature-based methods, however, do not need the complete genomes or existing databases and thus, can potentially be very useful for the comparison of metagenomic samples using NGS read data. Still, the applications of sequence signature methods for the comparison of metagenomic samples have not been well studied. Results We studied several dissimilarity measures, including d2, d2* and d2S recently developed from our group, a measure (hereinafter noted as Hao used in CVTree developed from Hao’s group (Qi et al., 2004, measures based on relative di-, tri-, and tetra-nucleotide frequencies as in Willner et al. (2009, as well as standard lp measures between the frequency vectors, for the comparison of metagenomic samples using sequence signatures. We compared their performance using a series of extensive simulations and three real next-generation sequencing (NGS metagenomic datasets: 39 fecal samples from 33 mammalian host species, 56 marine samples across the world, and 13 fecal samples from human individuals. Results showed that the dissimilarity measure d2S can achieve superior performance when comparing metagenomic samples by clustering them into different groups as well as recovering environmental gradients affecting microbial samples. New insights into the environmental factors affecting microbial compositions in metagenomic samples

  6. A neurocomputational model of automatic sequence production.

    Science.gov (United States)

    Helie, Sebastien; Roeder, Jessica L; Vucovich, Lauren; Rünger, Dennis; Ashby, F Gregory

    2015-07-01

    Most behaviors unfold in time and include a sequence of submovements or cognitive activities. In addition, most behaviors are automatic and repeated daily throughout life. Yet, relatively little is known about the neurobiology of automatic sequence production. Past research suggests a gradual transfer from the associative striatum to the sensorimotor striatum, but a number of more recent studies challenge this role of the BG in automatic sequence production. In this article, we propose a new neurocomputational model of automatic sequence production in which the main role of the BG is to train cortical-cortical connections within the premotor areas that are responsible for automatic sequence production. The new model is used to simulate four different data sets from human and nonhuman animals, including (1) behavioral data (e.g., RTs), (2) electrophysiology data (e.g., single-neuron recordings), (3) macrostructure data (e.g., TMS), and (4) neurological circuit data (e.g., inactivation studies). We conclude with a comparison of the new model with existing models of automatic sequence production and discuss a possible new role for the BG in automaticity and its implication for Parkinson's disease.

  7. Reporting Differences Between Spacecraft Sequence Files

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy E.; Fisher, Forest W.

    2010-01-01

    A suite of computer programs, called seq diff suite, reports differences between the products of other computer programs involved in the generation of sequences of commands for spacecraft. These products consist of files of several types: replacement sequence of events (RSOE), DSN keyword file [DKF (wherein DSN signifies Deep Space Network)], spacecraft activities sequence file (SASF), spacecraft sequence file (SSF), and station allocation file (SAF). These products can include line numbers, request identifications, and other pieces of information that are not relevant when generating command sequence products, though these fields can result in the appearance of many changes to the files, particularly when using the UNIX diff command to inspect file differences. The outputs of prior software tools for reporting differences between such products include differences in these non-relevant pieces of information. In contrast, seq diff suite removes the fields containing the irrelevant pieces of information before processing to extract differences, so that only relevant differences are reported. Thus, seq diff suite is especially useful for reporting changes between successive versions of the various products and in particular flagging difference in fields relevant to the sequence command generation and review process.

  8. Fault location using synchronized sequence measurements

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Chun; Jia, Qing-Quan; Li, Xin-Bin; Dou, Chun-Xia [Department of Power Electrical Engineering, Yanshan University, Qinhuangdao 066004 (China)

    2008-02-15

    This paper proposes fault location formulas using synchronized sequence measurements. For earth faults, zero-sequence voltages and currents at two terminals of faulted line are applied to fault location. Negative-sequence measurements are utilized for asymmetrical faults and positive-sequence measurements are used for three-phase faults. The fault location formulas are derived from a fault location technique [Wang C, Dou C, Li X, Jia Q. A WAMS/PMU-based fault location technique. Elect Power Syst Res 2007;77(8):936-945] based on WAMS/PMU. The technique uses synchronized fault voltages measured by PMUs in power network. The formulas are simple and are easy for application. Case studies on a testing network with 500 kV transmission lines including ATP/EMTP simulations are presented. Various fault types and fault resistances are also considered. (author)

  9. Sequencing Information Management System (SIMS). Final report

    Energy Technology Data Exchange (ETDEWEB)

    Fields, C.

    1996-02-15

    A feasibility study to develop a requirements analysis and functional specification for a data management system for large-scale DNA sequencing laboratories resulted in a functional specification for a Sequencing Information Management System (SIMS). This document reports the results of this feasibility study, and includes a functional specification for a SIMS relational schema. The SIMS is an integrated information management system that supports data acquisition, management, analysis, and distribution for DNA sequencing laboratories. The SIMS provides ad hoc query access to information on the sequencing process and its results, and partially automates the transfer of data between laboratory instruments, analysis programs, technical personnel, and managers. The SIMS user interfaces are designed for use by laboratory technicians, laboratory managers, and scientists. The SIMS is designed to run in a heterogeneous, multiplatform environment in a client/server mode. The SIMS communicates with external computational and data resources via the internet.

  10. Automated genome sequence analysis and annotation.

    Science.gov (United States)

    Andrade, M A; Brown, N P; Leroy, C; Hoersch, S; de Daruvar, A; Reich, C; Franchini, A; Tamames, J; Valencia, A; Ouzounis, C; Sander, C

    1999-05-01

    Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized. Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences. However, the installation and application of these methods require experience and are time consuming. We present here an automatic system for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts. The GeneQuiz system includes a Web-based browser that allows examination of the evidence leading to an automatic annotation and offers additional information, views of the results, and links to biological databases that complement the automatic analysis. System structure and operating principles concerning the use of multiple sequence databases, underlying sequence analysis tools, lexical analyses of database annotations and decision criteria for functional assignments are detailed. The system makes automatic quality assessments of results based on prior experience with the underlying sequence analysis tools; overall error rates in functional assignment are estimated at 2.5-5% for cases annotated with highest reliability ('clear' cases). Sources of over-interpretation of results are discussed with proposals for improvement. A conservative definition for reporting 'new findings' that takes account of database maturity is presented along with examples of possible kinds of discoveries (new function, family and superfamily) made by the system. System performance in relation to sequence database coverage, database dynamics and database search methods is analysed, demonstrating the inherent advantages of an integrated automatic approach using multiple databases and search methods applied in an objective and repeatable manner. The GeneQuiz system

  11. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  12. Metal resistance sequences and transgenic plants

    Science.gov (United States)

    Meagher, Richard Brian; Summers, Anne O.; Rugh, Clayton L.

    1999-10-12

    The present invention provides nucleic acid sequences encoding a metal ion resistance protein, which are expressible in plant cells. The metal resistance protein provides for the enzymatic reduction of metal ions including but not limited to divalent Cu, divalent mercury, trivalent gold, divalent cadmium, lead ions and monovalent silver ions. Transgenic plants which express these coding sequences exhibit increased resistance to metal ions in the environment as compared with plants which have not been so genetically modified. Transgenic plants with improved resistance to organometals including alkylmercury compounds, among others, are provided by the further inclusion of plant-expressible organometal lyase coding sequences, as specifically exemplified by the plant-expressible merB coding sequence. Furthermore, these transgenic plants which have been genetically modified to express the metal resistance coding sequences of the present invention can participate in the bioremediation of metal contamination via the enzymatic reduction of metal ions. Transgenic plants resistant to organometals can further mediate remediation of organic metal compounds, for example, alkylmetal compounds including but not limited to methyl mercury, methyl lead compounds, methyl cadmium and methyl arsenic compounds, in the environment by causing the freeing of mercuric or other metal ions and the reduction of the ionic mercury or other metal ions to the less toxic elemental mercury or other metals.

  13. Preliminary hazard analysis using sequence tree method

    International Nuclear Information System (INIS)

    Huang Huiwen; Shih Chunkuan; Hung Hungchih; Chen Minghuei; Yih Swu; Lin Jiinming

    2007-01-01

    A system level PHA using sequence tree method was developed to perform Safety Related digital I and C system SSA. The conventional PHA is a brainstorming session among experts on various portions of the system to identify hazards through discussions. However, this conventional PHA is not a systematic technique, the analysis results strongly depend on the experts' subjective opinions. The analysis quality cannot be appropriately controlled. Thereby, this research developed a system level sequence tree based PHA, which can clarify the relationship among the major digital I and C systems. Two major phases are included in this sequence tree based technique. The first phase uses a table to analyze each event in SAR Chapter 15 for a specific safety related I and C system, such as RPS. The second phase uses sequence tree to recognize what I and C systems are involved in the event, how the safety related systems work, and how the backup systems can be activated to mitigate the consequence if the primary safety systems fail. In the sequence tree, the defense-in-depth echelons, including Control echelon, Reactor trip echelon, ESFAS echelon, and Indication and display echelon, are arranged to construct the sequence tree structure. All the related I and C systems, include digital system and the analog back-up systems are allocated in their specific echelon. By this system centric sequence tree based analysis, not only preliminary hazard can be identified systematically, the vulnerability of the nuclear power plant can also be recognized. Therefore, an effective simplified D3 evaluation can be performed as well. (author)

  14. A vision for ubiquitous sequencing.

    Science.gov (United States)

    Erlich, Yaniv

    2015-10-01

    Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors--miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors. © 2015 Erlich; Published by Cold Spring Harbor Laboratory Press.

  15. Psychoacoustic Properties of Fibonacci Sequences

    Directory of Open Access Journals (Sweden)

    J. Sokoll

    2008-01-01

    Full Text Available 1202, Fibonacci set up one of the most interesting sequences in number theory. This sequence can be represented by so-called Fibonacci Numbers, and by a binary sequence of zeros and ones. If such a binary Fibonacci Sequence is played back as an audio file, a very dissonant sound results. This is caused by the “almost-periodic”, “self-similar” property of the binary sequence. The ratio of zeros and ones converges to the golden ratio, as do the primary and secondary spectral components intheir frequencies and amplitudes. These Fibonacci Sequences will be characterized using listening tests and psychoacoustic analyses. 

  16. Structural Optimization Including Centrifugal and Coriolis Effects

    Science.gov (United States)

    1988-01-01

    the desired frequency changes with excellent accuracy. MSC/ NASTRAN finite element solution sequences were modified to incorporate rotary effects. DMAP ...properties can be altered by a nonlinear change factor. These manipulations may be done by selective use of the MATMOD DMAP module. In the MSC/ NASTRAN ...Examples were carried out using the general purpose software package MSC/ NASTRAN and ADS (Automated Design Synthesis). "I OTIC copy INSpE TE 6

  17. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  18. Comparison of next generation sequencing technologies for transcriptome characterization

    Directory of Open Access Journals (Sweden)

    Soltis Douglas E

    2009-08-01

    Full Text Available Abstract Background We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared simulation results for traditional capillary sequencing with "Next Generation" (NG ultra high-throughput technologies. The simulation model was parameterized using mappings of 130,000 cDNA sequence reads to the Arabidopsis genome (NCBI Accession SRA008180.19. We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica and the magnoliid avocado (Persea americana using a variety of methods for cDNA synthesis. Results The Arabidopsis reads tagged more than 15,000 genes, including new splice variants and extended UTR regions. Of the total 134,791 reads (13.8 MB, 119,518 (88.7% mapped exactly to known exons, while 1,117 (0.8% mapped to introns, 11,524 (8.6% spanned annotated intron/exon boundaries, and 3,066 (2.3% extended beyond the end of annotated UTRs. Sequence-based inference of relative gene expression levels correlated significantly with microarray data. As expected, NG sequencing of normalized libraries tagged more genes than non-normalized libraries, although non-normalized libraries yielded more full-length cDNA sequences. The Arabidopsis data were used to simulate additional rounds of NG and traditional EST sequencing, and various combinations of each. Our simulations suggest a combination of FLX and Solexa sequencing for optimal transcriptome coverage at modest cost. We have also developed ESTcalc http://fgp.huck.psu.edu/NG_Sims/ngsim.pl, an online webtool, which allows users to explore the results of this study by specifying individualized costs and sequencing characteristics. Conclusion NG sequencing technologies are a highly flexible set of platforms that can be scaled to suit different project goals. In terms of sequence coverage alone, the NG sequencing is a dramatic advance

  19. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  20. Protein Sequencing with Tandem Mass Spectrometry

    Science.gov (United States)

    Ziady, Assem G.; Kinter, Michael

    The recent introduction of electrospray ionization techniques that are suitable for peptides and whole proteins has allowed for the design of mass spectrometric protocols that provide accurate sequence information for proteins. The advantages gained by these approaches over traditional Edman Degradation sequencing include faster analysis and femtomole, sometimes attomole, sensitivity. The ability to efficiently identify proteins has allowed investigators to conduct studies on their differential expression or modification in response to various treatments or disease states. In this chapter, we discuss the use of electrospray tandem mass spectrometry, a technique whereby protein-derived peptides are subjected to fragmentation in the gas phase, revealing sequence information for the protein. This powerful technique has been instrumental for the study of proteins and markers associated with various disorders, including heart disease, cancer, and cystic fibrosis. We use the study of protein expression in cystic fibrosis as an example.

  1. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large and com...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....... and complex genomes. Recent developments in strategies for target-enrichment, transcriptome re-sequencing, and partial genome re-sequencing allows for enrichment for regions of interest at a scale that is matched to the throughput of next-generation sequencing platforms, and has emerged as a promising...

  2. Spaces of ideal convergent sequences.

    Science.gov (United States)

    Mursaleen, M; Sharma, Sunil K

    2014-01-01

    In the present paper, we introduce some sequence spaces using ideal convergence and Musielak-Orlicz function ℳ = (M(k)). We also examine some topological properties of the resulting sequence spaces.

  3. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  4. A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data

    Directory of Open Access Journals (Sweden)

    Masanori Kakuta

    2017-10-01

    Full Text Available Sequence similarity searches have been widely used in the analyses of metagenomic sequencing data. Finding homologous sequences in a reference database enables the estimation of taxonomic and functional characteristics of each query sequence. Because current metagenomic sequencing data consist of a large number of nucleotide sequences, the time required for sequence similarity searches account for a large proportion of the total time. This time-consuming step makes it difficult to perform large-scale analyses. To analyze large-scale metagenomic data, such as those found in the human oral microbiome, we developed GHOST-MP (Genome-wide HOmology Search Tool on Massively Parallel system, a parallel sequence similarity search tool for massively parallel computing systems. This tool uses a fast search algorithm based on suffix arrays of query and database sequences and a hierarchical parallel search to accelerate the large-scale sequence similarity search of metagenomic sequencing data. The parallel computing efficiency and the search speed of this tool were evaluated. GHOST-MP was shown to be scalable over 10,000 CPU (Central Processing Unit cores, and achieved over 80-fold acceleration compared with mpiBLAST using the same computational resources. We applied this tool to human oral metagenomic data, and the results indicate that the oral cavity, the oral vestibule, and plaque have different characteristics based on the functional gene category.

  5. Putting instruction sequences into effect

    NARCIS (Netherlands)

    Bergstra, J.A.

    2011-01-01

    An attempt is made to define the concept of execution of an instruction sequence. It is found to be a special case of directly putting into effect of an instruction sequence. Directly putting into effect of an instruction sequences comprises interpretation as well as execution. Directly putting into

  6. Sequencing Games with Repeated Players

    NARCIS (Netherlands)

    Estevez Fernandez, M.A.; Borm, P.; Calleja, P.; Hamers, H.

    2008-01-01

    Two classes of one machine sequencing situations are considered in which each job corresponds to exactly one player but a player may have more than one job to be processed, so called RP(repeated player) sequencing situations. In max-RP sequencing situations it is assumed that each player's cost

  7. Blazar Sequence in Fermi Era

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power-high-synchrotron-peaked ...

  8. ASAP: Amplification, sequencing & annotation of plastomes

    Directory of Open Access Journals (Sweden)

    Folta Kevin M

    2005-12-01

    Full Text Available Abstract Background Availability of DNA sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Traditionally, the first step in mining the valuable information within a chloroplast genome requires sequencing a chloroplast plasmid library or BAC clones. These activities involve complicated preparatory procedures like chloroplast DNA isolation or identification of the appropriate BAC clones to be sequenced. Rolling circle amplification (RCA is being used currently to amplify the chloroplast genome from purified chloroplast DNA and the resulting products are sheared and cloned prior to sequencing. Herein we present a universal high-throughput, rapid PCR-based technique to amplify, sequence and assemble plastid genome sequence from diverse species in a short time and at reasonable cost from total plant DNA, using the large inverted repeat region from strawberry and peach as proof of concept. The method exploits the highly conserved coding regions or intergenic regions of plastid genes. Using an informatics approach, chloroplast DNA sequence information from 5 available eudicot plastomes was aligned to identify the most conserved regions. Cognate primer pairs were then designed to generate ~1 – 1.2 kb overlapping amplicons from the inverted repeat region in 14 diverse genera. Results 100% coverage of the inverted repeat region was obtained from Arabidopsis, tobacco, orange, strawberry, peach, lettuce, tomato and Amaranthus. Over 80% coverage was obtained from distant species, including Ginkgo, loblolly pine and Equisetum. Sequence from the inverted repeat region of strawberry and peach plastome was obtained, annotated and analyzed. Additionally, a polymorphic region identified from gel electrophoresis was sequenced from tomato and Amaranthus. Sequence analysis revealed large deletions in these species relative to tobacco plastome thus exhibiting the utility of this method for structural and

  9. Refined Pichia pastoris reference genome sequence

    Science.gov (United States)

    Sturmberger, Lukas; Chappell, Thomas; Geier, Martina; Krainer, Florian; Day, Kasey J.; Vide, Ursa; Trstenjak, Sara; Schiefer, Anja; Richardson, Toby; Soriaga, Leah; Darnhofer, Barbara; Birner-Gruenberger, Ruth; Glick, Benjamin S.; Tolstorukov, Ilya; Cregg, James; Madden, Knut; Glieder, Anton

    2016-01-01

    Strains of the species Komagataella phaffii are the most frequently used “Pichia pastoris” strains employed for recombinant protein production as well as studies on peroxisome biogenesis, autophagy and secretory pathway analyses. Genome sequencing of several different P. pastoris strains has provided the foundation for understanding these cellular functions in recent genomics, transcriptomics and proteomics experiments. This experimentation has identified mistakes, gaps and incorrectly annotated open reading frames in the previously published draft genome sequences. Here, a refined reference genome is presented, generated with genome and transcriptome sequencing data from multiple P. pastoris strains. Twelve major sequence gaps from 20 to 6000 base pairs were closed and 5111 out of 5256 putative open reading frames were manually curated and confirmed by RNA-seq and published LC-MS/MS data, including the addition of new open reading frames (ORFs) and a reduction in the number of spliced genes from 797 to 571. One chromosomal fragment of 76 kbp between two previous gaps on chromosome 1 and another 134 kbp fragment at the end of chromosome 4, as well as several shorter fragments needed re-orientation. In total more than 500 positions in the genome have been corrected. This reference genome is presented with new chromosomal numbering, positioning ribosomal repeats at the distal ends of the four chromosomes, and includes predicted chromosomal centromeres as well as the sequence of two linear cytoplasmic plasmids of 13.1 and 9.5 kbp found in some strains of P. pastoris. PMID:27084056

  10. Progressive multiple sequence alignments from triplets

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2007-07-01

    Full Text Available Abstract Background The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation steps. Adjacent insertions and deletions necessarily appear in arbitrary order in pairwise alignments and hence form an unavoidable source of errors. Research Here we present a modified variant of progressive sequence alignments that addresses both issues. Instead of pairwise alignments we use exact dynamic programming to align sequence or profile triples. This avoids a large fractions of the ambiguities arising in pairwise alignments. In the subsequent aggregation steps we follow the logic of the Neighbor-Net algorithm, which constructs a phylogenetic network by step-wisely replacing triples by pairs instead of combining pairs to singletons. To this end the three-way alignments are subdivided into two partial alignments, at which stage all-gap columns are naturally removed. This alleviates the "once a gap, always a gap" problem of progressive alignment procedures. Conclusion The three-way Neighbor-Net based alignment program aln3nn is shown to compare favorably on both protein sequences and nucleic acids sequences to other progressive alignment tools. In the latter case one easily can include scoring terms that consider secondary structure features. Overall, the quality of resulting alignments in general exceeds that of clustalw or other multiple alignments tools even though our software does not included heuristics for context dependent (mismatch scores.

  11. A Main Sequence for Quasars

    Directory of Open Access Journals (Sweden)

    Paola Marziani

    2018-03-01

    Full Text Available The last 25 years saw a major step forward in the analysis of optical and UV spectroscopic data of large quasar samples. Multivariate statistical approaches have led to the definition of systematic trends in observational properties that are the basis of physical and dynamical modeling of quasar structure. We discuss the empirical correlates of the so-called “main sequence” associated with the quasar Eigenvector 1, its governing physical parameters and several implications on our view of the quasar structure, as well as some luminosity effects associated with the virialized component of the line emitting regions. We also briefly discuss quasars in a segment of the main sequence that includes the strongest FeII emitters. These sources show a small dispersion around a well-defined Eddington ratio value, a property which makes them potential Eddington standard candles.

  12. The 2016 Kumamoto earthquake sequence.

    Science.gov (United States)

    Kato, Aitaro; Nakamura, Kouji; Hiyama, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An M j 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an M j 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest.

  13. The 2016 Kumamoto earthquake sequence

    Science.gov (United States)

    KATO, Aitaro; NAKAMURA, Kouji; HIYAMA, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An Mj 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an Mj 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest. PMID:27725474

  14. Sequencing Closterium moniliferum: Future prospects in nuclear ...

    African Journals Online (AJOL)

    Akanksha Pandey

    2012-10-06

    Oct 6, 2012 ... disorders. A remarkable feat has been achieved by the recent advancements in sequencing technologies that has revolution- ized the conceptual foundations in a wide range of scientific fields including archaeology, anthropology, genetics, molecu- lar biology, evolutionary genomics and forensic sciences.

  15. Spent fuel bundle counter sequence error manual - BRUCE NGS

    International Nuclear Information System (INIS)

    Nicholson, L.E.

    1992-01-01

    The Spent Fuel Bundle Counter (SFBC) is used to count the number and type of spent fuel transfers that occur into or out of controlled areas at CANDU reactor sites. However if the transfers are executed in a non-standard manner or the SFBC is malfunctioning, the transfers are recorded as sequence errors. Each sequence error message typically contains adequate information to determine the cause of the message. This manual provides a guide to interpret the various sequence error messages that can occur and suggests probable cause or causes of the sequence errors. Each likely sequence error is presented on a 'card' in Appendix A. Note that it would be impractical to generate a sequence error card file with entries for all possible combinations of faults. Therefore the card file contains sequences with only one fault at a time. Some exceptions have been included however where experience has indicated that several faults can occur simultaneously

  16. Spent fuel bundle counter sequence error manual - DARLINGTON NGS

    International Nuclear Information System (INIS)

    Nicholson, L.E.

    1992-01-01

    The Spent Fuel Bundle Counter (SFBC) is used to count the number and type of spent fuel transfers that occur into or out of controlled areas at CANDU reactor sites. However if the transfers are executed in a non-standard manner or the SFBC is malfunctioning, the transfers are recorded as sequence errors. Each sequence error message typically contains adequate information to determine the cause of the message. This manual provides a guide to interpret the various sequence error messages that can occur and suggests probable cause or causes of the sequence errors. Each likely sequence error is presented on a 'card' in Appendix A. Note that it would be impractical to generate a sequence error card file with entries for all possible combinations of faults. Therefore the card file contains sequences with only one fault at a time. Some exceptions have been included however where experience has indicated that several faults can occur simultaneously

  17. Sequence analysis on microcomputers.

    Science.gov (United States)

    Cannon, G C

    1987-10-02

    Overall, each of the program packages performed their tasks satisfactorily. For analyses where there was a well-defined answer, such as a search for a restriction site, there were few significant differences between the program sets. However, for tasks in which a degree of flexibility is desirable, such as homology or similarity determinations and database searches, DNASTAR consistently afforded the user more options in conducting the required analysis than did the other two packages. However, for laboratories where sequence analysis is not a major effort and the expense of a full sequence analysis workstation cannot be justified, MicroGenie and IBI-Pustell offer a satisfactory alternative. MicroGenie is a polished program system. Many may find that its user interface is more "user friendly" than the standard menu-driven interfaces. Its system of filing sequences under individual passwords facilitates use by more than one person. MicroGenie uses a hardware device for software protection that occupies a card slot in the computer on which it is used. Although I am sympathetic to the problem of software piracy, I feel that a less drastic solution is in order for a program likely to be sharing limited computer space with other software packages. The IBI-Pustell package performs the required analysis functions as accurately and quickly as MicroGenie but it lacks the clearness and ease of use. The menu system seems disjointed, and new or infrequent users often find themselves at apparent "dead-end menus" where the only clear alternative is to restart the entire program package. It is suggested from published accounts that the user interface is going to be upgraded and perhaps when that version is available, use of the system will be improved. The documentation accompanying each package was relatively clear as to how to run the programs, but all three packages assumed that the user was familiar with the computational techniques employed. MicroGenie and IBI-Pustell further

  18. Sequence-Based Identification of Aerobic Actinomycetes

    Science.gov (United States)

    Patel, Jean Baldus; Wallace, Richard J.; Brown-Elliott, Barbara A.; Taylor, Tony; Imperatrice, Carol; Leonard, Deborah G. B.; Wilson, Rebecca W.; Mann, Linda; Jost, Kenneth C.; Nachamkin, Irving

    2004-01-01

    We investigated the utility of 500-bp 16S rRNA gene sequencing for identifying clinically significant species of aerobic actinomycetes. A total of 28 reference strains and 71 clinical isolates that included members of the genera Streptomyces, Gordonia, and Tsukamurella and 10 taxa of Nocardia were studied. Methods of nonsequencing analyses included growth and biochemical analysis, PCR-restriction enzyme analysis of the 439-bp Telenti fragment of the 65 hsp gene, susceptibility testing, and, for selected isolates, high-performance liquid chromatography. Many of the isolates were included in prior taxonomic studies. Sequencing of Nocardia species revealed that members of the group were generally most closely related to the American Type Culture Collection (ATCC) type strains. However, the sequences of Nocardia transvalensis, N. otitidiscaviarum, and N. nova isolates were highly variable; and it is likely that each of these species contains multiple species. We propose that these three species be designated complexes until they are more taxonomically defined. The sequences of several taxa did not match any recognized species. Among other aerobic actinomycetes, each group most closely resembled the associated reference strain, but with some divergence. The study demonstrates the ability of partial 16S rRNA gene sequencing to identify members of the aerobic actinomycetes, but the study also shows that a high degree of sequence divergence exists within many species and that many taxa within the Nocardia spp. are unnamed at present. A major unresolved issue is the type strain of N. asteroides, as the present one (ATCC 19247), chosen before the availability of molecular analysis, does not represent any of the common taxa associated with clinical nocardiosis. PMID:15184431

  19. New MR pulse sequence

    International Nuclear Information System (INIS)

    Harms, S.E.; Flamig, D.P.; Griffey, R.H.

    1990-01-01

    This paper describes a method for fat suppression for three-dimensional MR imaging. The FATS (fat-suppressed acquisition with echo time shortened) sequence employs a pair of opposing adiabatic half-passage RF pulses tuned on fat resonance. The imaging parameters are as follows: TR, 20 msec; TE, 21.7-3.2 msec; 1,024 x 128 x 128 acquired matrix; imaging time, approximately 11 minutes. A series of 54 examinations were performed. Excellent fat suppression with water excitation is achieved in all cases. The orbital images demonstrate superior resolution of small orbital lesions. The high signal-to-noise ratio (SNR) in cranial studies demonstrates excellent petrous bone and internal auditory canal anatomy

  20. The evolution of nanopore sequencing

    Science.gov (United States)

    Wang, Yue; Yang, Qiuping; Wang, Zhimin

    2014-01-01

    The “$1000 Genome” project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the “$1000 Genome” while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards. PMID:25610451

  1. The Evolution of Nanopore Sequencing

    Directory of Open Access Journals (Sweden)

    Yue eWang

    2015-01-01

    Full Text Available The $1,000 Genome project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the $1,000 Genome while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.

  2. The value of qualitative and quantitative assessment of lesion to cerebral cortex signal ratio on double inversion recovery sequence in the differentiation of demyelinating plaques from non-specific T2 hyperintensities

    Energy Technology Data Exchange (ETDEWEB)

    Hamcan, Salih; Battal, Bilal; Akgun, Veysel; Sari, Sebahattin; Tasar, Mustafa [Gulhane Military Medical School, Department of Radiology, Etlik, Ankara (Turkey); Oz, Oguzhan; Tasdemir, Serdar [Gulhane Military Medical School, Department of Neurology, Ankara (Turkey); Bozkurt, Yalcin [Golcuk Military Hospital, Department of Radiology, Kocaeli (Turkey)

    2017-02-15

    To assess the usefulness of the visual assessment and to determine diagnostic value of the lesion-to-cerebral cortex signal ratio (LCSR) measurement in the differentiation of demyelinating plaques and non-specific T2 hyperintensities on double inversion recovery (DIR) sequence. DIR and fluid-attenuated inversion recovery (FLAIR) sequences of 25 clinically diagnosed multiple sclerosis (MS) patients and 25 non-MS patients with non-specific T2-hyperintense lesions were evaluated visually and LCSRs were measured by two observers independently. On DIR sequence, the calculated mean LCSR ± SD for demyelinating plaques and non-specific T2-hyperintense lesions were 1.60 ± 0.26 and 0.75 ± 0.19 for observer1, and 1.61 ± 0.27 and 0.74 ± 0.19 for observer2. LCSRs of demyelinating plaques were significantly higher than other non-specific T2-hyperintense lesions on DIR sequence. By using the visual assessment demyelinating plaques were differentiated from non-specific T2-hyperintensities with 92.8 % sensitivity, 97.5 % specificity and 95.1 % accuracy for observer1 and 92.8 % sensitivity, 95 % specificity and 93.9 % accuracy for observer2. Visual assessment and LCSR measurement on DIR sequence seems to be useful for differentiating demyelinating MS plaques from supratentorial non-specific T2 hyperintensities. This feature can be used for diagnosis of MS particularly in patients with only supratentorial T2-hyperintense lesions who are categorized as radiologically possible MS. (orig.)

  3. Tools for integrated sequence-structure analysis with UCSF Chimera

    Directory of Open Access Journals (Sweden)

    Huang Conrad C

    2006-07-01

    Full Text Available Abstract Background Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit; (c can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals. Results The molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided. Conclusion The tools described here apply to many problems involving comparison and analysis of protein structures and their sequences. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines. UCSF Chimera is free for non-commercial use and is

  4. Bilateral maculopathy associated with Pierre Robin sequence.

    Science.gov (United States)

    Witmer, Matthew T; Vasan, Ryan; Levy, Richard; Davis, Jessica; Chan, R V Paul

    2012-08-01

    Pierre Robin sequence has been associated with a number of ocular complications, including myopia, strabismus, Möbius syndrome, nasolacrimal duct obstruction, glaucoma, cataract, microphthalmos, coloboma of choroid, and retinal detachment. We report a 10-day-old boy who presented with micrognathia, glossoptosis, and cleft palate as well as multiple congenital anomalies. Ophthalmic examination was notable for bilateral maculopathy, with focal areas of retinal and retinal pigment epithelial atrophy. The association of Pierre Robin sequence and maculopathy has been reported only twice previously. Copyright © 2012 American Association for Pediatric Ophthalmology and Strabismus. Published by Mosby, Inc. All rights reserved.

  5. ANDES: Statistical tools for the ANalyses of DEep Sequencing

    Directory of Open Access Journals (Sweden)

    Denison Mark R

    2010-07-01

    Full Text Available Abstract Background The advancements in DNA sequencing technologies have allowed researchers to progress from the analyses of a single organism towards the deep sequencing of a sample of organisms. With sufficient sequencing depth, it is now possible to detect subtle variations between members of the same species, or between mixed species with shared biomarkers, such as the 16S rRNA gene. However, traditional sequencing analyses of samples from largely homogeneous populations are often still based on multiple sequence alignments (MSA, where each sequence is placed along a separate row and similarities between aligned bases can be followed down each column. While this visual format is intuitive for a small set of aligned sequences, the representation quickly becomes cumbersome as sequencing depths cover loci hundreds or thousands of reads deep. Findings We have developed ANDES, a software library and a suite of applications, written in Perl and R, for the statistical ANalyses of DEep Sequencing. The fundamental data structure underlying ANDES is the position profile, which contains the nucleotide distributions for each genomic position resultant from a multiple sequence alignment (MSA. Tools include the root mean square deviation (RMSD plot, which allows for the visual comparison of multiple samples on a position-by-position basis, and the computation of base conversion frequencies (transition/transversion rates, variation (Shannon entropy, inter-sample clustering and visualization (dendrogram and multidimensional scaling (MDS plot, threshold-driven consensus sequence generation and polymorphism detection, and the estimation of empirically determined sequencing quality values. Conclusions As new sequencing technologies evolve, deep sequencing will become increasingly cost-efficient and the inter and intra-sample comparisons of largely homogeneous sequences will become more common. We have provided a software package and demonstrated its

  6. Memory for sequences of events impaired in typical aging

    Science.gov (United States)

    Allen, Timothy A.; Morris, Andrea M.; Stark, Shauna M.; Fortin, Norbert J.

    2015-01-01

    Typical aging is associated with diminished episodic memory performance. To improve our understanding of the fundamental mechanisms underlying this age-related memory deficit, we previously developed an integrated, cross-species approach to link converging evidence from human and animal research. This novel approach focuses on the ability to remember sequences of events, an important feature of episodic memory. Unlike existing paradigms, this task is nonspatial, nonverbal, and can be used to isolate different cognitive processes that may be differentially affected in aging. Here, we used this task to make a comprehensive comparison of sequence memory performance between younger (18–22 yr) and older adults (62–86 yr). Specifically, participants viewed repeated sequences of six colored, fractal images and indicated whether each item was presented “in sequence” or “out of sequence.” Several out of sequence probe trials were used to provide a detailed assessment of sequence memory, including: (i) repeating an item from earlier in the sequence (“Repeats”; e.g., ABADEF), (ii) skipping ahead in the sequence (“Skips”; e.g., ABDDEF), and (iii) inserting an item from a different sequence into the same ordinal position (“Ordinal Transfers”; e.g., AB3DEF). We found that older adults performed as well as younger controls when tested on well-known and predictable sequences, but were severely impaired when tested using novel sequences. Importantly, overall sequence memory performance in older adults steadily declined with age, a decline not detected with other measures (RAVLT or BPS-O). We further characterized this deficit by showing that performance of older adults was severely impaired on specific probe trials that required detailed knowledge of the sequence (Skips and Ordinal Transfers), and was associated with a shift in their underlying mnemonic representation of the sequences. Collectively, these findings provide unambiguous evidence that the

  7. NOSEP: Nonoverlapping Sequence Pattern Mining With Gap Constraints.

    Science.gov (United States)

    Wu, Youxi; Tong, Yao; Zhu, Xingquan; Wu, Xindong

    2017-09-28

    Sequence pattern mining aims to discover frequent subsequences as patterns in a single sequence or a sequence database. By combining gap constraints (or flexible wildcards), users can specify special characteristics of the patterns and discover meaningful subsequences suitable for their own application domains, such as finding gene transcription sites from DNA sequences or discovering patterns for time series data classification. Due to the inherent complexity of sequence patterns, including the exponential candidate space with respect to pattern letters and gap constraints, to date, existing sequence pattern mining methods are either incomplete or do not support the Apriori property because the support ratio of a pattern may be greater than that of its subpatterns. Most importantly, patterns discovered by these methods are either too restrictive or too general and cannot represent underlying meaningful knowledge in the sequences. In this paper, we focus on a nonoverlapping sequence pattern (NOSEP) mining task with gap constraints, where an NOSEP allows sequence letters to be flexibly and maximally utilized for pattern discovery. A new Apriori-based NOSEP mining algorithm is proposed. NOSEP is a complete pattern mining algorithm, which uses a specially designed data structure, Nettree, to calculate the exact occurrence of a pattern in the sequence. Experimental results and comparisons on biology DNA sequences, time series data, and Gazelle datasets demonstrate the efficiency of the proposed algorithm and the uniqueness of NOSEPs compared to other methods.

  8. Management of High-Throughput DNA Sequencing Projects: Alpheus.

    Science.gov (United States)

    Miller, Neil A; Kingsmore, Stephen F; Farmer, Andrew; Langley, Raymond J; Mudge, Joann; Crow, John A; Gonzalez, Alvaro J; Schilkey, Faye D; Kim, Ryan J; van Velkinburgh, Jennifer; May, Gregory D; Black, C Forrest; Myers, M Kathy; Utsey, John P; Frost, Nicholas S; Sugarbaker, David J; Bueno, Raphael; Gullans, Stephen R; Baxter, Susan M; Day, Steve W; Retzel, Ernest F

    2008-12-26

    High-throughput DNA sequencing has enabled systems biology to begin to address areas in health, agricultural and basic biological research. Concomitant with the opportunities is an absolute necessity to manage significant volumes of high-dimensional and inter-related data and analysis. Alpheus is an analysis pipeline, database and visualization software for use with massively parallel DNA sequencing technologies that feature multi-gigabase throughput characterized by relatively short reads, such as Illumina-Solexa (sequencing-by-synthesis), Roche-454 (pyrosequencing) and Applied Biosystem's SOLiD (sequencing-by-ligation). Alpheus enables alignment to reference sequence(s), detection of variants and enumeration of sequence abundance, including expression levels in transcriptome sequence. Alpheus is able to detect several types of variants, including non-synonymous and synonymous single nucleotide polymorphisms (SNPs), insertions/deletions (indels), premature stop codons, and splice isoforms. Variant detection is aided by the ability to filter variant calls based on consistency, expected allele frequency, sequence quality, coverage, and variant type in order to minimize false positives while maximizing the identification of true positives. Alpheus also enables comparisons of genes with variants between cases and controls or bulk segregant pools. Sequence-based differential expression comparisons can be developed, with data export to SAS JMP Genomics for statistical analysis.

  9. Quantum-Sequencing: Fast electronic single DNA molecule sequencing

    Science.gov (United States)

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

  10. 10KP: A phylodiverse genome sequencing plan

    Science.gov (United States)

    Cheng, Shifeng; Melkonian, Michael; Brockington, Samuel; Archibald, John M; Delaux, Pierre-Marc; Melkonian, Barbara; Mavrodiev, Evgeny V; Sun, Wenjing; Fu, Yuan; Yang, Huanming; Soltis, Douglas E; Graham, Sean W; Soltis, Pamela S; Liu, Xin; Xu, Xun

    2018-01-01

    Abstract Understanding plant evolution and diversity in a phylogenomic context is an enormous challenge due, in part, to limited availability of genome-scale data across phylodiverse species. The 10KP (10,000 Plants) Genome Sequencing Project will sequence and characterize representative genomes from every major clade of embryophytes, green algae, and protists (excluding fungi) within the next 5 years. By implementing and continuously improving leading-edge sequencing technologies and bioinformatics tools, 10KP will catalogue the genome content of plant and protist diversity and make these data freely available as an enduring foundation for future scientific discoveries and applications. 10KP is structured as an international consortium, open to the global community, including botanical gardens, plant research institutes, universities, and private industry. Our immediate goal is to establish a policy framework for this endeavor, the principles of which are outlined here. PMID:29618049

  11. Protein sequence database for pathogenic arenaviruses

    Science.gov (United States)

    Bui, Huynh-Hoa; Botten, Jason; Fusseder, Nicolas; Pasquetto, Valerie; Mothe, Bianca; Buchmeier, Michael J; Sette, Alessandro

    2007-01-01

    Background Arenaviruses are a family of rodent-borne viruses that cause several hemorrhagic fevers. These diseases can be devastating and are often lethal. Herein, to aid in the design and development of diagnostics, treatments and vaccines for arenavirus infections, we have developed a database containing protein sequences from the seven pathogenic arenaviruses (Junin, Guanarito, Sabia, Machupo, Whitewater Arroyo, Lassa and LCMV). Results The database currently contains a non-redundant set of 333 protein sequences which were manually annotated. All entries were linked to NCBI and cited PubMed references. The database has a convenient query interface including BLAST search. Sequence variability analyses were also performed and the results are hosted in the database. Conclusion The database is available at and can be used to aid in studies that require proteomic information from pathogenic arenaviruses. PMID:17288609

  12. Fetal Kidney Anomalies: Next Generation Sequencing

    DEFF Research Database (Denmark)

    Rasmussen, Maria; Sunde, Lone; Nielsen, Marlene Louise

    Aim and Introduction Identification of abnormal kidneys in the fetus may lead to termination of the pregnancy and raises questions about the underlying cause and recurrence risk in future pregnancies. In this study, we investigate the effectiveness of targeted next generation sequencing in fetuse...... no mutations were identified, have been selected for exome sequencing in order to uncover novel genes associated to fetal kidney anomalies.......Aim and Introduction Identification of abnormal kidneys in the fetus may lead to termination of the pregnancy and raises questions about the underlying cause and recurrence risk in future pregnancies. In this study, we investigate the effectiveness of targeted next generation sequencing in fetuses...... postmortem examination. The approximately 110 genes included in the targeted panel were chosen on the basis of their potential involvement in embryonic kidney development, cystic kidney disease, or the renin-angiotensin system. DNA was extracted from fetal tissue samples or cultured chorion villus cells...

  13. 10KP: A phylodiverse genome sequencing plan.

    Science.gov (United States)

    Cheng, Shifeng; Melkonian, Michael; Smith, Stephen A; Brockington, Samuel; Archibald, John M; Delaux, Pierre-Marc; Li, Fay-Wei; Melkonian, Barbara; Mavrodiev, Evgeny V; Sun, Wenjing; Fu, Yuan; Yang, Huanming; Soltis, Douglas E; Graham, Sean W; Soltis, Pamela S; Liu, Xin; Xu, Xun; Wong, Gane Ka-Shu

    2018-03-01

    Understanding plant evolution and diversity in a phylogenomic context is an enormous challenge due, in part, to limited availability of genome-scale data across phylodiverse species. The 10KP (10,000 Plants) Genome Sequencing Project will sequence and characterize representative genomes from every major clade of embryophytes, green algae, and protists (excluding fungi) within the next 5 years. By implementing and continuously improving leading-edge sequencing technologies and bioinformatics tools, 10KP will catalogue the genome content of plant and protist diversity and make these data freely available as an enduring foundation for future scientific discoveries and applications. 10KP is structured as an international consortium, open to the global community, including botanical gardens, plant research institutes, universities, and private industry. Our immediate goal is to establish a policy framework for this endeavor, the principles of which are outlined here.

  14. Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments

    Directory of Open Access Journals (Sweden)

    Bass Ellen J

    2010-03-01

    model can also be used to generate novel alignments by using the probabilities in lieu of a scoring matrix. These alignments are typically better than the optimal sequence alignment, and include novel correct structural edges. We find that the probA alignments sample a larger variety of alignments than the Zuker set, which more frequently results in alignments that are closer to the structural alignments, but that using the probA alignments as input to the regression model does not increase performance. Conclusions The pool of suboptimal pairwise protein sequence alignments substantially overlaps structure-based alignments for pairs with statistically significant similarity, and a regression model based on information contained in this alignment pool improves the accuracy of pairwise alignments with respect to structure-based alignments.

  15. Static, Lightweight Includes Resolution for PHP

    NARCIS (Netherlands)

    M.A. Hills (Mark); P. Klint (Paul); J.J. Vinju (Jurgen)

    2014-01-01

    htmlabstractDynamic languages include a number of features that are challenging to model properly in static analysis tools. In PHP, one of these features is the include expression, where an arbitrary expression provides the path of the file to include at runtime. In this paper we present two

  16. Article Including Environmental Barrier Coating System

    Science.gov (United States)

    Lee, Kang N. (Inventor)

    2015-01-01

    An enhanced environmental barrier coating for a silicon containing substrate. The enhanced barrier coating may include a bond coat doped with at least one of an alkali metal oxide and an alkali earth metal oxide. The enhanced barrier coating may include a composite mullite bond coat including BSAS and another distinct second phase oxide applied over said surface.

  17. Rare thoracic cancers, including peritoneum mesothelioma

    NARCIS (Netherlands)

    Siesling, Sabine; van der Zwan, Jan Maarten; Izarzugaza, Isabel; Jaal, Jana; Treasure, Tom; Foschi, Roberto; Ricardi, Umberto; Groen, Harry; Tavilla, Andrea; Ardanaz, Eva

    Rare thoracic cancers include those of the trachea, thymus and mesothelioma (including peritoneum mesothelioma). The aim of this study was to describe the incidence, prevalence and survival of rare thoracic tumours using a large database, which includes cancer patients diagnosed from 1978 to 2002,

  18. Rare thoracic cancers, including peritoneum mesothelioma

    NARCIS (Netherlands)

    Siesling, Sabine; Zwan, J.M.V.D.; Izarzugaza, I.; Jaal, J.; Treasure, T.; Foschi, R.; Ricardi, U.; Groen, H.; Tavilla, A.; Ardanaz, E.

    2012-01-01

    Rare thoracic cancers include those of the trachea, thymus and mesothelioma (including peritoneum mesothelioma). The aim of this study was to describe the incidence, prevalence and survival of rare thoracic tumours using a large database, which includes cancer patients diagnosed from 1978 to 2002,

  19. Transcriptome sequencing of the Microarray Quality Control (MAQC RNA reference samples using next generation sequencing

    Directory of Open Access Journals (Sweden)

    Thierry-Mieg Danielle

    2009-06-01

    Full Text Available Abstract Background Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC reference RNA samples using Roche's 454 Genome Sequencer FLX. Results We generated more that 3.6 million sequence reads of average length 250 bp for the MAQC A and B samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values ≤ 10-20. We measured gene expression levels in the A and B samples by counting the numbers of reads that mapped to individual RefSeq genes in multiple sequencing runs to evaluate the MAQC quality metrics for reproducibility, sensitivity, specificity, and accuracy and compared the results with DNA microarrays and Quantitative RT-PCR (QRTPCR from the MAQC studies. In addition, 88% of the reads were successfully aligned directly to the human genome using the AceView alignment programs with an average 90% sequence similarity to identify 137,899 unique exon junctions, including 22,193 new exon junctions not yet contained in the RefSeq database. Conclusion Using the MAQC metrics for evaluating the performance of gene expression platforms, the ExpressSeq results for gene expression levels showed excellent reproducibility, sensitivity, and specificity that improved systematically with increasing shotgun sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRTPCR. In addition, a careful mapping of the reads to the genome using the AceView alignment programs shed new light on the complexity of the human transcriptome including the discovery of thousands of new splice variants.

  20. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  1. Nonlinear analysis of biological sequences

    Energy Technology Data Exchange (ETDEWEB)

    Torney, D.C.; Bruno, W.; Detours, V. [and others

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The main objectives of this project involved deriving new capabilities for analyzing biological sequences. The authors focused on tabulating the statistical properties exhibited by Human coding DNA sequences and on techniques of inferring the phylogenetic relationships among protein sequences related by descent.

  2. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  3. Composite Pressure Vessel Including Crack Arresting Barrier

    Science.gov (United States)

    DeLay, Thomas K. (Inventor)

    2013-01-01

    A pressure vessel includes a ported fitting having an annular flange formed on an end thereof and a tank that envelopes the annular flange. A crack arresting barrier is bonded to and forming a lining of the tank within the outer surface thereof. The crack arresting barrier includes a cured resin having a post-curing ductility rating of at least approximately 60% through the cured resin, and further includes randomly-oriented fibers positioned in and throughout the cured resin.

  4. Sequence Classification: 894222 [

    Lifescience Database Archive (English)

    Full Text Available the holoenzyme also contains CKA1, CKA2 and CKB1, the many substrates include transcription factors and all RNA polymerases; Ckb2p || http://www.ncbi.nlm.nih.gov/protein/6324613 ...

  5. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  6. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  7. Including Organizational Cultural Parameters in Work Processes

    National Research Council Canada - National Science Library

    Handley, Holly A; Heacox, Nancy J

    2004-01-01

    .... In order to represent the organizational impact on the work process, five organizational cultural parameters were identified and included in an algorithm for modeling and simulation of cultural...

  8. Haemophilus influenzae Disease (Including Hib) Symptoms

    Science.gov (United States)

    ... Links Global Hib Vaccination Hib Vaccination Meningitis Pneumonia Sepsis ... Haemophilus influenzae , including H. influenzae type b or Hib, can cause many different kinds of infections . Symptoms depend on ...

  9. Fibre-optic laser-assisted infrared tumour diagnostics (FLAIR)

    International Nuclear Information System (INIS)

    Bindig, U; Mueller, G

    2005-01-01

    Laser based fibre-optic surgery procedures are commonly used in minimal invasive surgery. Despite the development of precise and efficient laser systems there are also innovative attempts in the field of bio-medical diagnostics. As a direct result of the tissue's optical properties most applications are focused on the visible wavelength range of the spectrum. The extension of the spectrum up to the mid-infrared (IR) region will offer a broad range of possibilities for novel strategies with a view to non-invasive diagnostics in medicine. We describe a method to detect differences between diseased and normal tissues, which involve Fourier transform IR microspectroscopy and fibre-optics methods. Regions of interest on 10 μm thin tissue sections were mapped using an IR microscope in transmission mode. After IR-mapping, the samples were analysed using standard pathological techniques. Quadratic discriminant and correlation analyses were applied to the IR maps obtained allowing differentiation between cancerous and normal tissue. The use of optical fibres, transparent in the mid-IR, allowed measurements to be made in the attenuated total reflectance (ATR)-mode at a remote location. The IR sensor is in contact with the sample that shows characteristic absorption lines. The total transmission of the fibre and the sample will decrease at these lines. This method can be used to determine the absorption of a sample in a non-destructive manner. In this paper we report on our efforts to develop an IR fibre-optic sensor for tissue identification as well as to differentiate between malignant and healthy tissue in vivo. We also describe the technical design of the laboratory set-up and the results of developments made. Silver halide fibres and a special sensor tip were used for the ATR measurements on tissue specimens. The results indicate that fibre-optic IR spectrometry will be a useful tool for bio-diagnostics

  10. Fibre-optic laser-assisted infrared tumour diagnostics (FLAIR)

    Science.gov (United States)

    Bindig, U.; Müller, G.

    2005-08-01

    Laser based fibre-optic surgery procedures are commonly used in minimal invasive surgery. Despite the development of precise and efficient laser systems there are also innovative attempts in the field of bio-medical diagnostics. As a direct result of the tissue's optical properties most applications are focused on the visible wavelength range of the spectrum. The extension of the spectrum up to the mid-infrared (IR) region will offer a broad range of possibilities for novel strategies with a view to non-invasive diagnostics in medicine. We describe a method to detect differences between diseased and normal tissues, which involve Fourier transform IR microspectroscopy and fibre-optics methods. Regions of interest on 10 µm thin tissue sections were mapped using an IR microscope in transmission mode. After IR-mapping, the samples were analysed using standard pathological techniques. Quadratic discriminant and correlation analyses were applied to the IR maps obtained allowing differentiation between cancerous and normal tissue. The use of optical fibres, transparent in the mid-IR, allowed measurements to be made in the attenuated total reflectance (ATR)-mode at a remote location. The IR sensor is in contact with the sample that shows characteristic absorption lines. The total transmission of the fibre and the sample will decrease at these lines. This method can be used to determine the absorption of a sample in a non-destructive manner. In this paper we report on our efforts to develop an IR fibre-optic sensor for tissue identification as well as to differentiate between malignant and healthy tissue in vivo. We also describe the technical design of the laboratory set-up and the results of developments made. Silver halide fibres and a special sensor tip were used for the ATR measurements on tissue specimens. The results indicate that fibre-optic IR spectrometry will be a useful tool for bio-diagnostics.

  11. Storytelling for Fluency and Flair: A Performance-Based Approach

    Science.gov (United States)

    Campbell, Terry; Hlusek, Michelle

    2015-01-01

    In the classroom experiences described in this article, grade three students were introduced to storytelling through the interactive read aloud of a mentor text and a storytelling demonstration, followed by daily collaborative activities involving listening, speaking, reading, and writing, culminating in dramatic storytelling performances. The…

  12. Helping Students to Add Detail and Flair to Their Stories

    Science.gov (United States)

    Patel, Pooja; Laud, Leslie

    2009-01-01

    This action research case study measured the effectiveness of a writing strategy designed to enhance imagery in stories that 3 students with severe writing difficulties (2 were identified as learning disabled, 1 was undergoing assessment) produced during their resource room sessions. The authors combined the use of the self-regulated strategy…

  13. Impact of Negative Sequence Current Injection by Wind Power Plants

    DEFF Research Database (Denmark)

    Chaudhary, Sanjay; Göksu, Ömer; Teodorescu, Remus

    2013-01-01

    This paper presents an analysis of the impact from negative sequence current injection by wind power plants in power systems under steady-state and short-term unbalanced conditions, including faults. The separate positive and negative sequence current control capability of the grid-side converters...

  14. Biological sequence analysis: probabilistic models of proteins and nucleic acids

    National Research Council Canada - National Science Library

    Durbin, Richard

    1998-01-01

    ... analysis methods are now based on principles of probabilistic modelling. Examples of such methods include the use of probabilistically derived score matrices to determine the significance of sequence alignments, the use of hidden Markov models as the basis for profile searches to identify distant members of sequence families, and the inference...

  15. The COG database: an updated version includes eukaryotes

    Directory of Open Access Journals (Sweden)

    Sverdlov Alexander V

    2003-09-01

    Full Text Available Abstract Background The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Results We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens, one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe, and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the

  16. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...

  17. Methods and compositions for efficient nucleic acid sequencing

    Science.gov (United States)

    Drmanac, Radoje

    2002-01-01

    Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

  18. Sequencing small RNA: introduction and data analysis fundamentals.

    Science.gov (United States)

    Mehta, Jai Prakash

    2014-01-01

    Small RNAs are important transcriptional regulators within cells. With the advent of powerful Next Generation Sequencing platforms, sequencing small RNAs seems to be an obvious choice to understand their expression and its downstream effect. Additionally, sequencing provides an opportunity to identify novel and polymorphic miRNA. However, the biggest challenge is the appropriate data analysis pipeline, which is still in phase of active development by various academic groups. This chapter describes basic and advanced steps for small RNA sequencing analysis including quality control, small RNA alignment and quantification, differential expression analysis, novel small RNA identification, target prediction, and downstream analysis. We also provide a list of various resources for small RNA analysis.

  19. Design of Mariner 9 Science Sequences using Interactive Graphics Software

    Science.gov (United States)

    Freeman, J. E.; Sturms, F. M, Jr.; Webb, W. A.

    1973-01-01

    This paper discusses the analyst/computer system used to design the daily science sequences required to carry out the desired Mariner 9 science plan. The Mariner 9 computer environment, the development and capabilities of the science sequence design software, and the techniques followed in the daily mission operations are discussed. Included is a discussion of the overall mission operations organization and the individual components which played an essential role in the sequence design process. A summary of actual sequences processed, a discussion of problems encountered, and recommendations for future applications are given.

  20. Sequence and expression analysis of gaps in human chromosome 20

    DEFF Research Database (Denmark)

    Minocherhomji, Sheroy; Seemann, Stefan; Mang, Yuan

    2012-01-01

    /or overlap disease-associated loci, including the DLGAP4 locus. In this study, we sequenced ~99% of all three unfinished gaps on human chr 20, determined their complete genomic sizes and assessed epigenetic profiles using a combination of Sanger sequencing, mate pair paired-end high-throughput sequencing......The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 (chr 20) currently has three unfinished gaps remaining on its q-arm. All three gaps are within gene-dense regions and...

  1. GRAIL and GenQuest Sequence Annotation Tools

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Ying; Shah, Manesh B.; Einstein, J. Ralph; Parang, Morey; Snoddy, Jay; Petrov, Sergey; Olman, Victor; Zhang, Ge; Mural, Richard J.; Uberbacher, Edward C.

    1997-12-31

    Our goal is to develop and implement an integrated intelligent system which can recognize biologically significant features in DNA sequence and provide insight into the organization and function of regions of genomic DNA. GRAIL is a modular expert system which facilitates the recognition of gene features and provides an environment for the construction of sequence annotation. The last several years have seen a rapid evolution of the technology for analyzing genomic DNA sequences. The current GRAIL systems (including the e-mail, XGRAIL, JAVA-GRAIL and genQuest systems) are perhaps the most widely used, comprehensive, and user friendly systems available for computational characterization of genomic DNA sequence.

  2. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

    Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

  3. Generating Exome Enriched Sequencing Libraries from Formalin-Fixed, Paraffin-Embedded Tissue DNA for Next-Generation Sequencing.

    Science.gov (United States)

    Marosy, Beth A; Craig, Brian D; Hetrick, Kurt N; Witmer, P Dane; Ling, Hua; Griffith, Sean M; Myers, Benjamin; Ostrander, Elaine A; Stanford, Janet L; Brody, Lawrence C; Doheny, Kimberly F

    2017-01-11

    This unit describes a technique for generating exome-enriched sequencing libraries using DNA extracted from formalin-fixed paraffin-embedded (FFPE) samples. Utilizing commercially available kits, we present a low-input FFPE workflow starting with 50 ng of DNA. This procedure includes a repair step to address damage caused by FFPE preservation that improves sequence quality. Subsequently, libraries undergo an in-solution-targeted selection for exons, followed by sequencing using the Illumina next-generation short-read sequencing platform. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  4. An Integrated Biochemistry Laboratory, Including Molecular Modeling

    Science.gov (United States)

    Hall, Adele J. Wolfson Mona L.; Branham, Thomas R.

    1996-11-01

    ) experience with methods of protein purification; (iii) incorporation of appropriate controls into experiments; (iv) use of basic statistics in data analysis; (v) writing papers and grant proposals in accepted scientific style; (vi) peer review; (vii) oral presentation of results and proposals; and (viii) introduction to molecular modeling. Figure 1 illustrates the modular nature of the lab curriculum. Elements from each of the exercises can be separated and treated as stand-alone exercises, or combined into short or long projects. We have been able to offer the opportunity to use sophisticated molecular modeling in the final module through funding from an NSF-ILI grant. However, many of the benefits of the research proposal can be achieved with other computer programs, or even by literature survey alone. Figure 1.Design of project-based biochemistry laboratory. Modules (projects, or portions of projects) are indicated as boxes. Each of these can be treated independently, or used as part of a larger project. Solid lines indicate some suggested paths from one module to the next. The skills and knowledge required for protein purification and design are developed in three units: (i) an introduction to critical assays needed to monitor degree of purification, including an evaluation of assay parameters; (ii) partial purification by ion-exchange techniques; and (iii) preparation of a grant proposal on protein design by mutagenesis. Brief descriptions of each of these units follow, with experimental details of each project at the end of this paper. Assays for Lysozyme Activity and Protein Concentration (4 weeks) The assays mastered during the first unit are a necessary tool for determining the purity of the enzyme during the second unit on purification by ion exchange. These assays allow an introduction to the concept of specific activity (units of enzyme activity per milligram of total protein) as a measure of purity. In this first sequence, students learn a turbidimetric assay

  5. Diesel Mechanics: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a diesel mechanics vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  6. Farey sequences and resistor networks

    Indian Academy of Sciences (India)

    c Indian Academy of Sciences. Farey sequences and resistor networks. SAMEEN AHMED KHAN. Department of Engineering, Salalah College of Technology, Post Box No. 608, ..... 2.61n, strictly fixed by the Farey sequence method. For n ≥ 7, all the three basic sets have odd number of elements since A(n) is odd for n ≥ 6.

  7. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  8. DNA Sequencing Sensors: An Overview

    Directory of Open Access Journals (Sweden)

    Jose Antonio Garrido-Cardenas

    2017-03-01

    Full Text Available The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass sequencing sensors, or new generation sequencing (NGS meant a quantitative leap both in the volume of genetic material that was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies, already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each run. All of this would be impossible without sensors and detection systems becoming smaller and more precise. This article provides a comprehensive overview on sensors for DNA sequencing developed within the last 40 years.

  9. Chameleon sequences in neurodegenerative diseases.

    Science.gov (United States)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Combinatorial representations of token sequences

    NARCIS (Netherlands)

    Elzinga, C.H.

    2005-01-01

    This paper presents new representations of token sequences, with and without associated quantities, in Euclidean space. The representations are free of assumptions about the nature of the sequences or the processes that generate them. Algorithms and applications from the domains of structured

  11. A criterion for regular sequences

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Note that every sequence is a strongly regular as well as regular sequence on the zero ... following statement given in Chapter II, 6.1 of [4]. .... for financial support. The authors sincerely thank Harmut Wiebe for stimulating discus- sions. References. [1] Bruns W and Herzog J, Cohen–Macaulay rings (Cambridge Studies in ...

  12. Chameleon sequences in neurodegenerative diseases

    International Nuclear Information System (INIS)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-01-01

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  13. DNA Sequencing by Capillary Electrophoresis

    Science.gov (United States)

    Karger, Barry L.; Guttman, Andras

    2009-01-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

  14. Sequence Classification: 732582 [

    Lifescience Database Archive (English)

    Full Text Available Non-TMB Non-TMH TMB Non-TMB Non-TMB Non-TMB >gi|45443438|ref|NP_994977.1| riboflavin... biosynthesis protein (includes: riboflavin kinase and FMN adenyltransferase) || http://www.ncbi.nlm.nih.gov/protein/45443438 ...

  15. Sequence Classification: 721488 [

    Lifescience Database Archive (English)

    Full Text Available Non-TMB Non-TMH TMB Non-TMB Non-TMB Non-TMB >gi|16120803|ref|NP_404116.1| riboflavin... biosynthesis protein (includes: riboflavin kinase and FMN adenyltransferase) || http://www.ncbi.nlm.nih.gov/protein/16120803 ...

  16. Sequence Classification: 889975 [

    Lifescience Database Archive (English)

    Full Text Available se, controls turnover of a specific class of unstable nuclear proteins including Sir4p but not Sir2p or Sir3p; san1 mutations... suppress sir4, spt16, and cdc68 mutations, suggesting a role in chromatin silencing; San1p || http://www.ncbi.nlm.nih.gov/protein/6320347 ...

  17. Sequence Classification: 889423 [

    Lifescience Database Archive (English)

    Full Text Available ; Ca++ binding protein that regulates Ca++ independent processes (mitosis, bud growth, actin organization, e...ndocytosis, etc.) and Ca++ dependent processes (stress-activated pathways), targets include Nuf1p, Myo2p and calcineurin; Cmd1p || http://www.ncbi.nlm.nih.gov/protein/6319585 ...

  18. The surgery of peripheral nerves (including tumors)

    DEFF Research Database (Denmark)

    Fugleholm, Kåre

    2013-01-01

    Surgical pathology of the peripheral nervous system includes traumatic injury, entrapment syndromes, and tumors. The recent significant advances in the understanding of the pathophysiology and cellular biology of peripheral nerve degeneration and regeneration has yet to be translated into improved...

  19. Including Indigenous Minorities in Decision-Making

    DEFF Research Database (Denmark)

    Pristed Nielsen, Helene

    Based on theories of public sphere participation and deliberative democracy, this book presents empirical results from a study of experiences with including Aboriginal and Maori groups in political decision-making in respectively Western Australia and New Zealand...

  20. Lung Disease Including Asthma and Adult Vaccination

    Science.gov (United States)

    ... Diseases Resources Lung Disease including Asthma and Adult Vaccination Language: English (US) Español (Spanish) Recommend on Facebook ... more about health insurance options. Learn about adult vaccination and other health conditions Asplenia Diabetes Heart Disease, ...

  1. Births and deaths including fetal deaths

    Data.gov (United States)

    U.S. Department of Health & Human Services — Access to a variety of United States birth and death files including fetal deaths: Birth Files, 1968-2009; 1995-2005; Fetal death file, 1982-2005; Mortality files,...

  2. Accident sequence quantification with KIRAP

    International Nuclear Information System (INIS)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong.

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP's cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs

  3. Echinoderm phylogeny including Xyloplax, a progenetic asteroid.

    Science.gov (United States)

    Janies, Daniel A; Voight, Janet R; Daly, Marymegan

    2011-07-01

    Reconstruction of the phylogeny of the five extant classes of the phylum Echinodermata has proven difficult. Results concerning higher-level taxonomic relationships among echinoderms are sensitive to the choice of analytical parameters and methods. Moreover, the proposal of a putative sixth class based on a small enigmatic disc-shaped echinoderm, Xyloplax, from the deep seas of the Bahamas and New Zealand in the 1980s further complicated the problem. Although clearly an echinoderm, Xyloplax did not have clear affinity among known groups. Using molecular sequence and developmental data from recently collected Xyloplax adults and embryos, we show that rather than representing an ancient distinct lineage as implied by its status as a class, Xyloplax is simply a starfish that is closely related to the asteroid family Pterasteridae. Many members of the Pterasteridae and all Xyloplax inhabit deep or polar seas and brood young. Brooding pterasterids and Xyloplax hold their young in specialized adult chambers until the young reach an advanced juvenile stage after which they are released as free-living individuals. We hypothesize that the unique morphology of Xyloplax evolved via progenesis--the truncation of somatic growth at a juvenile body plan but with gonadal growth to maturity. Although the overall phylogeny of extant echinoderms remains sensitive to the choice of analytical methods, the placement of Xyloplax as sister to pterasterid asteroids is unequivocal. Based on this, we argue that the proposed class and infraclass status of Xyloplax should be suppressed. © The Author(s) 2011. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.

  4. Expression and sequence characterization of growth hormone ...

    African Journals Online (AJOL)

    Qadeer

    2012-01-03

    Jan 3, 2012 ... Bhd., Malaysia. DTCS Quick start kit (Beckman Coulter) was used for sequencing of the gene. The vectors used for cloning and expression of BbGHBP include pTZ57R/T (Fermentas Inc. USA) and pET22b(+) (Novagen EMD Biosciences, Germany). E. coli host strains used in this study were DH5α and BL21 ...

  5. Next-Generation Sequencing in Intellectual Disability

    OpenAIRE

    Carvill, Gemma L.; Mefford, Heather C.

    2015-01-01

    Next-generation sequencing technologies have revolutionized gene discovery in patients with intellectual disability (ID) and led to an unprecedented expansion in the number of genes implicated in this disorder. We discuss the strategies that have been used to identify these novel genes for both syndromic and nonsyndromic ID and highlight the phenotypic and genetic heterogeneity that underpin this condition. Finally, we discuss the future of defining the genetic etiology of ID, including the r...

  6. Exploring the correlations between sequence evolution rate and ...

    Indian Academy of Sciences (India)

    2012-10-15

    islands'. We suggest research directions that ... sequence evolution rate and are correlated with each other are important for several reasons. ... 2011). This included the acquisition of many traits used to define the respective orders.

  7. Protein sequences bound to mineral surfaces persist into deep time

    DEFF Research Database (Denmark)

    Demarchi, Beatrice; Hall, Shaun; Roncal-Herrero, Teresa

    2016-01-01

    Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites...

  8. Roche genome sequencer FLX based high-throughput sequencing of ancient DNA

    DEFF Research Database (Denmark)

    Alquezar-Planas, David E; Fordyce, Sarah Louise

    2012-01-01

    Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure tha...

  9. Isolators Including Main Spring Linear Guide Systems

    Science.gov (United States)

    Goold, Ryan (Inventor); Buchele, Paul (Inventor); Hindle, Timothy (Inventor); Ruebsamen, Dale Thomas (Inventor)

    2017-01-01

    Embodiments of isolators, such as three parameter isolators, including a main spring linear guide system are provided. In one embodiment, the isolator includes first and second opposing end portions, a main spring mechanically coupled between the first and second end portions, and a linear guide system extending from the first end portion, across the main spring, and toward the second end portion. The linear guide system expands and contracts in conjunction with deflection of the main spring along the working axis, while restricting displacement and rotation of the main spring along first and second axes orthogonal to the working axis.

  10. Electrochemical cell structure including an ionomeric barrier

    Science.gov (United States)

    Lambert, Timothy N.; Hibbs, Michael

    2017-06-20

    An apparatus includes an electrochemical half-cell comprising: an electrolyte, an anode; and an ionomeric barrier positioned between the electrolyte and the anode. The anode may comprise a multi-electron vanadium phosphorous alloy, such as VP.sub.x, wherein x is 1-5. The electrochemical half-cell is configured to oxidize the vanadium and phosphorous alloy to release electrons. A method of mitigating corrosion in an electrochemical cell includes disposing an ionomeric barrier in a path of electrolyte or ion flow to an anode and mitigating anion accumulation on the surface of the anode.

  11. Electric Power Monthly, August 1990. [Glossary included

    Energy Technology Data Exchange (ETDEWEB)

    1990-11-29

    The Electric Power Monthly (EPM) presents monthly summaries of electric utility statistics at the national, Census division, and State level. The purpose of this publication is to provide energy decisionmakers with accurate and timely information that may be used in forming various perspectives on electric issues that lie ahead. Data includes generation by energy source (coal, oil, gas, hydroelectric, and nuclear); generation by region; consumption of fossil fuels for power generation; sales of electric power, cost data; and unusual occurrences. A glossary is included.

  12. Multiple echo multi-shot diffusion sequence.

    Science.gov (United States)

    Chabert, Steren; Galindo, César; Tejos, Cristian; Uribe, Sergio A

    2014-04-01

    To measure both transversal relaxation time (T2 ) and diffusion coefficients within a single scan using a multi-shot approach. Both measurements have drawn interest in many applications, especially in skeletal muscle studies, which have short T2 values. Multiple echo single-shot schemes have been proposed to obtain those variables simultaneously within a single scan, resulting in a reduction of the scanning time. However, one problem with those approaches is the associated long echo read-out. Consequently, the minimum achievable echo time tends to be long, limiting the application of these sequences to tissues with relatively long T2 . To address this problem, we propose to extend the multi-echo sequences using a multi-shot approach, so that to allow shorter echo times. A multi-shot dual-echo EPI sequence with diffusion gradients and echo navigators was modified to include independent diffusion gradients in any of the two echoes. The multi-shot approach allows us to drastically reduce echo times. Results showed a good agreement for the T2 and mean diffusivity measurements with gold standard sequences in phantoms and in vivo data of calf muscles from healthy volunteers. A fast and accurate method is proposed to measure T2 and diffusion coefficients simultaneously, tested in vitro and in healthy volunteers. Copyright © 2013 Wiley Periodicals, Inc.

  13. Retrosynthetic Reaction Prediction Using Neural Sequence-to-Sequence Models.

    Science.gov (United States)

    Liu, Bowen; Ramsundar, Bharath; Kawthekar, Prasad; Shi, Jade; Gomes, Joseph; Luu Nguyen, Quang; Ho, Stephen; Sloane, Jack; Wender, Paul; Pande, Vijay

    2017-10-25

    We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder-decoder architecture that consists of two recurrent neural networks, which has previously shown great success in solving other sequence-to-sequence prediction tasks such as machine translation. The model is trained on 50,000 experimental reaction examples from the United States patent literature, which span 10 broad reaction types that are commonly used by medicinal chemists. We find that our model performs comparably with a rule-based expert system baseline model, and also overcomes certain limitations associated with rule-based expert systems and with any machine learning approach that contains a rule-based expert system component. Our model provides an important first step toward solving the challenging problem of computational retrosynthetic analysis.

  14. Diversification of Smallholder Tobacco Systems to include ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Tobacco is the mainstay of the economy of Malawi, accounting for over 70% of export earnings. Of the 100 000 members of the National Smallholder Farmers' Association of Malawi (NASFAM), 60% rely on tobacco for their sole source of income. Like their counterparts elsewhere, they face many difficulties, including: ...

  15. BIOLOGIC AND ECONOMIC EFFECTS OF INCLUDING DIFFERENT ...

    African Journals Online (AJOL)

    The biologic and economic effects of including three agro-industrial by-products as ingredients in turkey poult diets were investigated using 48 turkey poults in a completely randomised design experiment. Diets were formulated to contain the three by-products – wheat offal, rice husk and palm kernel meal, each at 20% level ...

  16. Extending flood damage assessment methodology to include ...

    African Journals Online (AJOL)

    Optimal and sustainable flood plain management, including flood control, can only be achieved when the impacts of flood control measures are considered for both the man-made and natural environments, and the sociological aspects are fully considered. Until now, methods/models developed to determine the influences ...

  17. Including Children Dependent on Ventilators in School.

    Science.gov (United States)

    Levine, Jack M.

    1996-01-01

    Guidelines for including ventilator-dependent children in school are offered, based on experience with six such students at a New York State school. Guidelines stress adherence to the medical management plan, the school-family partnership, roles of the social worker and psychologist, orientation, transportation, classroom issues, and steps toward…

  18. Musculoskeletal ultrasound including definitions for ultrasonographic pathology

    DEFF Research Database (Denmark)

    Wakefield, RJ; Balint, PV; Szkudlarek, Marcin

    2005-01-01

    Ultrasound (US) has great potential as an outcome in rheumatoid arthritis trials for detecting bone erosions, synovitis, tendon disease, and enthesopathy. It has a number of distinct advantages over magnetic resonance imaging, including good patient tolerability and ability to scan multiple joint...

  19. Modernizing Agrifood Markets : Including Small Producers in ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Against this baseline data, they will endeavor to identify success stories or examples of interventions that ensure small farmers' access to modernizing agrifood markets. The research will inform a set of policy recommendations to be promoted through policy platforms in a large number of developing countries, including but ...

  20. Including Students with Visual Impairments: Softball

    Science.gov (United States)

    Brian, Ali; Haegele, Justin A.

    2014-01-01

    Research has shown that while students with visual impairments are likely to be included in general physical education programs, they may not be as active as their typically developing peers. This article provides ideas for equipment modifications and game-like progressions for one popular physical education unit, softball. The purpose of these…

  1. Numerical simulation of spark ignition including ionization

    NARCIS (Netherlands)

    Thiele, M; Selle, S; Riedel, U; Warnatz, J; Maas, U

    2000-01-01

    A detailed understanding of the processes associated Midi spark ignition, as a first step during combustion, is of great importance fur clean operation of spark ignition engines. In the past 10 years. a growing concern for environmental protection, including low emission of pollutants, has increased

  2. Sequencing genes in silico using single nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Zhang Xinyi

    2012-01-01

    Full Text Available Abstract Background The advent of high throughput sequencing technology has enabled the 1000 Genomes Project Pilot 3 to generate complete sequence data for more than 906 genes and 8,140 exons representing 697 subjects. The 1000 Genomes database provides a critical opportunity for further interpreting disease associations with single nucleotide polymorphisms (SNPs discovered from genetic association studies. Currently, direct sequencing of candidate genes or regions on a large number of subjects remains both cost- and time-prohibitive. Results To accelerate the translation from discovery to functional studies, we propose an in silico gene sequencing method (ISS, which predicts phased sequences of intragenic regions, using SNPs. The key underlying idea of our method is to infer diploid sequences (a pair of phased sequences/alleles at every functional locus utilizing the deep sequencing data from the 1000 Genomes Project and SNP data from the HapMap Project, and to build prediction models using flanking SNPs. Using this method, we have developed a database of prediction models for 611 known genes. Sequence prediction accuracy for these genes is 96.26% on average (ranges 79%-100%. This database of prediction models can be enhanced and scaled up to include new genes as the 1000 Genomes Project sequences additional genes on additional individuals. Applying our predictive model for the KCNJ11 gene to the Wellcome Trust Case Control Consortium (WTCCC Type 2 diabetes cohort, we demonstrate how the prediction of phased sequences inferred from GWAS SNP genotype data can be used to facilitate interpretation and identify a probable functional mechanism such as protein changes. Conclusions Prior to the general availability of routine sequencing of all subjects, the ISS method proposed here provides a time- and cost-effective approach to broadening the characterization of disease associated SNPs and regions, and facilitating the prioritization of candidate

  3. Sequencing of the Hepatitis C Virus: A Systematic Review.

    Directory of Open Access Journals (Sweden)

    Brendan Jacka

    Full Text Available Since the identification of hepatitis C virus (HCV, viral sequencing has been important in understanding HCV classification, epidemiology, evolution, transmission clustering, treatment response and natural history. The length and diversity of the HCV genome has resulted in analysis of certain regions of the virus, however there has been little standardisation of protocols. This systematic review was undertaken to map the location and frequency of sequencing on the HCV genome in peer reviewed publications, with the aim to produce a database of sequencing primers and amplicons to inform future research. Medline and Scopus databases were searched for English language publications based on keyword/MeSH terms related to sequence analysis (9 terms or HCV (3 terms, plus "primer" as a general search term. Exclusion criteria included non-HCV research, review articles, duplicate records, and incomplete description of HCV sequencing methods. The PCR primer locations of accepted publications were noted, and purpose of sequencing was determined. A total of 450 studies were accepted from the 2099 identified, with 629 HCV sequencing amplicons identified and mapped on the HCV genome. The most commonly sequenced region was the HVR-1 region, often utilised for studies of natural history, clustering/transmission, evolution and treatment response. Studies related to genotyping/classification or epidemiology of HCV genotype generally targeted the 5'UTR, Core and NS5B regions, while treatment response/resistance was assessed mainly in the NS3-NS5B region with emphasis on the Interferon sensitivity determining region (ISDR region of NS5A. While the sequencing of HCV is generally constricted to certain regions of the HCV genome there is little consistency in the positioning of sequencing primers, with the exception of a few highly referenced manuscripts. This study demonstrates the heterogeneity of HCV sequencing, providing a comprehensive database of previously

  4. Identification of trains of sleep sequences in adult rats.

    Science.gov (United States)

    Piscopo, S; Mandile, P; Montagnese, P; Cotugno, M; Giuditta, A; Vescia, S

    2001-02-15

    In previous studies based on high resolution EEG analyses of the 7 h baseline session of 18 adult male Wistar rats [6,14], we have identified four sleep sequences initiating with slow wave sleep (SS) and terminating with waking (W) or paradoxical sleep (PS). Two of these sequences contained an intervening episode of transition sleep (TS). Several variables of these sequences (SS-->W, SS-->TS-->W, SS-->TS-->PS, and SS-->PS) were selectively correlated with the capacity of rats to learn a two-way active avoidance task the following day, and were differently distributed in fast learning, slow learning and non learning rats [21]. The temporal organization of different sleep components in sequences suggested that a comparable temporal organization might concern the different sleep sequences, albeit on a longer time scale. We have now used waking periods longer than 60 s to separate clusters of baseline sleep sequences (trains) in the same rats. Trains containing the same sleep sequence (homogeneous trains) have been distinguished from trains containing different sleep sequences (mixed trains). In addition, mixed trains including the SS-->TS-->W sequence (+TSW trains) have been separated from mixed trains lacking that sequence (-TSW trains). Mixed trains of the +TSW type were longest and most numerous, while homogeneous trains were shortest and least abundant. Mixed trains of the -TSW type displayed intermediate values. Several variables of sleep sequences and sleep components differed within mixed trains and among mixed and homogeneous trains. The data indicate that baseline sleep sequences aggregate in relatively long strings in a non random fashion. The mechanism of this association is discussed.

  5. High-throughput sequence alignment using Graphics Processing Units

    Directory of Open Access Journals (Sweden)

    Trapnell Cole

    2007-12-01

    Full Text Available Abstract Background The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. Results This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Conclusion MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU.

  6. The Release 6 reference sequence of the Drosophila melanogaster genome.

    Science.gov (United States)

    Hoskins, Roger A; Carlson, Joseph W; Wan, Kenneth H; Park, Soo; Mendez, Ivonne; Galle, Samuel E; Booth, Benjamin W; Pfeiffer, Barret D; George, Reed A; Svirskas, Robert; Krzywinski, Martin; Schein, Jacqueline; Accardo, Maria Carmela; Damia, Elisabetta; Messina, Giovanni; Méndez-Lago, María; de Pablos, Beatriz; Demakova, Olga V; Andreyeva, Evgeniya N; Boldyreva, Lidiya V; Marra, Marco; Carvalho, A Bernardo; Dimitri, Patrizio; Villasante, Alfredo; Zhimulev, Igor F; Rubin, Gerald M; Karpen, Gary H; Celniker, Susan E

    2015-03-01

    Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads. © 2015 Hoskins et al.; Published by Cold Spring Harbor Laboratory Press.

  7. mufasa: the assembly of the red sequence

    Science.gov (United States)

    Davé, Romeel; Rafieferantsoa, Mika H.; Thompson, Robert J.

    2017-10-01

    We examine the growth and evolution of quenched galaxies in the mufasa cosmological hydrodynamic simulations that include an evolving halo mass-based quenching prescription, with galaxy colours computed accounting for line-of-sight extinction to individual star particles. mufasa reproduces the observed present-day red sequence reasonably well, including its slope, amplitude and scatter. In mufasa, the red sequence slope is driven entirely by the steep stellar mass-stellar metallicity relation, which independently agrees with observations. High-mass star-forming galaxies blend smoothly on to the red sequence, indicating the lack of a well-defined green valley at M* ≳ 1010.5 M⊙. The most massive galaxies quench the earliest and then grow very little in mass via dry merging; they attain their high masses at earlier epochs when cold inflows more effectively penetrate hot haloes. To higher redshifts, the red sequence becomes increasingly contaminated with massive dusty star-forming (SF) galaxies; UVJ selection subtly but effectively separates these populations. We then examine the evolution of the mass functions of central and satellite galaxies split into passive and star-forming via UVJ. Massive quenched systems show good agreement with observations out to z ∼ 2, despite not including a rapid early quenching mode associated with mergers. However, low-mass quenched galaxies are far too numerous at z ≲ 1 in mufasa, indicating that mufasa strongly overquenches satellites. A challenge for hydrodynamic simulations is to devise a quenching model that produces enough early massive quenched galaxies and keeps them quenched to z = 0, while not being so strong as to overquench satellites; mufasa's current scheme fails at the latter.

  8. Duplication in DNA Sequences

    Science.gov (United States)

    Ito, Masami; Kari, Lila; Kincaid, Zachary; Seki, Shinnosuke

    The duplication and repeat-deletion operations are the basis of a formal language theoretic model of errors that can occur during DNA replication. During DNA replication, subsequences of a strand of DNA may be copied several times (resulting in duplications) or skipped (resulting in repeat-deletions). As formal language operations, iterated duplication and repeat-deletion of words and languages have been well studied in the literature. However, little is known about single-step duplications and repeat-deletions. In this paper, we investigate several properties of these operations, including closure properties of language families in the Chomsky hierarchy and equations involving these operations. We also make progress toward a characterization of regular languages that are generated by duplicating a regular language.

  9. Photoactive devices including porphyrinoids with coordinating additives

    Science.gov (United States)

    Forrest, Stephen R; Zimmerman, Jeramy; Yu, Eric K; Thompson, Mark E; Trinh, Cong; Whited, Matthew; Diev, Vlacheslav

    2015-05-12

    Coordinating additives are included in porphyrinoid-based materials to promote intermolecular organization and improve one or more photoelectric characteristics of the materials. The coordinating additives are selected from fullerene compounds and organic compounds having free electron pairs. Combinations of different coordinating additives can be used to tailor the characteristic properties of such porphyrinoid-based materials, including porphyrin oligomers. Bidentate ligands are one type of coordinating additive that can form coordination bonds with a central metal ion of two different porphyrinoid compounds to promote porphyrinoid alignment and/or pi-stacking. The coordinating additives can shift the absorption spectrum of a photoactive material toward higher wavelengths, increase the external quantum efficiency of the material, or both.

  10. Electric power monthly, September 1990. [Glossary included

    Energy Technology Data Exchange (ETDEWEB)

    1990-12-17

    The purpose of this report is to provide energy decision makers with accurate and timely information that may be used in forming various perspectives on electric issues. The power plants considered include coal, petroleum, natural gas, hydroelectric, and nuclear power plants. Data are presented for power generation, fuel consumption, fuel receipts and cost, sales of electricity, and unusual occurrences at power plants. Data are compared at the national, Census division, and state levels. 4 figs., 52 tabs. (CK)

  11. Power generation method including membrane separation

    Science.gov (United States)

    Lokhandwala, Kaaeid A.

    2000-01-01

    A method for generating electric power, such as at, or close to, natural gas fields. The method includes conditioning natural gas containing C.sub.3+ hydrocarbons and/or acid gas by means of a membrane separation step. This step creates a leaner, sweeter, drier gas, which is then used as combustion fuel to run a turbine, which is in turn used for power generation.

  12. Should Trade Agreements Include Environmental Policy?

    OpenAIRE

    Josh Ederington

    2010-01-01

    This article examines the extent to which environmental and trade policies should be treated equally, or symmetrically, in international negotiations. It reviews the recent economics literature on trade and the environment to address two questions. First, should trade negotiations include negotiations over environmental policies and the setting of binding environmental standards? Second, if there are grounds for international environmental negotiations, should environmental agreements b...

  13. Jet-calculus approach including coherence effects

    International Nuclear Information System (INIS)

    Jones, L.M.; Migneron, R.; Narayanan, K.S.S.

    1987-01-01

    We show how integrodifferential equations typical of jet calculus can be combined with an averaging procedure to obtain jet-calculus-based results including the Mueller interference graphs. Results in longitudinal-momentum fraction x for physical quantities are higher at intermediate x and lower at large x than with the conventional ''incoherent'' jet calculus. These results resemble those of Marchesini and Webber, who used a Monte Carlo approach based on the same dynamics

  14. Revisiting Hansen Solubility Parameters by Including Thermodynamics.

    Science.gov (United States)

    Louwerse, Manuel J; Maldonado, Ana; Rousseau, Simon; Moreau-Masselon, Chloe; Roux, Bernard; Rothenberg, Gadi

    2017-11-03

    The Hansen solubility parameter approach is revisited by implementing the thermodynamics of dissolution and mixing. Hansen's pragmatic approach has earned its spurs in predicting solvents for polymer solutions, but for molecular solutes improvements are needed. By going into the details of entropy and enthalpy, several corrections are suggested that make the methodology thermodynamically sound without losing its ease of use. The most important corrections include accounting for the solvent molecules' size, the destruction of the solid's crystal structure, and the specificity of hydrogen-bonding interactions, as well as opportunities to predict the solubility at extrapolated temperatures. Testing the original and the improved methods on a large industrial dataset including solvent blends, fit qualities improved from 0.89 to 0.97 and the percentage of correct predictions rose from 54 % to 78 %. Full Matlab scripts are included in the Supporting Information, allowing readers to implement these improvements on their own datasets. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS

    Directory of Open Access Journals (Sweden)

    Alves-Ferreira Marcelo

    2008-09-01

    Full Text Available Abstract Background Genome survey sequences (GSS offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive regions of the genome. A more precise estimation of the nature, quantity and variability of repetitive sequences very early in a genome sequencing project is of considerable importance, as such data strongly influence the estimation of genome coverage, library quality and progress in scaffold construction. Also, the elimination of repetitive sequences from the initial assembly process is important to avoid errors and unnecessary complexity. Repetitive sequences are also of interest in a variety of other studies, for instance as molecular markers. Results We designed and implemented a straightforward pipeline called ReRep, which combines bioinformatics tools for identifying repetitive structures in a GSS dataset. In a case study, we first applied the pipeline to a set of 970 GSSs, sequenced in our laboratory from the human pathogen Leishmania braziliensis, the causative agent of leishmaniosis, an important public health problem in Brazil. We also verified the applicability of ReRep to new sequencing technologies using a set of 454-reads of an Escheria coli. The behaviour of several parameters in the algorithm is evaluated and suggestions are made for tuning of the analysis. Conclusion The ReRep approach for identification of repetitive elements in GSS datasets proved to be straightforward and efficient. Several potential repetitive sequences were found in a L. braziliensis GSS dataset generated in our laboratory, and further validated by the analysis of a more complete genomic dataset from the EMBL and Sanger Centre databases. ReRep also identified most of the E. coli K12 repeats prior to assembly in an example dataset obtained by automated sequencing using 454 technology. The parameters controlling the algorithm behaved consistently and may be tuned to the properties

  16. De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies

    DEFF Research Database (Denmark)

    2014-01-01

    analyzed exome-sequencing data of 356 trios with the "classical" epileptic encephalopathies, infantile spasms and Lennox Gastaut syndrome, including 264 trios previously analyzed by the Epi4K/EPGP consortium. In this expanded cohort, we find 429 de novo mutations, including de novo mutations in DNM1...

  17. The Dynamics of DNA Sequencing.

    Science.gov (United States)

    Morvillo, Nancy

    1997-01-01

    Describes a paper-and-pencil activity that helps students understand DNA sequencing and expands student understanding of DNA structure, replication, and gel electrophoresis. Appropriate for advanced biology students who are familiar with the Sanger method. (DDR)

  18. Fractal nature of stratigraphic sequences

    NARCIS (Netherlands)

    Schlager, W.

    2004-01-01

    Orders of stratigraphic sequences are being used loosely and with widely varying definitions. The orders seem to be subdivisions of convenience rather than an indication of natural structure. It is proposed that, at least at time scales of 10

  19. Sequence analysis of Leukemia DNA

    Science.gov (United States)

    Nacong, Nasria; Lusiyanti, Desy; Irawan, Muhammad. Isa

    2018-03-01

    Cancer is a very deadly disease, one of which is leukemia disease or better known as blood cancer. The cancer cell can be detected by taking DNA in laboratory test. This study focused on local alignment of leukemia and non leukemia data resulting from NCBI in the form of DNA sequences by using Smith-Waterman algorithm. SmithWaterman algorithm was invented by TF Smith and MS Waterman in 1981. These algorithms try to find as much as possible similarity of a pair of sequences, by giving a negative value to the unequal base pair (mismatch), and positive values on the same base pair (match). So that will obtain the maximum positive value as the end of the alignment, and the minimum value as the initial alignment. This study will use sequences of leukemia and 3 sequences of non leukemia.

  20. Characterization of simple sequence repeats (SSRs from Phlebotomus papatasi (Diptera: Psychodidae expressed sequence tags (ESTs

    Directory of Open Access Journals (Sweden)

    Hamarsheh Omar

    2011-09-01

    Full Text Available Abstract Background Phlebotomus papatasi is a natural vector of Leishmania major, which causes cutaneous leishmaniasis in many countries. Simple sequence repeats (SSRs, or microsatellites, are common in eukaryotic genomes and are short, repeated nucleotide sequence elements arrayed in tandem and flanked by non-repetitive regions. The enrichment methods used previously for finding new microsatellite loci in sand flies remain laborious and time consuming; in silico mining, which includes retrieval and screening of microsatellites from large amounts of sequence data from sequence data bases using microsatellite search tools can yield many new candidate markers. Results Simple sequence repeats (SSRs were characterized in P. papatasi expressed sequence tags (ESTs derived from a public database, National Center for Biotechnology Information (NCBI. A total of 42,784 sequences were mined, and 1,499 SSRs were identified with a frequency of 3.5% and an average density of 15.55 kb per SSR. Dinucleotide motifs were the most common SSRs, accounting for 67% followed by tri-, tetra-, and penta-nucleotide repeats, accounting for 31.1%, 1.5%, and 0.1%, respectively. The length of microsatellites varied from 5 to 16 repeats. Dinucleotide types; AG and CT have the highest frequency. Dinucleotide SSR-ESTs are relatively biased toward an excess of (AXn repeats and a low GC base content. Forty primer pairs were designed based on motif lengths for further experimental validation. Conclusion The first large-scale survey of SSRs derived from P. papatasi is presented; dinucleotide SSRs identified are more frequent than other types. EST data mining is an effective strategy to identify functional microsatellites in P. papatasi.

  1. From sequencer to supercomputer: an automatic pipeline for managing and processing next generation sequencing data.

    Science.gov (United States)

    Camerlengo, Terry; Ozer, Hatice Gulcin; Onti-Srinivasan, Raghuram; Yan, Pearlly; Huang, Tim; Parvin, Jeffrey; Huang, Kun

    2012-01-01

    Next Generation Sequencing is highly resource intensive. NGS Tasks related to data processing, management and analysis require high-end computing servers or even clusters. Additionally, processing NGS experiments requires suitable storage space and significant manual interaction. At The Ohio State University's Biomedical Informatics Shared Resource, we designed and implemented a scalable architecture to address the challenges associated with the resource intensive nature of NGS secondary analysis built around Illumina Genome Analyzer II sequencers and Illumina's Gerald data processing pipeline. The software infrastructure includes a distributed computing platform consisting of a LIMS called QUEST (http://bisr.osumc.edu), an Automation Server, a computer cluster for processing NGS pipelines, and a network attached storage device expandable up to 40TB. The system has been architected to scale to multiple sequencers without requiring additional computing or labor resources. This platform provides demonstrates how to manage and automate NGS experiments in an institutional or core facility setting.

  2. Graphene Nanopores for Protein Sequencing

    Science.gov (United States)

    Wilson, James; Sloman, Leila; He, Zhiren

    2016-01-01

    An inexpensive, reliable method for protein sequencing is essential to unraveling the biological mechanisms governing cellular behavior and disease. Current protein sequencing methods suffer from limitations associated with the size of proteins that can be sequenced, the time, and the cost of the sequencing procedures. Here, we report the results of all-atom molecular dynamics simulations that investigated the feasibility of using graphene nanopores for protein sequencing. We focus our study on the biologically significant phenylalanine-glycine repeat peptides (FG-nups)—parts of the nuclear pore transport machinery. Surprisingly, we found FG-nups to behave similarly to single stranded DNA: the peptides adhere to graphene and exhibit step-wise translocation when subject to a transmembrane bias or a hydrostatic pressure gradient. Reducing the peptide’s charge density or increasing the peptide’s hydrophobicity was found to decrease the translocation speed. Yet, unidirectional and stepwise translocation driven by a transmembrane bias was observed even when the ratio of charged to hydrophobic amino acids was as low as 1:8. The nanopore transport of the peptides was found to produce stepwise modulations of the nanopore ionic current correlated with the type of amino acids present in the nanopore, suggesting that protein sequencing by measuring ionic current blockades may be possible. PMID:27746710

  3. Drug delivery device including electrolytic pump

    KAUST Repository

    Foulds, Ian G.

    2016-03-31

    Systems and methods are provided for a drug delivery device and use of the device for drug delivery. In various aspects, the drug delivery device combines a “solid drug in reservoir” (SDR) system with an electrolytic pump. In various aspects an improved electrolytic pump is provided including, in particular, an improved electrolytic pump for use with a drug delivery device, for example an implantable drug delivery device. A catalytic reformer can be incorporated in a periodically pulsed electrolytic pump to provide stable pumping performance and reduced actuation cycle.

  4. Stress triggering and the Canterbury earthquake sequence

    Science.gov (United States)

    Steacy, Sandy; Jiménez, Abigail; Holden, Caroline

    2014-01-01

    The Canterbury earthquake sequence, which includes the devastating Christchurch event of 2011 February, has to date led to losses of around 40 billion NZ dollars. The location and severity of the earthquakes was a surprise to most inhabitants as the seismic hazard model was dominated by an expected Mw > 8 earthquake on the Alpine fault and an Mw 7.5 earthquake on the Porters Pass fault, 150 and 80 km to the west of Christchurch. The sequence to date has included an Mw = 7.1 earthquake and 3 Mw ≥ 5.9 events which migrated from west to east. Here we investigate whether the later events are consistent with stress triggering and whether a simple stress map produced shortly after the first earthquake would have accurately indicated the regions where the subsequent activity occurred. We find that 100 per cent of M > 5.5 earthquakes occurred in positive stress areas computed using a slip model for the first event that was available within 10 d of its occurrence. We further find that the stress changes at the starting points of major slip patches of post-Darfield main events are consistent with triggering although this is not always true at the hypocentral locations. Our results suggest that Coulomb stress changes contributed to the evolution of the Canterbury sequence and we note additional areas of increased stress in the Christchurch region and on the Porters Pass fault.

  5. Genome sequence and analysis of Lactobacillus helveticus

    Directory of Open Access Journals (Sweden)

    Paola eCremonesi

    2013-01-01

    Full Text Available The microbiological characterization of lactobacilli is historically well developed, but the genomic analysis is recent. Because of the widespread use of L. helveticus in cheese technology, information concerning the heterogeneity in this species is accumulating rapidly. Recently, the genome of five L. helveticus strains was sequenced to completion and compared with other genomically characterized lactobacilli. The genomic analysis of the first sequenced strain, L. helveticus DPC 4571, isolated from cheese and selected for its characteristics of rapid lysis and high proteolytic activity, has revealed a plethora of genes with industrial potential including those responsible for key metabolic functions such as proteolysis, lipolysis, and cell lysis. These genes and their derived enzymes can facilitate the production of cheese and cheese derivatives with potential for use as ingredients in consumer foods. In addition, L. helveticus has the potential to produce peptides with a biological function, such as angiotensin converting enzyme (ACE inhibitory activity, in fermented dairy products, demonstrating the therapeutic value of this species. A most intriguing feature of the genome of L. helveticus is the remarkable similarity in gene content with many intestinal lactobacilli. Comparative genomics has allowed the identification of key gene sets that facilitate a variety of lifestyles including adaptation to food matrices or the gastrointestinal tract.As genome sequence and functional genomic information continues to explode, key features of the genomes of L. helveticus strains continue to be discovered, answering many questions but also raising many new ones.

  6. Method for priming and DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Mugasimangalam, R.C.; Ulanovsky, L.E.

    1997-12-01

    A method is presented for improving the priming specificity of an oligonucleotide primer that is non-unique in a nucleic acid template which includes selecting a continuous stretch of several nucleotides in the template DNA where one of the four bases does not occur in the stretch. This also includes bringing the template DNA in contract with a non-unique primer partially or fully complimentary to the sequence immediately upstream of the selected sequence stretch. This results in polymerase-mediated differential extension of the primer in the presence of a subset of deoxyribonucleotide triphosphates that does not contain the base complementary to the base absent in the selected sequence stretch. These reactions occur at a temperature sufficiently low for allowing the extension of the non-unique primer. The method causes polymerase-mediated extension reactions in the presence of all four natural deoxyribonucleotide triphosphates or modifications. At this high temperature discrimination occurs against priming sites of the non-unique primer where the differential extension has not made the primer sufficiently stable to prime. However, the primer extended at the selected stretch is sufficiently stable to prime.

  7. Aerosol simulation including chemical and nuclear reactions

    International Nuclear Information System (INIS)

    Marwil, E.S.; Lemmon, E.C.

    1985-01-01

    The numerical simulation of aerosol transport, including the effects of chemical and nuclear reactions presents a challenging dynamic accounting problem. Particles of different sizes agglomerate and settle out due to various mechanisms, such as diffusion, diffusiophoresis, thermophoresis, gravitational settling, turbulent acceleration, and centrifugal acceleration. Particles also change size, due to the condensation and evaporation of materials on the particle. Heterogeneous chemical reactions occur at the interface between a particle and the suspending medium, or a surface and the gas in the aerosol. Homogeneous chemical reactions occur within the aersol suspending medium, within a particle, and on a surface. These reactions may include a phase change. Nuclear reactions occur in all locations. These spontaneous transmutations from one element form to another occur at greatly varying rates and may result in phase or chemical changes which complicate the accounting process. This paper presents an approach for inclusion of these effects on the transport of aerosols. The accounting system is very complex and results in a large set of stiff ordinary differential equations (ODEs). The techniques for numerical solution of these ODEs require special attention to achieve their solution in an efficient and affordable manner. 4 refs

  8. Long-range barcode labeling-sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Feng; Zhang, Tao; Singh, Kanwar K.; Pennacchio, Len A.; Froula, Jeff L.; Eng, Kevin S.

    2016-10-18

    Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

  9. Including gauge corrections to thermal leptogenesis

    International Nuclear Information System (INIS)

    Huetig, Janine

    2013-01-01

    This thesis provides the first approach of a systematic inclusion of gauge corrections to leading order to the ansatz of thermal leptogenesis. We have derived a complete expression for the integrated lepton number matrix including all resummations needed. For this purpose, a new class of diagram has been invented, namely the cylindrical diagram, which allows diverse investigations into the topic of leptogenesis such as the case of resonant leptogenesis. After a brief introduction of the topic of the baryon asymmetry in the universe and a discussion of its most promising solutions as well as their advantages and disadvantages, we have presented our framework of thermal leptogenesis. An effective model was described as well as the associated Feynman rules. The basis for using nonequilibrium quantum field theory has been built in chapter 3. At first, the main definitions have been presented for equilibrium thermal field theory, afterwards we have discussed the Kadanoff-Baym equations for systems out of equilibrium using the example of the Majorana neutrino. The equations have also been solved in the context of leptogenesis in chapter 4. Since gauge corrections play a crucial role throughout this thesis, we have also repeated the naive ansatz by replacing the free equilibrium propagator by propagators including thermal damping rates due to the Standard Model damping widths for lepton and Higgs fields. It is shown that this leads to a comparable result to the solutions of the Boltzmann equations for thermal leptogenesis. Thus it becomes obvious that Standard Model corrections are not negligible for thermal leptogenesis and therefore need to be included systematically from first principles. In order to achieve this we have started discussing the calculation of ladder rung diagrams for Majorana neutrinos using the HTL and the CTL approach in chapter 5. All gauge corrections are included in this framework and thus it has become the basis for the following considerations

  10. Initial sequencing and comparative analysis of the mouse genome.

    Science.gov (United States)

    Waterston, Robert H; Lindblad-Toh, Kerstin; Birney, Ewan; Rogers, Jane; Abril, Josep F; Agarwal, Pankaj; Agarwala, Richa; Ainscough, Rachel; Alexandersson, Marina; An, Peter; Antonarakis, Stylianos E; Attwood, John; Baertsch, Robert; Bailey, Jonathon; Barlow, Karen; Beck, Stephan; Berry, Eric; Birren, Bruce; Bloom, Toby; Bork, Peer; Botcherby, Marc; Bray, Nicolas; Brent, Michael R; Brown, Daniel G; Brown, Stephen D; Bult, Carol; Burton, John; Butler, Jonathan; Campbell, Robert D; Carninci, Piero; Cawley, Simon; Chiaromonte, Francesca; Chinwalla, Asif T; Church, Deanna M; Clamp, Michele; Clee, Christopher; Collins, Francis S; Cook, Lisa L; Copley, Richard R; Coulson, Alan; Couronne, Olivier; Cuff, James; Curwen, Val; Cutts, Tim; Daly, Mark; David, Robert; Davies, Joy; Delehaunty, Kimberly D; Deri, Justin; Dermitzakis, Emmanouil T; Dewey, Colin; Dickens, Nicholas J; Diekhans, Mark; Dodge, Sheila; Dubchak, Inna; Dunn, Diane M; Eddy, Sean R; Elnitski, Laura; Emes, Richard D; Eswara, Pallavi; Eyras, Eduardo; Felsenfeld, Adam; Fewell, Ginger A; Flicek, Paul; Foley, Karen; Frankel, Wayne N; Fulton, Lucinda A; Fulton, Robert S; Furey, Terrence S; Gage, Diane; Gibbs, Richard A; Glusman, Gustavo; Gnerre, Sante; Goldman, Nick; Goodstadt, Leo; Grafham, Darren; Graves, Tina A; Green, Eric D; Gregory, Simon; Guigó, Roderic; Guyer, Mark; Hardison, Ross C; Haussler, David; Hayashizaki, Yoshihide; Hillier, LaDeana W; Hinrichs, Angela; Hlavina, Wratko; Holzer, Timothy; Hsu, Fan; Hua, Axin; Hubbard, Tim; Hunt, Adrienne; Jackson, Ian; Jaffe, David B; Johnson, L Steven; Jones, Matthew; Jones, Thomas A; Joy, Ann; Kamal, Michael; Karlsson, Elinor K; Karolchik, Donna; Kasprzyk, Arkadiusz; Kawai, Jun; Keibler, Evan; Kells, Cristyn; Kent, W James; Kirby, Andrew; Kolbe, Diana L; Korf, Ian; Kucherlapati, Raju S; Kulbokas, Edward J; Kulp, David; Landers, Tom; Leger, J P; Leonard, Steven; Letunic, Ivica; Levine, Rosie; Li, Jia; Li, Ming; Lloyd, Christine; Lucas, Susan; Ma, Bin; Maglott, Donna R; Mardis, Elaine R; Matthews, Lucy; Mauceli, Evan; Mayer, John H; McCarthy, Megan; McCombie, W Richard; McLaren, Stuart; McLay, Kirsten; McPherson, John D; Meldrim, Jim; Meredith, Beverley; Mesirov, Jill P; Miller, Webb; Miner, Tracie L; Mongin, Emmanuel; Montgomery, Kate T; Morgan, Michael; Mott, Richard; Mullikin, James C; Muzny, Donna M; Nash, William E; Nelson, Joanne O; Nhan, Michael N; Nicol, Robert; Ning, Zemin; Nusbaum, Chad; O'Connor, Michael J; Okazaki, Yasushi; Oliver, Karen; Overton-Larty, Emma; Pachter, Lior; Parra, Genís; Pepin, Kymberlie H; Peterson, Jane; Pevzner, Pavel; Plumb, Robert; Pohl, Craig S; Poliakov, Alex; Ponce, Tracy C; Ponting, Chris P; Potter, Simon; Quail, Michael; Reymond, Alexandre; Roe, Bruce A; Roskin, Krishna M; Rubin, Edward M; Rust, Alistair G; Santos, Ralph; Sapojnikov, Victor; Schultz, Brian; Schultz, Jörg; Schwartz, Matthias S; Schwartz, Scott; Scott, Carol; Seaman, Steven; Searle, Steve; Sharpe, Ted; Sheridan, Andrew; Shownkeen, Ratna; Sims, Sarah; Singer, Jonathan B; Slater, Guy; Smit, Arian; Smith, Douglas R; Spencer, Brian; Stabenau, Arne; Stange-Thomann, Nicole; Sugnet, Charles; Suyama, Mikita; Tesler, Glenn; Thompson, Johanna; Torrents, David; Trevaskis, Evanne; Tromp, John; Ucla, Catherine; Ureta-Vidal, Abel; Vinson, Jade P; Von Niederhausern, Andrew C; Wade, Claire M; Wall, Melanie; Weber, Ryan J; Weiss, Robert B; Wendl, Michael C; West, Anthony P; Wetterstrand, Kris; Wheeler, Raymond; Whelan, Simon; Wierzbowski, Jamey; Willey, David; Williams, Sophie; Wilson, Richard K; Winter, Eitan; Worley, Kim C; Wyman, Dudley; Yang, Shan; Yang, Shiaw-Pyng; Zdobnov, Evgeny M; Zody, Michael C; Lander, Eric S

    2002-12-05

    The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

  11. Implementation of Targeted Next Generation Sequencing in Clinical Diagnostics

    DEFF Research Database (Denmark)

    Larsen, Martin Jakob; Burton, Mark; Thomassen, Mads

    advantage of targeted NGS is that multiple disease-specific genes can easily be sequenced simultaneously, which is favorable in genetic heterogeneous diseases. Prior to implementation in our diagnostic setting, we aimed to assess the sensitivity and specificity of targeted NGS by sequencing a collection......, respectively. For diagnostics, the sequencing coverage is essential, wherefore a minimum coverage of 30x per nucleotide in the coding regions was used as our primary quality criterion. For the majority of the included genes, we obtained adequate gene coverage, in which we were able to detect 100% of the known......Accurate mutation detection is essential in clinical genetic diagnostics of monogenic hereditary diseases. Targeted next generation sequencing (NGS) provides a promising and cost-effective alternative to Sanger sequencing and MLPA analysis currently used in most diagnostic laboratories. One...

  12. Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

    Directory of Open Access Journals (Sweden)

    Giorgio Palù

    2011-11-01

    Full Text Available Novel DNA sequencing techniques, referred to as “next-generation” sequencing (NGS, provide high speed and throughput that can produce an enormous volume of sequences with many possible applications in research and diagnostic settings. In this article, we provide an overview of the many applications of NGS in diagnostic virology. NGS techniques have been used for high-throughput whole viral genome sequencing, such as sequencing of new influenza viruses, for detection of viral genome variability and evolution within the host, such as investigation of human immunodeficiency virus and human hepatitis C virus quasispecies, and monitoring of low-abundance antiviral drug-resistance mutations. NGS techniques have been applied to metagenomics-based strategies for the detection of unexpected disease-associated viruses and for the discovery of novel human viruses, including cancer-related viruses. Finally, the human virome in healthy and disease conditions has been described by NGS-based metagenomics.

  13. Grand unified models including extra Z bosons

    International Nuclear Information System (INIS)

    Li Tiezhong

    1989-01-01

    The grand unified theories (GUT) of the simple Lie groups including extra Z bosons are discussed. Under authors's hypothesis there are only SU 5+m SO 6+4n and E 6 groups. The general discussion of SU 5+m is given, then the SU 6 and SU 7 are considered. In SU 6 the 15+6 * +6 * fermion representations are used, which are not same as others in fermion content, Yukawa coupling and broken scales. A conception of clans of particles, which are not families, is suggested. These clans consist of extra Z bosons and the corresponding fermions of the scale. The all of fermions in the clans are down quarks except for the standard model which consists of Z bosons and 15 fermions, therefore, the spectrum of the hadrons which are composed of these down quarks are different from hadrons at present

  14. CLIC expands to include the Southern Hemisphere

    CERN Multimedia

    Roberto Cantoni

    2010-01-01

    Australia has recently joined the CLIC collaboration: the enlargement will bring new expertise and resources to the project, and is especially welcome in the wake of CERN budget redistributions following the recent adoption of the Medium Term Plan.   The countries involved in CLIC collaboration With the signing of a Memorandum of Understanding on 26 August 2010, the ACAS network (Australian Collaboration for Accelerator Science) became the 40th member of in the multilateral CLIC collaboration making Australia the 22nd country to join the collaboration. “The new MoU was signed by the ACAS network, which includes the Australian Synchrotron and the University of Melbourne”, explains Jean-Pierre Delahaye, CLIC Study Leader. “Thanks to their expertise, the Australian institutes will contribute greatly to the CLIC damping rings and the two-beam test modules." Institutes from any country wishing to join the CLIC collaboration are invited to assume responsibility o...

  15. Musculoskeletal ultrasound including definitions for ultrasonographic pathology

    DEFF Research Database (Denmark)

    Wakefield, RJ; Balint, PV; Szkudlarek, Marcin

    2005-01-01

    Ultrasound (US) has great potential as an outcome in rheumatoid arthritis trials for detecting bone erosions, synovitis, tendon disease, and enthesopathy. It has a number of distinct advantages over magnetic resonance imaging, including good patient tolerability and ability to scan multiple joints...... in a short period of time. However, there are scarce data regarding its validity, reproducibility, and responsiveness to change, making interpretation and comparison of studies difficult. In particular, there are limited data describing standardized scanning methodology and standardized definitions of US...... pathologies. This article presents the first report from the OMERACT ultrasound special interest group, which has compared US against the criteria of the OMERACT filter. Also proposed for the first time are consensus US definitions for common pathological lesions seen in patients with inflammatory arthritis....

  16. Education Program on Fossil Resources Including Coal

    Science.gov (United States)

    Usami, Masahiro

    Fossil fuels including coal play a key role as crucial energies in contributing to economic development in Asia. On the other hand, its limited quantity and the environmental problems causing from its usage have become a serious global issue and a countermeasure to solve such problems is very much demanded. Along with the pursuit of sustainable development, environmentally-friendly use of highly efficient fossil resources should be therefore, accompanied. Kyushu-university‧s sophisticated research through long years of accumulated experience on the fossil resources and environmental sectors together with the advanced large-scale commercial and empirical equipments will enable us to foster cooperative research and provide internship program for the future researchers. Then, this program is executed as a consignment business from the Ministry of Economy, Trade and Industry from 2007 fiscal year to 2009 fiscal year. The lecture that uses the textbooks developed by this program is scheduled to be started a course in fiscal year 2010.

  17. Should Broca's area include Brodmann area 47?

    Science.gov (United States)

    Ardila, Alfredo; Bernal, Byron; Rosselli, Monica

    2017-02-01

    Understanding brain organization of speech production has been a principal goal of neuroscience. Historically, brain speech production has been associated with so-called Broca’s area (Brodmann area –BA- 44 and 45), however, modern neuroimaging developments suggest speech production is associated with networks rather than with areas. The purpose of this paper was to analyze the connectivity of BA47 ( pars orbitalis) in relation to language . A meta-analysis was conducted to assess the language network in which BA47 is involved. The Brainmap database was used. Twenty papers corresponding to 29 experimental conditions with a total of 373 subjects were included. Our results suggest that BA47 participates in a “frontal language production system” (or extended Broca’s system). The BA47  connectivity found is also concordant with a minor role in language semantics. BA47 plays a central role in the language production system.

  18. Pulmonary disorders, including vocal cord dysfunction.

    Science.gov (United States)

    Greenberger, Paul A; Grammer, Leslie C

    2010-02-01

    The lung is a very complex immunologic organ and responds in a variety of ways to inhaled antigens, organic or inorganic materials, infectious or saprophytic agents, fumes, and irritants. There might be airways obstruction, restriction, neither, or both accompanied by inflammatory destruction of the pulmonary interstitium, alveoli, or bronchioles. This review focuses on diseases organized by their predominant immunologic responses, either innate or acquired. Pulmonary innate immune conditions include transfusion-related acute lung injury, World Trade Center cough, and acute respiratory distress syndrome. Adaptive immunity responses involve the systemic and mucosal immune systems, activated lymphocytes, cytokines, and antibodies that produce CD4(+) T(H)1 phenotypes, such as for tuberculosis or acute forms of hypersensitivity pneumonitis, and CD4(+) T(H)2 phenotypes, such as for asthma, Churg-Strauss syndrome, and allergic bronchopulmonary aspergillosis. Copyright 2010 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

  19. CERN Technical Training: LABVIEW courses include RADE

    CERN Multimedia

    HR Department

    2009-01-01

    The contents of the "LabView Basic I" and "LabView Intermediate II" courses have recently been changed to include, respectively, an introduction to and expert training in the Rapid Application Development Environment (RADE). RADE is a LabView-based application developed at CERN to integrate LabView in the accelerator and experiment control infrastructure. It is a suitable solution to developing expert tools, machine development analysis and independent test facilities. The course names have also been changed to "LabVIEW Basics I with RADE Introduction" and "LabVIEW Intermediate II with Advanced RADE Application". " LabVIEW Basics I with RADE Introduction" is designed for: Users preparing to develop applications using LabVIEW, or NI Developer Suite; users and technical managers evaluating LabVIEW or NI Developer Suite in purchasing decisions; users pursuing the Certified LabVIEW Developer certification. The course pr...

  20. CERN Technical Training: LABVIEW courses include RADE

    CERN Multimedia

    HR Department

    2009-01-01

    The contents of "LabView Basic I" and "LabView Intermediate II" trainings have been recently changed to include, respectively, an introduction and an expert training on the Rapid Application Development Environment (RADE). RADE is a LabView-based application developed at CERN to integrate LabView in the accelerator and experiment control infrastructure. It is a suitable solution to develop expert tools, machine development analysis and independent test facilities. The course names have also been changed to "LabVIEW Basics I with RADE Introduction" and "LabVIEW Intermediate II with Advanced RADE Application". " LabVIEW Basics I with RADE Introduction" is designed for: Users preparing to develop applications using LabVIEW, or NI Developer Suite; users and technical managers evaluating LabVIEW or NI Developer Suite in purchasing decisions; users pursuing the Certified LabVIEW Developer certification. The course prepare...

  1. CERN Technical Training: LABVIEW courses include RADE

    CERN Multimedia

    HR Department

    2009-01-01

    The contents of the "LabView Basic I" and "LabView Intermediate II" courses have recently been changed to include, respectively, an introduction to and expert training in the Rapid Application Development Environment (RADE). RADE is a LabView-based application developed at CERN to integrate LabView in the accelerator and experiment control infrastructure. It is a suitable solution to developing expert tools, machine development analysis and independent test facilities. The course names have also been changed to "LabVIEW Basics I with RADE Introduction" and "LabVIEW Intermediate II with Advanced RADE Application". " LabVIEW Basics I with RADE Introduction" is designed for: Users preparing to develop applications using LabVIEW, or NI Developer Suite; users and technical managers evaluating LabVIEW or NI Developer Suite in purchasing decisions; users pursuing the Certified LabVIEW Developer certification. The course prepares participants to develop test and measurement, da...

  2. AMS at the ANU including biomedical applications

    International Nuclear Information System (INIS)

    Fifield, L.K.; Allan, G.L.; Cresswell, R.G.; Ophel, T.R.; King, S.J.; Day, J.P.

    1993-01-01

    An extensive accelerator mass spectrometry program has been conducted on the 14UD accelerator at the Australian National University since 1986. In the two years since the previous conference, the research program has expanded significantly to include biomedical applications of 26 Al and studies of landform evolution using isotopes produced in situ in surface rocks by cosmic ray bombardment. The system is now used for the measurement of 10 Be, 14 C, 26 Al, 36 Cl, 59 Ni and 129 I, and research is being undertaken in hydrology, environmental geochemistry, archaeology and biomedicine. On the technical side, a new test system has permitted the successful off-line development of a high-intensity ion source. A new injection line to the 14UD has been established and the new source is now in position and providing beams to the accelerator. 4 refs

  3. AMS at the ANU including biomedical applications

    Energy Technology Data Exchange (ETDEWEB)

    Fifield, L.K.; Allan, G.L.; Cresswell, R.G.; Ophel, T.R. [Australian National Univ., Canberra, ACT (Australia); King, S.J.; Day, J.P. [Manchester Univ. (United Kingdom). Dept. of Chemistry

    1993-12-31

    An extensive accelerator mass spectrometry program has been conducted on the 14UD accelerator at the Australian National University since 1986. In the two years since the previous conference, the research program has expanded significantly to include biomedical applications of {sup 26}Al and studies of landform evolution using isotopes produced in situ in surface rocks by cosmic ray bombardment. The system is now used for the measurement of {sup 10}Be, {sup 14}C, {sup 26}Al, {sup 36}Cl, {sup 59}Ni and {sup 129}I, and research is being undertaken in hydrology, environmental geochemistry, archaeology and biomedicine. On the technical side, a new test system has permitted the successful off-line development of a high-intensity ion source. A new injection line to the 14UD has been established and the new source is now in position and providing beams to the accelerator. 4 refs.

  4. Targeted exome sequencing of suspected mitochondrial disorders.

    Science.gov (United States)

    Lieber, Daniel S; Calvo, Sarah E; Shanahan, Kristy; Slate, Nancy G; Liu, Shangtao; Hershman, Steven G; Gold, Nina B; Chapman, Brad A; Thorburn, David R; Berry, Gerard T; Schmahmann, Jeremy D; Borowsky, Mark L; Mueller, David M; Sims, Katherine B; Mootha, Vamsi K

    2013-05-07

    To evaluate the utility of targeted exome sequencing for the molecular diagnosis of mitochondrial disorders, which exhibit marked phenotypic and genetic heterogeneity. We considered a diverse set of 102 patients with suspected mitochondrial disorders based on clinical, biochemical, and/or molecular findings, and whose disease ranged from mild to severe, with varying age at onset. We sequenced the mitochondrial genome (mtDNA) and the exons of 1,598 nuclear-encoded genes implicated in mitochondrial biology, mitochondrial disease, or monogenic disorders with phenotypic overlap. We prioritized variants likely to underlie disease and established molecular diagnoses in accordance with current clinical genetic guidelines. Targeted exome sequencing yielded molecular diagnoses in established disease loci in 22% of cases, including 17 of 18 (94%) with prior molecular diagnoses and 5 of 84 (6%) without. The 5 new diagnoses implicated 2 genes associated with canonical mitochondrial disorders (NDUFV1, POLG2), and 3 genes known to underlie other neurologic disorders (DPYD, KARS, WFS1), underscoring the phenotypic and biochemical overlap with other inborn errors. We prioritized variants in an additional 26 patients, including recessive, X-linked, and mtDNA variants that were enriched 2-fold over background and await further support of pathogenicity. In one case, we modeled patient mutations in yeast to provide evidence that recessive mutations in ATP5A1 can underlie combined respiratory chain deficiency. The results demonstrate that targeted exome sequencing is an effective alternative to the sequential testing of mtDNA and individual nuclear genes as part of the investigation of mitochondrial disease. Our study underscores the ongoing challenge of variant interpretation in the clinical setting.

  5. Comparative chloroplast genomics: Analyses including new sequencesfrom the angiosperms Nuphar advena and Ranunculus macranthus

    Energy Technology Data Exchange (ETDEWEB)

    Raubeso, Linda A.; Peery, Rhiannon; Chumley, Timothy W.; Dziubek,Chris; Fourcade, H. Matthew; Boore, Jeffrey L.; Jansen, Robert K.

    2007-03-01

    The number of completely sequenced plastid genomes available is growing rapidly. This new array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is most useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the new genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (from the basal group of eudicots). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition.

  6. Ossification sequence heterochrony among amphibians.

    Science.gov (United States)

    Harrington, Sean M; Harrison, Luke B; Sheil, Christopher A

    2013-01-01

    Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia. In this study, a new version of the program Parsimov-based genetic inference (PGi) was used to identify shifts in ossification sequences across all extant orders of amphibians, for all major structural units of the skeleton. PGi identified a number of heterochronic sequence shifts in all analyses, the most interesting of which seem to be tied to differences in metamorphic patterns among major clades. Early ossification of the vomer, premaxilla, and dentary is retained by Apateon caducus and members of Gymnophiona and Urodela, which lack the strongly biphasic development seen in anurans. In contrast, bones associated with the jaws and face were identified as shifting late in the ancestor of Anura. The bones that do not shift late, and thereby occupy the earliest positions in the anuran cranial sequence, are those in regions of the skull that undergo the least restructuring throughout anuran metamorphosis. Additionally, within Anura, bones of the hind limb and pelvic girdle were also identified as shifting early in the sequence of ossification, which may be a result of functional constraints imposed by the drastic metamorphosis of most anurans. © 2013 Wiley Periodicals, Inc.

  7. Sequence Factorization with Multiple References.

    Science.gov (United States)

    Wandelt, Sebastian; Leser, Ulf

    2015-01-01

    The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1) the size of the factorization, 2) the time for factorization, and 3) the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%), factorization speed (0.01 MB/s to more than 600 MB/s), and main memory usage (few dozen MB to dozens of GB). Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  8. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  9. DNA Sequence Analysis in Clinical Medicine, Proceeding Cautiously

    Directory of Open Access Journals (Sweden)

    Moyra Smith

    2017-05-01

    Full Text Available Delineation of underlying genomic and genetic factors in a specific disease may be valuable in establishing a definitive diagnosis and may guide patient management and counseling. In addition, genetic information may be useful in identification of at risk family members. Gene mapping and initial genome sequencing data enabled the development of microarrays to analyze genomic variants. The goal of this review is to consider different generations of sequencing techniques and their application to exome sequencing and whole genome sequencing and their clinical applications. In recent decades, exome sequencing has primarily been used in patient studies. Discussed in some detail, are important measures that have been developed to standardize variant calling and to assess pathogenicity of variants. Examples of cases where exome sequencing has facilitated diagnosis and led to improved medical management are presented. Whole genome sequencing and its clinical relevance are presented particularly in the context of analysis of nucleotide and structural genomic variants in large population studies and in certain patient cohorts. Applications involving analysis of cell free DNA in maternal blood for prenatal diagnosis of specific autosomal trisomies are reviewed. Applications of DNA sequencing to diagnosis and therapeutics of cancer are presented. Also discussed are important recent diagnostic applications of DNA sequencing in cancer, including analysis of tumor derived cell free DNA and exosomes that are present in body fluids. Insights gained into underlying pathogenetic mechanisms of certain complex common diseases, including schizophrenia, macular degeneration, neurodegenerative disease are presented. The relevance of different types of variants, rare, uncommon, and common to disease pathogenesis, and the continuum of causality, are addressed. Pharmogenetic variants detected by DNA sequence analysis are gaining in importance and are particularly relevant

  10. The neural correlates of speech motor sequence learning.

    Science.gov (United States)

    Segawa, Jennifer A; Tourville, Jason A; Beal, Deryk S; Guenther, Frank H

    2015-04-01

    Speech is perhaps the most sophisticated example of a species-wide movement capability in the animal kingdom, requiring split-second sequencing of approximately 100 muscles in the respiratory, laryngeal, and oral movement systems. Despite the unique role speech plays in human interaction and the debilitating impact of its disruption, little is known about the neural mechanisms underlying speech motor learning. Here, we studied the behavioral and neural correlates of learning new speech motor sequences. Participants repeatedly produced novel, meaningless syllables comprising illegal consonant clusters (e.g., GVAZF) over 2 days of practice. Following practice, participants produced the sequences with fewer errors and shorter durations, indicative of motor learning. Using fMRI, we compared brain activity during production of the learned illegal sequences and novel illegal sequences. Greater activity was noted during production of novel sequences in brain regions linked to non-speech motor sequence learning, including the BG and pre-SMA. Activity during novel sequence production was also greater in brain regions associated with learning and maintaining speech motor programs, including lateral premotor cortex, frontal operculum, and posterior superior temporal cortex. Measures of learning success correlated positively with activity in left frontal operculum and white matter integrity under left posterior superior temporal sulcus. These findings indicate speech motor sequence learning relies not only on brain areas involved generally in motor sequencing learning but also those associated with feedback-based speech motor learning. Furthermore, learning success is modulated by the integrity of structural connectivity between these motor and sensory brain regions.

  11. T1- Thresholds in Black Holes Increase Clinical-Radiological Correlation in Multiple Sclerosis Patients.

    Science.gov (United States)

    Thaler, Christian; Faizy, Tobias; Sedlacik, Jan; Holst, Brigitte; Stellmann, Jan-Patrick; Young, Kim Lea; Heesen, Christoph; Fiehler, Jens; Siemonsen, Susanne

    2015-01-01

    Magnetic Resonance Imaging (MRI) is an established tool in diagnosing and evaluating disease activity in Multiple Sclerosis (MS). While clinical-radiological correlations are limited in general, hypointense T1 lesions (also known as Black Holes (BH)) have shown some promising results. The definition of BHs is very heterogeneous and depends on subjective visual evaluation. We aimed to improve clinical-radiological correlations by defining BHs using T1 relaxation time (T1-RT) thresholds to achieve best possible correlation between BH lesion volume and clinical disability. 40 patients with mainly relapsing-remitting MS underwent MRI including 3-dimensional fluid attenuated inversion recovery (FLAIR), magnetization-prepared rapid gradient echo (MPRAGE) before and after Gadolinium (GD) injection and double inversion-contrast magnetization-prepared rapid gradient echo (MP2RAGE) sequences. BHs (BHvis) were marked by two raters on native T1-weighted (T1w)-MPRAGE, contrast-enhancing lesions (CE lesions) on T1w-MPRAGE after GD and FLAIR lesions (total-FLAIR lesions) were detected separately. BHvis and total-FLAIR lesion maps were registered to MP2RAGE images, and the mean T1-RT were calculated for all lesion ROIs. Mean T1 values of the cortex (CTX) were calculated for each patient. Subsequently, Spearman rank correlations between clinical scores (Expanded Disability Status Scale and Multiple Sclerosis Functional Composite) and lesion volume were determined for different T1-RT thresholds. Significant differences in T1-RT were obtained between all different lesion types with highest T1 values in visually marked BHs (BHvis: 1453.3±213.4 ms, total-FLAIR lesions: 1394.33±187.38 ms, CTX: 1305.6±35.8 ms; p1500 ms (Expanded Disability Status Scale vs. lesion volume: rBHvis = 0.442 and rtotal-FLAIR = 0.497, p<0.05; Multiple Sclerosis Functional Composite vs. lesion volume: rBHvis = -0.53 and rtotal-FLAIR = -0.627, p<0.05). Clinical-radiological correlations in MS patients are

  12. How Next-Generation Sequencing Has Aided Our Understanding of the Sequence Composition and Origin of B Chromosomes

    Directory of Open Access Journals (Sweden)

    Alevtina Ruban

    2017-10-01

    Full Text Available Accessory, supernumerary, or—most simply—B chromosomes, are found in many eukaryotic karyotypes. These small chromosomes do not follow the usual pattern of segregation, but rather are transmitted in a higher than expected frequency. As increasingly being demonstrated by next-generation sequencing (NGS, their structure comprises fragments of standard (A chromosomes, although in some plant species, their sequence also includes contributions from organellar genomes. Transcriptomic analyses of various animal and plant species have revealed that, contrary to what used to be the common belief, some of the B chromosome DNA is protein-encoding. This review summarizes the progress in understanding B chromosome biology enabled by the application of next-generation sequencing technology and state-of-the-art bioinformatics. In particular, a contrast is drawn between a direct sequencing approach and a strategy based on a comparative genomics as alternative routes that can be taken towards the identification of B chromosome sequences.

  13. ARC Code TI: sequenceMiner

    Data.gov (United States)

    National Aeronautics and Space Administration — The sequenceMiner was developed to address the problem of detecting and describing anomalies in large sets of high-dimensional symbol sequences. sequenceMiner works...

  14. A Demonstration of Automated DNA Sequencing.

    Science.gov (United States)

    Latourelle, Sandra; Seidel-Rogol, Bonnie

    1998-01-01

    Details a simulation that employs a paper-and-pencil model to demonstrate the principles behind automated DNA sequencing. Discusses the advantages of automated sequencing as well as the chemistry of automated DNA sequencing. (DDR)

  15. A micromanipulation cell including a tool changer

    Science.gov (United States)

    Clévy, Cédric; Hubert, Arnaud; Agnus, Joël; Chaillet, Nicolas

    2005-10-01

    This paper deals with the design, fabrication and characterization of a tool changer for micromanipulation cells. This tool changer is part of a manipulation cell including a three linear axes robot and a piezoelectric microgripper. All these parts are designed to perform micromanipulation tasks in confined spaces such as a microfactory or in the chamber of a scanning electron microscope (SEM). The tool changer principle is to fix a pair of tools (i.e. the gripper tips) either on the tips of the microgripper actuator (piezoceramic bulk) or on a tool magazine. The temperature control of a thermal glue enables one to fix or release this pair of tools. Liquefaction and solidification are generated by surface mounted device (SMD) resistances fixed on the surface of the actuator or magazine. Based on this principle, the tool changer can be adapted to other kinds of micromanipulation cells. Hundreds of automatic tool exchanges were performed with a maximum positioning error between two consecutive tool exchanges of 3.2 µm, 2.3 µm and 2.8 µm on the X, Y and Z axes respectively (Z refers to the vertical axis). Finally, temperature measurements achieved under atmospheric pressure and in a vacuum environment and pressure measurements confirm the possibility of using this device in the air as well as in a SEM.

  16. Robust Unit Commitment Including Frequency Stability Constraints

    Directory of Open Access Journals (Sweden)

    Felipe Pérez-Illanes

    2016-11-01

    Full Text Available An increased use of variable generation technologies such as wind power and photovoltaic generation can have important effects on system frequency performance during normal operation as well as contingencies. The main reasons are the operational principles and inherent characteristics of these power plants like operation at maximum power point and no inertial response during power system imbalances. This has led to new challenges for Transmission System Operators in terms of ensuring system security during contingencies. In this context, this paper proposes a Robust Unit Commitment including a set of additional frequency stability constraints. To do this, a simplified dynamic model of the initial system frequency response is used in combination with historical frequency nadir data during contingencies. The proposed approach is especially suitable for power systems with cost-based economic dispatch like those in most Latin American countries. The study is done considering the Northern Interconnected System of Chile, a 50-Hz medium size isolated power system. The results obtained were validated by means of dynamic simulations of different system contingencies.

  17. Unifying all elementary particle forces including gravity

    International Nuclear Information System (INIS)

    Terazawa, H.

    1979-01-01

    It is a final goal in physics to unify all four basic forces, strong, weak, electromagnetic and gravitational. First, the unified gauge theories of strong, weak and electromagnetic interactions are discussed. There are two standard models, the model of Pati and Salam in which leptons have the fourth color, and the model of Georgi and Glashow in which a simple group SU (5) is assumed for grand unification. Two mass relations for leptons and quarks were derived, and the extension of the Georgi-Glashow model to a grand unified model of SU (6) gauge group has been made. The quantization of the electric charge of elementary particles is one of the most satisfactory features in grand unified gauge theories. The constraint relations between the gauge couplings, the weak mixing angle and the mass scale of symmetry breaking owing to the renormalization effect are not so severe as those in the grand unified models. However, the mass scale becomes far above the Planck mass in some cases. The baryon number non-conservation is one of the most intriguing features common to grand unified gauge theories. The unified models of all elementary particle forces including gravity are discussed. The discovery of weak vector bosons and the production of subquark pairs are anticipated. (Kako, I.)

  18. Computing distribution of scale independent motifs in biological sequences.

    Science.gov (United States)

    Almeida, Jonas S; Vinga, Susana

    2006-10-18

    The use of Chaos Game Representation (CGR) or its generalization, Universal Sequence Maps (USM), to describe the distribution of biological sequences has been found objectionable because of the fractal structure of that coordinate system. Consequently, the investigation of distribution of symbolic motifs at multiple scales is hampered by an inexact association between distance and sequence dissimilarity. A solution to this problem could unleash the use of iterative maps as phase-state representation of sequences where its statistical properties can be conveniently investigated. In this study a family of kernel density functions is described that accommodates the fractal nature of iterative function representations of symbolic sequences and, consequently, enables the exact investigation of sequence motifs of arbitrary lengths in that scale-independent representation. Furthermore, the proposed kernel density includes both Markovian succession and currently used alignment-free sequence dissimilarity metrics as special solutions. Therefore, the fractal kernel described is in fact a generalization that provides a common framework for a diverse suite of sequence analysis techniques.

  19. Computing distribution of scale independent motifs in biological sequences

    Directory of Open Access Journals (Sweden)

    Vinga Susana

    2006-10-01

    Full Text Available Abstract The use of Chaos Game Representation (CGR or its generalization, Universal Sequence Maps (USM, to describe the distribution of biological sequences has been found objectionable because of the fractal structure of that coordinate system. Consequently, the investigation of distribution of symbolic motifs at multiple scales is hampered by an inexact association between distance and sequence dissimilarity. A solution to this problem could unleash the use of iterative maps as phase-state representation of sequences where its statistical properties can be conveniently investigated. In this study a family of kernel density functions is described that accommodates the fractal nature of iterative function representations of symbolic sequences and, consequently, enables the exact investigation of sequence motifs of arbitrary lengths in that scale-independent representation. Furthermore, the proposed kernel density includes both Markovian succession and currently used alignment-free sequence dissimilarity metrics as special solutions. Therefore, the fractal kernel described is in fact a generalization that provides a common framework for a diverse suite of sequence analysis techniques.

  20. [Study on factors influencing DNA sequencing by automatic genetic analyzer].

    Science.gov (United States)

    Yan, Shaofei; Wang, Wei; Xu, Jin; Bai, Li; Gan, Xin; Li, Fengqin

    2015-05-01

    To acquire accurate and successful DNA sequencing in a cost-effective way by ABI3500xl automatic genetic analyzer. BigDye was diluted to 8, 16 and 32 times in PCR product sequencing. Three different methods including CENTRI-SEP kit, BigDye cleaning beads and ethanol-NaAc-EDTA were used to purify the sequencing PCR products. The results of DNA sequencing were correct when BigDye was diluted up to 16 times. The misreading of nucleic acid bases was found as BigDye was diluted to 32 times. All three purification methods provided acceptable DNA sequencing results. In terms of method for purification of PCR products, the CENTRI-SEP Kit was the most expensive but time-saving (0.5 h), while ethanol-NaAc-EDTA method was the most economical but time-consuming (2 h). The BigDye cleaning beads method was of a suitable purification time (1 h) but not fit for high-throughput DNA sequencing. BigDye should be diluted up to 16 times in DNA sequencing by ABI3500xl DNA analyzer. Although all three purification methods may promise DNA sequencing results with good quality, it is necessary to choose an appropriate one to keep the balance between time and cost on the basis of the lab condition.

  1. Transformed composite sequences for improved qubit addressing

    Science.gov (United States)

    Merrill, J. True; Doret, S. Charles; Vittorini, Grahame; Addison, J. P.; Brown, Kenneth R.

    2014-10-01

    Selective laser addressing of a single atom or atomic ion qubit can be improved using narrow-band composite pulse sequences. We describe a Lie-algebraic technique to generalize known narrow-band sequences and introduce sequences related by dilation and rotation of sequence generators. Our method improves known narrow-band sequences by decreasing both the pulse time and the residual error. Finally, we experimentally demonstrate these composite sequences using 40Ca+ ions trapped in a surface-electrode ion trap.

  2. SEEPAGE MODEL FOR PA INCLUDING DRIFT COLLAPSE

    International Nuclear Information System (INIS)

    C. Tsang

    2004-01-01

    The purpose of this report is to document the predictions and analyses performed using the seepage model for performance assessment (SMPA) for both the Topopah Spring middle nonlithophysal (Tptpmn) and lower lithophysal (Tptpll) lithostratigraphic units at Yucca Mountain, Nevada. Look-up tables of seepage flow rates into a drift (and their uncertainty) are generated by performing numerical simulations with the seepage model for many combinations of the three most important seepage-relevant parameters: the fracture permeability, the capillary-strength parameter 1/a, and the percolation flux. The percolation flux values chosen take into account flow focusing effects, which are evaluated based on a flow-focusing model. Moreover, multiple realizations of the underlying stochastic permeability field are conducted. Selected sensitivity studies are performed, including the effects of an alternative drift geometry representing a partially collapsed drift from an independent drift-degradation analysis (BSC 2004 [DIRS 166107]). The intended purpose of the seepage model is to provide results of drift-scale seepage rates under a series of parameters and scenarios in support of the Total System Performance Assessment for License Application (TSPA-LA). The SMPA is intended for the evaluation of drift-scale seepage rates under the full range of parameter values for three parameters found to be key (fracture permeability, the van Genuchten 1/a parameter, and percolation flux) and drift degradation shape scenarios in support of the TSPA-LA during the period of compliance for postclosure performance [Technical Work Plan for: Performance Assessment Unsaturated Zone (BSC 2002 [DIRS 160819], Section I-4-2-1)]. The flow-focusing model in the Topopah Spring welded (TSw) unit is intended to provide an estimate of flow focusing factors (FFFs) that (1) bridge the gap between the mountain-scale and drift-scale models, and (2) account for variability in local percolation flux due to

  3. [Contracts including performance and management of uncertainty].

    Science.gov (United States)

    Duru, G; Garassus, P; Auray, J-P

    2013-09-01

    Since many decades in France, the most important part of ambulatory health care expenditure is represented by drug consumption. By the fact, French patient is indeed the greatest world consumer of pharmaceuticals treatments. Therefore, the regulation authorities by successive strategies, attempt to limit or even restrict market access for new drugs in the health care sector secured by public social insurance coverage. Common objectives are to assess the reimbursement to scientific studies and to fix the price of therapeutics at an acceptable level for both industries and government. New trends try then to determine recently the drug price in a dual approach, as a component of global and effective contract, including performance and outcome. The first diffusion authorization is diffusion concerned, but this concept takes into account the eventual success of new produces in long-term survey. Signed for a fixed period as reciprocal partnership between regulation authorities and pharmaceutics industries, the contract integrates two dimensions of incertitude. The first one is represented by the strategy of new treatments development according to efficacy and adapted price, and the second one is linked to the result of diffusion and determines adapted rules if eventual non-respects of the previous engagement are registered. This paper discusses problems related to this new dimension of incertitude affected by conditional drug prices in market access strategy and the adapted follow-up of new treatment diffusion fixed by "outcome" contract between French regulation administration and pharmaceutics industries in our recent economic context. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  4. Resection of thymoma should include nodal sampling.

    Science.gov (United States)

    Weksler, Benny; Pennathur, Arjun; Sullivan, Jennifer L; Nason, Katie S

    2015-03-01

    Thymoma is best treated by surgical resection; however, no clear guidelines have been created regarding lymph node sampling at the time of resection. Additionally, the prognostic implications of nodal metastases are unclear. The aim of this study was to analyze the prognostic implications of nodal metastases in thymoma. The Surveillance, Epidemiology, and End Results database was queried for patients who underwent surgical resection of thymoma with documented pathologic examination of lymph nodes. The impact of nodal status on survival and thymoma staging was examined. We identified 442 patients who underwent thymoma resection with pathologic evaluation of 1 or more lymph nodes. A median of 2 nodes were sampled per patient. Fifty-nine patients (59 of 442, 13.3%) had ≥ 1 positive node. Patients with positive nodes were younger and had smaller tumors than node-negative patients. Median survival in the node-positive patients was 98 months, compared with 144 months in node-negative patients (P = .013). In multivariable analysis, the presence of positive nodes had a significant, independent, adverse impact on survival (hazard ratio 1.945, 95% confidence interval 1.296-2.919, P = .001). The presence of nodal metastases resulted in a change in classification to a higher stage in 80% of patients, the majority from Masaoka-Koga stage III to stage IV. Nodal status seems to be an important prognostic factor in patients with thymoma. Until the prognostic significance of nodal metastases is better understood, surgical therapy for thymoma should include sampling of regional lymph nodes. Copyright © 2015 The American Association for Thoracic Surgery. Published by Elsevier Inc. All rights reserved.

  5. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    . All but one sequence mapped to the MCP gene while the last sequence mapped to the Neurofilament gene. Approx. half of the sequences contained no errors while the rest differed with 88-99 percent similarity with most having 99% similarity. One sequence, when BLASTed, showed most similarity to European...... Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...

  6. Nucleotide sequence of the triosephosphate isomerase gene from Macaca mulatta

    Energy Technology Data Exchange (ETDEWEB)

    Old, S.E.; Mohrenweiser, H.W. (Univ. of Michigan, Ann Arbor (USA))

    1988-09-26

    The triosephosphate isomerase gene from a rhesus monkey, Macaca mulatta, charon 34 library was sequenced. The human and chimpanzee enzymes differ from the rhesus enzyme at ASN 20 and GLU 198. The nucleotide sequence identity between rhesus and human is 97% in the coding region and >94% in the flanking regions. Comparison of the rhesus and chimp genes, including the intron and flanking sequences, does not suggest a mechanism for generating the two TPI peptides of proliferating cells from hominoids and a single peptide from the rhesus gene.

  7. Operator Ideal of Cesaro Type Sequence Spaces Involving Lacunary Sequence

    Directory of Open Access Journals (Sweden)

    Awad A. Bakery

    2014-01-01

    Full Text Available The aim of this paper is to give the sufficient conditions on the sequence space Cesθ,p defined in Lim (1977 such that the class of all bounded linear operators between any arbitrary Banach spaces with nth approximation numbers of the bounded linear operators in Cesθ,p form an operator ideal.

  8. Constrained Optimization of MIMO Training Sequences

    Directory of Open Access Journals (Sweden)

    Coon Justin P

    2007-01-01

    Full Text Available Multiple-input multiple-output (MIMO systems have shown a huge potential for increased spectral efficiency and throughput. With an increasing number of transmitting antennas comes the burden of providing training for channel estimation for coherent detection. In some special cases optimal, in the sense of mean-squared error (MSE, training sequences have been designed. However, in many practical systems it is not feasible to analytically find optimal solutions and numerical techniques must be used. In this paper, two systems (unique word (UW single carrier and OFDM with nulled subcarriers are considered and a method of designing near-optimal training sequences using nonlinear optimization techniques is proposed. In particular, interior-point (IP algorithms such as the barrier method are discussed. Although the two systems seem unrelated, the cost function, which is the MSE of the channel estimate, is shown to be effectively the same for each scenario. Also, additional constraints, such as peak-to-average power ratio (PAPR, are considered and shown to be easily included in the optimization process. Numerical examples illustrate the effectiveness of the designed training sequences, both in terms of MSE and bit-error rate (BER.

  9. Sequence of tenses: playing with possibilities

    Directory of Open Access Journals (Sweden)

    Bohdan Ulašin

    2012-12-01

    Full Text Available The aim of this article is to analyse the sequence of tenses in Spanish, a phenomenon typical of the Romance languages. Our purpose is to systematize and formulate the rules of use by means of examples with graphical representations. We focus on such cases of use of the sequence of tenses where it is possible to apply a “double-access interpretation”, i. e. which allows the possibility of choosing between reference points: with the actual time (the moment of speech or with the main clause. This double interpretation is to be found in all three types of time relationships: simultaneousness, priority and posteriority. Some pairs differ semantically; others are used according to the preferences of the speaker with no change of meaning. Most examples are subordinate noun clauses, nonetheless we included examples of other types of clauses as well (e.g. relative, reason clauses. We also analyze the problem of the sequence of tenses where the main verb is in the conditional tense.

  10. Information theory applications for biological sequence analysis.

    Science.gov (United States)

    Vinga, Susana

    2014-05-01

    Information theory (IT) addresses the analysis of communication systems and has been widely applied in molecular biology. In particular, alignment-free sequence analysis and comparison greatly benefited from concepts derived from IT, such as entropy and mutual information. This review covers several aspects of IT applications, ranging from genome global analysis and comparison, including block-entropy estimation and resolution-free metrics based on iterative maps, to local analysis, comprising the classification of motifs, prediction of transcription factor binding sites and sequence characterization based on linguistic complexity and entropic profiles. IT has also been applied to high-level correlations that combine DNA, RNA or protein features with sequence-independent properties, such as gene mapping and phenotype analysis, and has also provided models based on communication systems theory to describe information transmission channels at the cell level and also during evolutionary processes. While not exhaustive, this review attempts to categorize existing methods and to indicate their relation with broader transversal topics such as genomic signatures, data compression and complexity, time series analysis and phylogenetic classification, providing a resource for future developments in this promising area.

  11. Categorizing accident sequences in the external radiotherapy for risk analysis

    OpenAIRE

    Kim, Jonghyun

    2013-01-01

    Purpose This study identifies accident sequences from the past accidents in order to help the risk analysis application to the external radiotherapy. Materials and Methods This study reviews 59 accidental cases in two retrospective safety analyses that have collected the incidents in the external radiotherapy extensively. Two accident analysis reports that accumulated past incidents are investigated to identify accident sequences including initiating events, failure of safety measures, and co...

  12. Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences

    Science.gov (United States)

    Barker, F. Keith; Oyler-McCance, Sara; Tomback, Diana F.

    2015-01-01

    Next generation sequencing methods allow rapid, economical accumulation of data that have many applications, even at relatively low levels of genome coverage. However, the utility of shotgun sequencing data sets for specific goals may vary depending on the biological nature of the samples sequenced. We show that the ability to assemble mitogenomes from three avian samples of two different tissue types varies widely. In particular, data with coverage typical of microsatellite development efforts (∼1×) from DNA extracted from avian blood failed to cover even 50% of the mitogenome, relative to at least 500-fold coverage from muscle-derived data. Researchers should consider possible applications of their data and select the tissue source for their work accordingly. Practitioners analyzing low-coverage shotgun sequencing data (including for microsatellite locus development) should consider the potential benefits of mitogenome assembly, including internal barcode verification of species identity, mitochondrial primer development, and phylogenetics.

  13. Motif discovery in ranked lists of sequences

    DEFF Research Database (Denmark)

    Nielsen, Morten Muhlig; Tataru, Paula; Madsen, Tobias

    2016-01-01

    a growing need for motif analysis methods that can exploit this coupled data structure and be tailored for specific biological questions. Here, we present an exploratory motif analysis tool, Regmex (REGular expression Motif EXplorer), which offers several methods to evaluate the correlation of motifs....... These features make Regmex well suited for a range of biological sequence analysis problems related to motif discovery, exemplified by microRNA seed enrichment, but also including enrichment problems involving complex motifs and combinations of motifs. We demonstrate a number of usage scenarios that take...

  14. An auditory display tool for DNA sequence analysis.

    Science.gov (United States)

    Temple, Mark D

    2017-04-24

    DNA Sonification refers to the use of an auditory display to convey the information content of DNA sequence data. Six sonification algorithms are presented that each produce an auditory display. These algorithms are logically designed from the simple through to the more complex. Three of these parse individual nucleotides, nucleotide pairs or codons into musical notes to give rise to 4, 16 or 64 notes, respectively. Codons may also be parsed degenerately into 20 notes with respect to the genetic code. Lastly nucleotide pairs can be parsed as two separate frames or codons can be parsed as three reading frames giving rise to multiple streams of audio. The most informative sonification algorithm reads the DNA sequence as codons in three reading frames to produce three concurrent streams of audio in an auditory display. This approach is advantageous since start and stop codons in either frame have a direct affect to start or stop the audio in that frame, leaving the other frames unaffected. Using these methods, DNA sequences such as open reading frames or repetitive DNA sequences can be distinguished from one another. These sonification tools are available through a webpage interface in which an input DNA sequence can be processed in real time to produce an auditory display playable directly within the browser. The potential of this approach as an analytical tool is discussed with reference to auditory displays derived from test sequences including simple nucleotide sequences, repetitive DNA sequences and coding or non-coding genes. This study presents a proof-of-concept that some properties of a DNA sequence can be identified through sonification alone and argues for their inclusion within the toolkit of DNA sequence browsers as an adjunct to existing visual and analytical tools.

  15. Combinatorial pooling enables selective sequencing of the barley gene space.

    Directory of Open Access Journals (Sweden)

    Stefano Lonardi

    2013-04-01

    Full Text Available For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

  16. Short read sequence typing (SRST: multi-locus sequence types from short reads

    Directory of Open Access Journals (Sweden)

    Inouye Michael

    2012-07-01

    software tool for accurate assignment of sequence types using short read data. Several uses for the tool are demonstrated, including quality control for high-throughput sequencing projects, plasmid MLST and analysis of genomic data during outbreak investigation. SRST is open-source, requires Python, BWA and SamTools, and is available from http://srst.sourceforge.net.

  17. Probabilistic studies of accident sequences

    International Nuclear Information System (INIS)

    Villemeur, A.; Berger, J.P.

    1986-01-01

    For several years, Electricite de France has carried out probabilistic assessment of accident sequences for nuclear power plants. In the framework of this program many methods were developed. As the interest in these studies was increasing and as adapted methods were developed, Electricite de France has undertaken a probabilistic safety assessment of a nuclear power plant [fr

  18. On primes in Lucas sequences

    Czech Academy of Sciences Publication Activity Database

    Křížek, Michal; Somer, L.

    2015-01-01

    Roč. 53, č. 1 (2015), s. 2-23 ISSN 0015-0517 R&D Projects: GA ČR GA14-02067S Institutional support: RVO:67985840 Keywords : Lucas sequence * primes Subject RIV: BA - General Math ematics http://www.fq. math .ca/Abstracts/53-1/somer.pdf

  19. MRI sequences and their parameters

    International Nuclear Information System (INIS)

    Teissier, J.M.

    1993-01-01

    Listing basic sequences and their present variants makes a synthetic classification of the various acquisition modes possible. The knowledge of the advantages of each of them, as well as of their disadvantages and restraints, seems to be an essential prerequisite to an optimal utilization of each magnetic resonance imaging system. (author)

  20. Curious Consequences of Simple Sequences

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 12; Issue 1. Curious Consequences of Simple Sequences. A K Mallik. General Article Volume 12 Issue 1 January 2007 pp ... Author Affiliations. A K Mallik1. Department of Mechanical Engineering, Indian Institute of Technology, Kanpur 208 016, India.

  1. On primes in Lucas sequences

    Czech Academy of Sciences Publication Activity Database

    Křížek, Michal; Somer, L.

    2015-01-01

    Roč. 53, č. 1 (2015), s. 2-23 ISSN 0015-0517 R&D Projects: GA ČR GA14-02067S Institutional support: RVO:67985840 Keywords : Lucas sequence * primes Subject RIV: BA - General Mathematics http://www.fq.math.ca/Abstracts/53-1/somer.pdf

  2. Crop Sequence Calculator, v. 3

    Science.gov (United States)

    Producers need to know how to sequence crops to develop sustainable dynamic cropping systems that take advantage of inherent internal resources, such as crop synergism, nutrient cycling, and soil water, and capitalize on external resources, such as weather, markets, and government programs. Version ...

  3. Sequences in language and text

    CERN Document Server

    Mikros, George K

    2015-01-01

    The aim of this volume is to present the diverse but highly interesting area of the quantitative analysis of the sequence of various linguistic structures. The collected articles present a wide spectrum of quantitative analyses of linguistic syntagmatic structures and explore novel sequential linguistic entities. This volume will be interesting to all researchers studying linguistics using quantitative methods.

  4. Exome sequencing for syndrome diagnostics

    DEFF Research Database (Denmark)

    Østergaard, Elsebet; Risom, Lotte; Ek, Jakob

    2017-01-01

    The majority of rare congenital disorders and syndromes have a genetic cause, but the diagnostic rate using standard workup is only around 50%. Whole exome and whole genome sequencing methods have improved the genetic diagnosis of syndromes during the latest few years. This article...

  5. Homogeneity of the 16S rDNA sequence among geographically disparate isolates of Taylorella equigenitalis.

    Science.gov (United States)

    Matsuda, M; Tazumi, A; Kagawa, S; Sekizuka, T; Murayama, O; Moore, J E; Millar, B C

    2006-01-06

    At present, six accessible sequences of 16S rDNA from Taylorella equigenitalis (T. equigenitalis) are available, whose sequence differences occur at a few nucleotide positions. Thus it is important to determine these sequences from additional strains in other countries, if possible, in order to clarify any anomalies regarding 16S rDNA sequence heterogeneity. Here, we clone and sequence the approximate full-length 16S rDNA from additional strains of T. equigenitalis isolated in Japan, Australia and France and compare these sequences to the existing published sequences. Clarification of any anomalies regarding 16S rDNA sequence heterogeneity of T. equigenitalis was carried out. When cloning, sequencing and comparison of the approximate full-length 16S rDNA from 17 strains of T. equigenitalis isolated in Japan, Australia and France, nucleotide sequence differences were demonstrated at the six loci in the 1,469 nucleotide sequence. Moreover, 12 polymorphic sites occurred among 23 sequences of the 16S rDNA, including the six reference sequences. High sequence similarity (99.5% or more) was observed throughout, except from nucleotide positions 138 to 501 where substitutions and deletions were noted.

  6. Homogeneity of the 16S rDNA sequence among geographically disparate isolates of Taylorella equigenitalis

    Directory of Open Access Journals (Sweden)

    Moore JE

    2006-01-01

    Full Text Available Abstract Background At present, six accessible sequences of 16S rDNA from Taylorella equigenitalis (T. equigenitalis are available, whose sequence differences occur at a few nucleotide positions. Thus it is important to determine these sequences from additional strains in other countries, if possible, in order to clarify any anomalies regarding 16S rDNA sequence heterogeneity. Here, we clone and sequence the approximate full-length 16S rDNA from additional strains of T. equigenitalis isolated in Japan, Australia and France and compare these sequences to the existing published sequences. Results Clarification of any anomalies regarding 16S rDNA sequence heterogeneity of T. equigenitalis was carried out. When cloning, sequencing and comparison of the approximate full-length 16S rDNA from 17 strains of T. equigenitalis isolated in Japan, Australia and France, nucleotide sequence differences were demonstrated at the six loci in the 1,469 nucleotide sequence. Moreover, 12 polymorphic sites occurred among 23 sequences of the 16S rDNA, including the six reference sequences. Conclusion High sequence similarity (99.5% or more was observed throughout, except from nucleotide positions 138 to 501 where substitutions and deletions were noted.

  7. Digital PCR provides sensitive and absolute calibration for high throughput sequencing

    Directory of Open Access Journals (Sweden)

    Fan H Christina

    2009-03-01

    Full Text Available Abstract Background Next-generation DNA sequencing on the 454, Solexa, and SOLiD platforms requires absolute calibration of the number of molecules to be sequenced. This requirement has two unfavorable consequences. First, large amounts of sample-typically micrograms-are needed for library preparation, thereby limiting the scope of samples which can be sequenced. For many applications, including metagenomics and the sequencing of ancient, forensic, and clinical samples, the quantity of input DNA can be critically limiting. Second, each library requires a titration sequencing run, thereby increasing the cost and lowering the throughput of sequencing. Results We demonstrate the use of digital PCR to accurately quantify 454 and Solexa sequencing libraries, enabling the preparation of sequencing libraries from nanogram quantities of input material while eliminating costly and time-consuming titration runs of the sequencer. We successfully sequenced low-nanogram scale bacterial and mammalian DNA samples on the 454 FLX and Solexa DNA sequencing platforms. This study is the first to definitively demonstrate the successful sequencing of picogram quantities of input DNA on the 454 platform, reducing the sample requirement more than 1000-fold without pre-amplification and the associated bias and reduction in library depth. Conclusion The digital PCR assay allows absolute quantification of sequencing libraries, eliminates uncertainties associated with the construction and application of standard curves to PCR-based quantification, and with a coefficient of variation close to 10%, is sufficiently precise to enable direct sequencing without titration runs.

  8. SU-E-I-67: Arachnoid Cysts: The Role of the BLADE Technique

    Energy Technology Data Exchange (ETDEWEB)

    Mavroidis, P [University of North Carolina, Chapel Hill, NC (United States); Vlachopoulou, A; Kostopoulos, S; Ninos, C; Glotsos, D; Bakas, A; Oikonomou, G; Roka, V; Lavdas, E [Technological Education Institute of Athens, Athens, Attika (Greece); Kapsalaki, E; Tsirika, A [University of Thessaly, Larissa, Thessaly (Greece); Papanikolaou, N [University of Texas HSC SA, San Antonio, TX (United States); Stathakis, S [Cancer Therapy and Research Center, San Antonio, TX (United States)

    2015-06-15

    Purpose: The purpose of this study is first to show the extent by which BLADE sequences can reduce all the image artifacts and second to verify that the usefulness of this technique in certain pathological conditions is significant. Methods: In this study, fourteen consecutive patients (5 females, 9 males), who routinely underwent MRI brain examination, between 2010–2014, were selected. The applied routine protocols for brain MR examination included the following sequences: 1) T2-W FLAIR axial; 2) T2-W TSE axial; 3) T2*-W axial, 4) T1-W TSE sagittal; 5) DWI-W axial; 6) T1-W TSE axial; 7) T1-W TSE axial+contrast. In cases of cystic tumors, the T2-W FLAIR BLADE sequence was added to the protocol. All the images were evaluated independently at two separate settings with 3 weeks interval by two radiologists. The radiologists also evaluated the presence of image artifacts (motion, flow, chemical shift, Gibbs ringing). To evaluate the size of the cyst, the two radiologists compared the two techniques (conventional and BLADE) by assessing the extent of the divergence in the measurements of the cysts. Results: Regarding the extent of the cyst size, BLADE measurements were found to be more reliable than the conventional ones with the differences being statistically significant (p<0.01). The qualitative measurements indicated that the T2 FLAIR BLADE sequences were superior to the conventional T2 FLAIR with statistically significant differences (p<0.001) in the following characteristics: 1) overall image quality, 2) CSF nulling; 3) contrast at the pathology and its surrounding; 4) limits of the pathology; 5) motion artifacts; 6) flow artifacts; 7) chemical shift artifacts and 8) Gibbs ringing artifacts. Conclusion: BLADE sequence was found to decrease both flow artifacts in the temporal lobes and motion artifacts from the orbits and it is proposed for clinical use.

  9. Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution.

    Directory of Open Access Journals (Sweden)

    Sara Imari Walker

    Full Text Available Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even earlier stage of chemical evolution, when polymer sequence diversity was generated and sustained before, and during, the onset of functional selection. The model includes regular environmental cycles (e.g. hydration-dehydration cycles that drive polymers between times of replication and functional activity, which coincide with times of different monomer and polymer diffusivity. Template-directed replication of informational polymers, which takes place during the dehydration stage of each cycle, is considered to be sequence-independent. New sequences are generated by spontaneous polymer formation, and all sequences compete for a finite monomer resource that is recycled via reversible polymerization. Kinetic Monte Carlo simulations demonstrate that this proposed prebiotic scenario provides a robust mechanism for the exploration of sequence space. Introduction of a polymer sequence with monomer synthetase activity illustrates that functional sequences can become established in a preexisting pool of otherwise non-functional sequences. Functional selection does not dominate system dynamics and sequence diversity remains high, permitting the emergence and spread of more than one functional sequence. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for

  10. Repdigits in k-Lucas sequences

    Indian Academy of Sciences (India)

    57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence ( L n ( 2 ) ) n . In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences ...

  11. An analysis of sequence alignment: heuristic algorithms.

    Science.gov (United States)

    Bucak, I Ö; Uslan, V

    2010-01-01

    Sequence alignment becomes challenging with an increase in size and number of sequences. Finding optimal or near optimal solutions for sequence alignment is one of the most important operations in bioinformatics. This study aims to survey heuristics applied for the sequence alignment problem summarized in a time line.

  12. Application of Quaternion in improving the quality of global sequence alignment scores for an ambiguous sequence target in Streptococcus pneumoniae DNA

    Science.gov (United States)

    Lestari, D.; Bustamam, A.; Novianti, T.; Ardaneswari, G.

    2017-07-01

    DNA sequence can be defined as a succession of letters, representing the order of nucleotides within DNA, using a permutation of four DNA base codes including adenine (A), guanine (G), cytosine (C), and thymine (T). The precise code of the sequences is determined using DNA sequencing methods and technologies, which have been developed since the 1970s and currently become highly developed, advanced and highly throughput sequencing technologies. So far, DNA sequencing has greatly accelerated biological and medical research and discovery. However, in some cases DNA sequencing could produce any ambiguous and not clear enough sequencing results that make them quite difficult to be determined whether these codes are A, T, G, or C. To solve these problems, in this study we can introduce other representation of DNA codes namely Quaternion Q = (PA, PT, PG, PC), where PA, PT, PG, PC are the probability of A, T, G, C bases that could appear in Q and PA + PT + PG + PC = 1. Furthermore, using Quaternion representations we are able to construct the improved scoring matrix for global sequence alignment processes, by applying a dot product method. Moreover, this scoring matrix produces better and higher quality of the match and mismatch score between two DNA base codes. In implementation, we applied the Needleman-Wunsch global sequence alignment algorithm using Octave, to analyze our target sequence which contains some ambiguous sequence data. The subject sequences are the DNA sequences of Streptococcus pneumoniae families obtained from the Genebank, meanwhile the target DNA sequence are received from our collaborator database. As the results we found the Quaternion representations improve the quality of the sequence alignment score and we can conclude that DNA sequence target has maximum similarity with Streptococcus pneumoniae.

  13. Plantagora: modeling whole genome sequencing and assembly of plant genomes.

    Directory of Open Access Journals (Sweden)

    Roger Barthelson

    Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

  14. Examination of equine glandular stomach lesions for bacteria, including Helicobacter spp by fluorescence in situ hybridisation

    DEFF Research Database (Denmark)

    husted, Louise; Jensen, Tim Kåre; Olsen, Susanne N.

    2010-01-01

    by cloning and sequencing. Mucosal lesions were found in 36/63 stomachs and included hyperplastic rugae, polypoid structures and focal erosions. None of the samples were tested positive for urease activity or for FISH using the Helicobacter genus specific probe. In samples of lesions, as well as normal...

  15. REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

    Directory of Open Access Journals (Sweden)

    Guy Leonard

    2009-01-01

    Full Text Available The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment fi le, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree fi les (with a user-defined combination of species name and/or database accession number. Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file and generation of species and accession number lists for use in supplementary materials or figure legends.

  16. REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

    Directory of Open Access Journals (Sweden)

    Guy Leonard

    2009-05-01

    Full Text Available The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment fi le, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree fi les (with a user-defined combination of species name and/or database accession number. Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file and generation of species and accession number lists for use in supplementary materials or figure legends.

  17. eShadow: A tool for comparing closely related sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ovcharenko, Ivan; Boffelli, Dario; Loots, Gabriela G.

    2004-01-15

    Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing, has been pioneered for predicting functional elements in the human genome through the analysis of multiple primate sequence alignments. We have expanded this theoretical approach to create a computational tool, eShadow, for the identification of elements under selective pressure in multiple sequence alignments of closely related genomes, such as in comparisons of human to primate or mouse to rat DNA. This tool integrates two different statistical methods and allows for the dynamic visualization of the resulting conservation profile. eShadow also includes a versatile optimization module capable of training the underlying Hidden Markov Model to differentially predict functional sequences. This module grants the tool high flexibility in the analysis of multiple sequence alignments and in comparing sequences with different divergence rates. Here, we describe the eShadow comparative tool and its potential uses for analyzing both multiple nucleotide and protein alignments to predict putative functional elements. The eShadow tool is publicly available at http://eshadow.dcode.org/

  18. Non-parametric algorithm to isolate chunks in response sequences

    Directory of Open Access Journals (Sweden)

    Andrea Alamia

    2016-09-01

    Full Text Available Chunking consists in grouping items of a sequence into small clusters, named chunks, with the assumed goal of lessening working memory load. Despite extensive research, the current methods used to detect chunks, and to identify different chunking strategies, remain discordant and difficult to implement. Here, we propose a simple and reliable method to identify chunks in a sequence and to determine their stability across blocks.This algorithm is based on a ranking method and its major novelty is that it provides concomitantly both the features of individual chunk in a given sequence, and an overall index that quantifies the chunking pattern consistency across sequences. The analysis of simulated data confirmed the validity of our method in different conditions of noise, chunk lengths and chunk numbers; moreover, we found that this algorithm was particularly efficient in the noise range observed in real data, provided that at least 4 sequence repetitions were included in each experimental block. Furthermore, we applied this algorithm to actual reaction time series gathered from 3 published experiments and were able to confirm the findings obtained in the original reports. In conclusion, this novel algorithm is easy to implement, is robust to outliers and provides concurrent and reliable estimation of chunk position and chunking dynamics, making it useful to study both sequence-specific and general chunking effects.The algorithm is available at: https://github.com/artipago/Non-parametric-algorithm-to-isolate-chunks-in-response-sequences

  19. Unveiling Mycoplasma hyopneumoniae Promoters: Sequence Definition and Genomic Distribution

    Science.gov (United States)

    Weber, Shana de Souto; Sant'Anna, Fernando Hayashi; Schrank, Irene Silveira

    2012-01-01

    Several Mycoplasma species have had their genome completely sequenced, including four strains of the swine pathogen Mycoplasma hyopneumoniae. Nevertheless, little is known about the nucleotide sequences that control transcriptional initiation in these microorganisms. Therefore, with the objective of investigating the promoter sequences of M. hyopneumoniae, 23 transcriptional start sites (TSSs) of distinct genes were mapped. A pattern that resembles the σ70 promoter −10 element was found upstream of the TSSs. However, no −35 element was distinguished. Instead, an AT-rich periodic signal was identified. About half of the experimentally defined promoters contained the motif 5′-TRTGn-3′, which was identical to the −16 element usually found in Gram-positive bacteria. The defined promoters were utilized to build position-specific scoring matrices in order to scan putative promoters upstream of all coding sequences (CDSs) in the M. hyopneumoniae genome. Two hundred and one signals were found associated with 169 CDSs. Most of these sequences were located within 100 nucleotides of the start codons. This study has shown that the number of promoter-like sequences in the M. hyopneumoniae genome is more frequent than expected by chance, indicating that most of the sequences detected are probably biologically functional. PMID:22334569

  20. Rapid multi-locus sequence typing using microfluidic biochips.

    Directory of Open Access Journals (Sweden)

    Timothy D Read

    2010-05-01

    Full Text Available Multiple locus sequence typing (MLST has become a central genotyping strategy for analysis of bacterial populations. The scheme involves de novo sequencing of 6-8 housekeeping loci to assign unique sequence types. In this work we adapted MLST to a rapid microfluidics platform in order to enhance speed and reduce laboratory labor time.Using two integrated microfluidic devices, DNA was purified from 100 Bacillus cereus soil isolates, used as a template for multiplex amplification of 7 loci and sequenced on forward and reverse strands. The time on instrument from loading genomic DNA to generation of electropherograms was only 1.5 hours. We obtained full-length sequence of all seven MLST alleles from 84 representing 46 different Sequence Types. At least one allele could be sequenced from a further 15 strains. The nucleotide diversity of B. cereus isolated in this study from one location in Rockville, Maryland (0.04 substitutions per site was found to be as great as the global collection of isolates.Biogeographical investigation of pathogens is only one of a panoply of possible applications of microfluidics based MLST; others include microbiologic forensics, biothreat identification, and rapid characterization of human clinical samples.

  1. Ionic liquids, electrolyte solutions including the ionic liquids, and energy storage devices including the ionic liquids

    Science.gov (United States)

    Gering, Kevin L.; Harrup, Mason K.; Rollins, Harry W.

    2015-12-08

    An ionic liquid including a phosphazene compound that has a plurality of phosphorus-nitrogen units and at least one pendant group bonded to each phosphorus atom of the plurality of phosphorus-nitrogen units. One pendant group of the at least one pendant group comprises a positively charged pendant group. Additional embodiments of ionic liquids are disclosed, as are electrolyte solutions and energy storage devices including the embodiments of the ionic liquid.

  2. Protein sequence analysis using Hewlett-Packard biphasic sequencing cartridges in an applied biosystems 473A protein sequencer.

    Science.gov (United States)

    Tang, S; Mozdzanowski, J; Anumula, K R

    1999-01-01

    Protein sequence analysis using an adsorptive biphasic sequencing cartridge, a set of two coupled columns introduced by Hewlett-Packard for protein sequencing by Edman degradation, in an Applied Biosystems 473A protein sequencer has been demonstrated. Samples containing salts, detergents, excipients, etc. (e.g., formulated protein drugs) can be easily analyzed using the ABI sequencer. Simple modifications to the ABI sequencer to accommodate the cartridge extend its utility in the analysis of difficult samples. The ABI sequencer solvents and reagents were compatible with the HP cartridge for sequencing. Sequence information up to ten residues can be easily generated by this nonoptimized procedure, and it is sufficient for identifying proteins by database search and for preparing a DNA probe for cloning novel proteins.

  3. Sequencing the exposome: A call to action

    Directory of Open Access Journals (Sweden)

    Dean P. Jones

    2016-01-01

    Full Text Available The exposome is a complement to the genome that includes non-genetic causes of disease. Multiple definitions are available, with salient points being global inclusion of exposures and behaviors, and cumulative integration of associated biologic responses. As such, the concept is both refreshingly simple and dauntingly complex. This article reviews high-resolution metabolomics (HRM as an affordable approach to routinely analyze samples for a broad spectrum of environmental chemicals and biologic responses. HRM has been successfully used in multiple exposome research paradigms and is suitable to implement in a prototype universal exposure surveillance system. Development of such a structure for systematic monitoring of environmental exposures is an important step toward sequencing the exposome because it builds upon successes of exposure science, naturally connects external exposure to body burden and partitions the exposome into workable components. Practical results would be repositories of quantitative data on chemicals according to geography and biology. This would support new opportunities for environmental health analysis and predictive modeling. Complementary approaches to hasten development of exposome theory and associated biologic response networks could include experimental studies with model systems, analysis of archival samples from longitudinal studies with outcome data and study of relatively short-lived animals, such as household pets (dogs and cats and non-human primates (common marmoset. International investment and cooperation to sequence the human exposome will advance scientific knowledge and also provide an important foundation to control adverse environmental exposures to sustain healthy living spaces and improve prediction and management of disease.

  4. Automation tools for control systems a network based sequencer

    International Nuclear Information System (INIS)

    Clout, P.; Geib, M.; Westervelt, R.

    1990-01-01

    This paper reports on development of a sequencer for control systems which works in conjunction with its realtime, distributed Vsystem database. Vsystem is a network-based data acquisition, monitoring and control system which has been applied successfully to many different types of projects. The network-based sequencer allows a user to simple define a thread of execution in any supported computer on the network. The scrip defining a sequence has a simple syntax designed for non-programmers, with facilities for selectively abbreviating the channel names for easy reference. The semantics of the script contains most of the familiar capabilities of conventional programming languages, including standard stream I/O and the ability to start other processes with parameters passed. The scrip is compiled to threaded code for execution efficiency. The implementation will be described in some detail and examples will be given of applications for which the sequencer has been used

  5. Deep Sequencing Analysis of Nucleolar Small RNAs: Bioinformatics.

    Science.gov (United States)

    Bai, Baoyan; Laiho, Marikki

    2016-01-01

    Small RNAs (size 20-30 nt) of various types have been actively investigated in recent years, and their subcellular compartmentalization and relative concentrations are likely to be of importance to their cellular and physiological functions. Comprehensive data on this subset of the transcriptome can only be obtained by application of high-throughput sequencing, which yields data that are inherently complex and multidimensional, as sequence composition, length, and abundance will all inform to the small RNA function. Subsequent data analysis, hypothesis testing, and presentation/visualization of the results are correspondingly challenging. We have constructed small RNA libraries derived from different cellular compartments, including the nucleolus, and asked whether small RNAs exist in the nucleolus and whether they are distinct from cytoplasmic and nuclear small RNAs, the miRNAs. Here, we present a workflow for analysis of small RNA sequencing data generated by the Ion Torrent PGM sequencer from samples derived from different cellular compartments.

  6. An improved high throughput sequencing method for studying oomycete communities

    DEFF Research Database (Denmark)

    Sapkota, Rumakanta; Nicolaisen, Mogens

    2015-01-01

    Culture-independent studies using next generation sequencing have revolutionizedmicrobial ecology, however, oomycete ecology in soils is severely lagging behind. The aimof this study was to improve and validate standard techniques for using high throughput sequencing as a tool for studying oomycete...... agricultural fields in Denmark, and 11 samples from carrot tissue with symptoms of Pythium infection. Sequence data from the Pythium and Phytophthora mock communities showed that our strategy successfully detected all included species. Taxonomic assignments of OTUs from 26 soil sample showed that 95...... the usefulness of the method not only in soil DNA but also in a plant DNA background. In conclusion, we demonstrate a successful approach for pyrosequencing of oomycete communities using ITS1 as the barcode sequence with well-known primers for oomycete DNA amplification....

  7. Nonparametric Inference for Periodic Sequences

    KAUST Repository

    Sun, Ying

    2012-02-01

    This article proposes a nonparametric method for estimating the period and values of a periodic sequence when the data are evenly spaced in time. The period is estimated by a "leave-out-one-cycle" version of cross-validation (CV) and complements the periodogram, a widely used tool for period estimation. The CV method is computationally simple and implicitly penalizes multiples of the smallest period, leading to a "virtually" consistent estimator of integer periods. This estimator is investigated both theoretically and by simulation.We also propose a nonparametric test of the null hypothesis that the data have constantmean against the alternative that the sequence of means is periodic. Finally, our methodology is demonstrated on three well-known time series: the sunspots and lynx trapping data, and the El Niño series of sea surface temperatures. © 2012 American Statistical Association and the American Society for Quality.

  8. Apparatus for improved DNA sequencing

    Science.gov (United States)

    Douthart, Richard J.; Crowell, Shannon L.

    1996-01-01

    This invention is a means for the rapid sequencing of DNA samples. More specifically, it consists of a new design direct blotting electrophoresis unit. The DNA sequence is deposited on a membrane attached to a rotating drum. Initial data compaction is facilitated by the use of a machined multi-channeled plate called a ribbon channel plate. Each channel is an isolated mini gel system much like a gel filled capillary. The system as a whole, however, is in a slab gel like format with the advantages of uniformity and easy reusability. The system can be used in different embodiments. The drum system is unique in that after deposition the drum rotates the deposited DNA into a large non-buffer open space where processing and detection can occur. The drum can also be removed in toto to special workstations for downstream processing, multiplexing and detection.

  9. Cassini Mission Sequence Subsystem (MSS)

    Science.gov (United States)

    Alland, Robert

    2011-01-01

    This paper describes my work with the Cassini Mission Sequence Subsystem (MSS) team during the summer of 2011. It gives some background on the motivation for this project and describes the expected benefit to the Cassini program. It then introduces the two tasks that I worked on - an automatic system auditing tool and a series of corrections to the Cassini Sequence Generator (SEQ_GEN) - and the specific objectives these tasks were to accomplish. Next, it details the approach I took to meet these objectives and the results of this approach, followed by a discussion of how the outcome of the project compares with my initial expectations. The paper concludes with a summary of my experience working on this project, lists what the next steps are, and acknowledges the help of my Cassini colleagues.

  10. Sequence correlations shape protein promiscuity

    Science.gov (United States)

    Lukatsky, David B.; Afek, Ariel; Shakhnovich, Eugene I.

    2011-08-01

    We predict analytically that diagonal correlations of amino acid positions within protein sequences statistically enhance protein propensity for nonspecific binding. We use the term "promiscuity" to describe such nonspecific binding. Diagonal correlations represent statistically significant repeats of sequence patterns where amino acids of the same type are clustered together. The predicted effect is qualitatively robust with respect to the form of the microscopic interaction potentials and the average amino acid composition. Our analytical results provide an explanation for the enhanced diagonal correlations observed in hubs of eukaryotic organismal proteomes [J. Mol. Biol. 409, 439 (2011)], 10.1016/j.jmb.2011.03.056. We suggest experiments that will allow direct testing of the predicted effect.

  11. Replacement collision sequences in metals

    International Nuclear Information System (INIS)

    Blewitt, T.H.; Kirk, M.A.; Scott, T.L.

    1975-10-01

    The concept of radiation-induced defects traveling large distances by focussed collision sequences (focusons) without thermal activation has important consequences in radiation effect studies. The focussed collision sequences are of two types: (1) ''Silsbee focussing'' or momentum focussing which can cause defect pairs to form large distances from the primary knock-on and (2) focussed replacement collisions also called ''dynamic crowdions'' where mass transport causes a large separation between the vacancy and its interstitial. Direct experimental evidence for focussed collision sequences is in short supply and conflicting. The sputtering patterns associated with close packed crystalline directions from the backscattering of charged particles seemed to substantiate long-range focussed collisions until it was pointed out that collision chains need not be long to yield such patterns. More recently, transmission sputtering has been used with conflicting results. Ecker et al. found no evidence for focusons greater than 17 atom distances whereas preliminary results of Siedman et al. suggest several hundred atom distances. Keil and co-workers found evidence for replacement collision sequences of 100 atom distances by stereo electron microscopy of interstitial agglomerates interjected by low energy heavy ion bombardment. Experiments by Kirk et al. and Becker and co-workers on ordered alloys, are only sensitive to dynamic crowdions. Kirk and co-workers result on the changes in magnetic properties of Ni 3 Mn induced by thermal neutron bombardment strongly support long range focusons (greater than 30 atom distances) whereas Wollenberger found no evidence for focusons with 1 and 3 MeV electron irradiation. Theoretical treatments of Liebfried suggest a maximum length of 30 atom distances whereas Holmes' modified treatment suggests less than 10 atom distances. (10 fig, 23 references)

  12. Channel plate for DNA sequencing

    Science.gov (United States)

    Douthart, Richard J.; Crowell, Shannon L.

    1998-01-01

    This invention is a channel plate that facilitates data compaction in DNA sequencing. The channel plate has a length, a width and a thickness, and further has a plurality of channels that are parallel. Each channel has a depth partially through the thickness of the channel plate. Additionally an interface edge permits electrical communication across an interface through a buffer to a deposition membrane surface.

  13. The complete sequence of human chromosome 5

    Energy Technology Data Exchange (ETDEWEB)

    Schmutz, Jeremy; Martin, Joel; Terry, Astrid; Couronne, Olivier; Grimwood, Jane; Lowry, State; Gordon, Laurie A.; Scott, Duncan; Xie, Gary; Huang, Wayne; Hellsten, Uffe; Tran-Gyamfi, Mary; She, Xinwei; Prabhakar, Shyam; Aerts, Andrea; Altherr, Michael; Bajorek, Eva; Black, Stacey; Branscomb, Elbert; Caoile, Chenier; Challacombe, Jean F.; Chan, Yee Man; Denys, Mirian; Detter, Chris; Escobar, Julio; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstenin, David; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Israni, Sanjay; Jett, Jamie; Kadner, Kristen; Kimbal, Heather; Kobayashi, Arthur; Lopez, Frederick; Lou, Yunian; Martinez, Diego; Medina, Catherine; Morgan, Jenna; Nandkeshwar, Richard; Noonan, James P.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Priest, James; Ramirez, Lucia; Rash, Sam; Retterer, James; Rodriguez, Alex; Rogers, Stephanie; Salamov, Asaf; Salazar, Angelica; Thayer, Nina; Tice, Hope; Tsai, Ming; Ustaszewska, Anna; Vo, Nu; Wheeler, Jeremy; Wu, Kevin; Yang, Joan; Dickson, Mark; Cheng, Jan-Fang; Eichler, Evan E.; Olsen, Anne; Pennacchio, Len A.; Rokhsar, Daniel S.; Richardson, Paul; Lucas, Susan M.; Myers, Richard M.; Rubin, Edward M.

    2004-04-15

    Chromosome 5 is one of the largest human chromosomes yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding and syntenic conservation with non-mammalian vertebrates, suggesting they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-encoding genes including the protocadherin and interleukin gene families and the first complete versions of each of the large chromosome 5 specific internal duplications. These duplications are very recent evolutionary events and play a likely mechanistic role, since deletions of these regions are the cause of debilitating disorders including spinal muscular atrophy (SMA).

  14. Entropic fluctuations in DNA sequences

    Science.gov (United States)

    Thanos, Dimitrios; Li, Wentian; Provata, Astero

    2018-03-01

    The Local Shannon Entropy (LSE) in blocks is used as a complexity measure to study the information fluctuations along DNA sequences. The LSE of a DNA block maps the local base arrangement information to a single numerical value. It is shown that despite this reduction of information, LSE allows to extract meaningful information related to the detection of repetitive sequences in whole chromosomes and is useful in finding evolutionary differences between organisms. More specifically, large regions of tandem repeats, such as centromeres, can be detected based on their low LSE fluctuations along the chromosome. Furthermore, an empirical investigation of the appropriate block sizes is provided and the relationship of LSE properties with the structure of the underlying repetitive units is revealed by using both computational and mathematical methods. Sequence similarity between the genomic DNA of closely related species also leads to similar LSE values at the orthologous regions. As an application, the LSE covariance function is used to measure the evolutionary distance between several primate genomes.

  15. Development of expressed sequence tag and expressed sequence tag-simple sequence repeat marker resources for Musa acuminata.

    Science.gov (United States)

    Passos, Marco A N; de Oliveira Cruz, Viviane; Emediato, Flavia L; de Camargo Teixeira, Cristiane; Souza, Manoel T; Matsumoto, Takashi; Rennó Azevedo, Vânia C; Ferreira, Claudia F; Amorim, Edson P; de Alencar Figueiredo, Lucio Flavio; Martins, Natalia F; de Jesus Barbosa Cavalcante, Maria; Baurens, Franc-Christophe; da Silva, Orzenil Bonfim; Pappas, Georgios J; Pignolet, Luc; Abadie, Catherine; Ciampi, Ana Y; Piffanelli, Pietro; Miller, Robert N G

    2012-01-01

    Banana (Musa acuminata) is a crop contributing to global food security. Many varieties lack resistance to biotic stresses, due to sterility and narrow genetic background. The objective of this study was to develop an expressed sequence tag (EST) database of transcripts expressed during compatible and incompatible banana-Mycosphaerella fijiensis (Mf) interactions. Black leaf streak disease (BLSD), caused by Mf, is a destructive disease of banana. Microsatellite markers were developed as a resource for crop improvement. cDNA libraries were constructed from in vitro-infected leaves from BLSD-resistant M. acuminata ssp. burmaniccoides Calcutta 4 (MAC4) and susceptible M. acuminata cv. Cavendish Grande Naine (MACV). Clones were 5'-end Sanger sequenced, ESTs assembled with TGICL and unigenes annotated using BLAST, Blast2GO and InterProScan. Mreps was used to screen for simple sequence repeats (SSRs), with markers evaluated for polymorphism using 20 diploid (AA) M. acuminata accessions contrasting in resistance to Mycosphaerella leaf spot diseases. A total of 9333 high-quality ESTs were obtained for MAC4 and 3964 for MACV, which assembled into 3995 unigenes. Of these, 2592 displayed homology to genes encoding proteins with known or putative function, and 266 to genes encoding proteins with unknown function. Gene ontology (GO) classification identified 543 GO terms, 2300 unigenes were assigned to EuKaryotic orthologous group categories and 312 mapped to Kyoto Encyclopedia of Genes and Genomes pathways. A total of 624 SSR loci were identified, with trinucleotide repeat motifs the most abundant in MAC4 (54.1 %) and MACV (57.6 %). Polymorphism across M. acuminata accessions was observed with 75 markers. Alleles per polymorphic locus ranged from 2 to 8, totalling 289. The polymorphism information content ranged from 0.08 to 0.81. This EST collection offers a resource for studying functional genes, including transcripts expressed in banana-Mf interactions. Markers are

  16. Now and next-generation sequencing techniques: future of sequence analysis using cloud computing.

    Science.gov (United States)

    Thakur, Radhe Shyam; Bandopadhyay, Rajib; Chaudhary, Bratati; Chatterjee, Sourav

    2012-01-01

    Advances in the field of sequencing techniques have resulted in the greatly accelerated production of huge sequence datasets. This presents immediate challenges in database maintenance at datacenters. It provides additional computational challenges in data mining and sequence analysis. Together these represent a significant overburden on traditional stand-alone computer resources, and to reach effective conclusions quickly and efficiently, the virtualization of the resources and computation on a pay-as-you-go concept (together termed "cloud computing") has recently appeared. The collective resources of the datacenter, including both hardware and software, can be available publicly, being then termed a public cloud, the resources being provided in a virtual mode to the clients who pay according to the resources they employ. Examples of public companies providing these resources include Amazon, Google, and Joyent. The computational workload is shifted to the provider, which also implements required hardware and software upgrades over time. A virtual environment is created in the cloud corresponding to the computational and data storage needs of the user via the internet. The task is then performed, the results transmitted to the user, and the environment finally deleted after all tasks are completed. In this discussion, we focus on the basics of cloud computing, and go on to analyze the prerequisites and overall working of clouds. Finally, the applications of cloud computing in biological systems, particularly in comparative genomics, genome informatics, and SNP detection are discussed with reference to traditional workflows.

  17. Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

    Energy Technology Data Exchange (ETDEWEB)

    Morgan, Jenna L.; Darling, Aaron E.; Eisen, Jonathan A.

    2009-12-01

    Background: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. Methodology/Principal Findings: We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. Conclusions/Significance: We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with

  18. Cyanobacteria gene and protein sequences in diurnal oscillation metabolic processes

    Science.gov (United States)

    Tremberger, George, Jr.; Holden, T.; Cheung, E.; Dehipawala, S.; Gadura, N.; Golebiewska, U.; Valentin, K.; Smulczeski, M.; Satizabal, W.; Schneider, P.; Lieberman, D.; Cheung, T.

    2010-09-01

    Daytime photosynthesis and nighttime nitrogen fixation metabolic processes have been reported in the bacterium, Cyanothece 51142. The organism's auto-fluorescence with 532 nm excitation would place cyanobacteria at the forefront in the remote sensing of microbial activity in astrobiology. The sensitivity of nitrogenase to oxygen was studied in terms of sequence nucleotide fluctuation. A nucleotide sequence fractal dimension can be calculated from a numerical series consisting of the atomic numbers of each nucleotide. The fractal dimension and Shannon entropy form a two-dimensional measure that is useful in assessing evolutionary pressures. The studied sequences include nitrogenase iron protein NifH, nitrogenase molybdenum-iron protein alpha chain NifD and beta chain NifK. The photosynthesis-lacking UCYN-A cyanobacterium as reported recently in the journal, Nature, was observed to have the lowest entropy with relatively high fractal dimension values in the studied NifH, NifD and NifH sequences. The fractal dimension of NifH sequences correlates with the NifD sequence values with an R-square of 0.91 (N = 8). The Shannon mononucleotide entropy of NifD sequences correlates with the NifK sequence values with an R-square value of 0.92 (N = 8). The observed strong correlation suggests the presence of gradual evolutionary pressure among the studied cyanobacteria, and throws light on the reported paradox in evolution for the case of UCYN-A. The results show that diurnal oscillation metabolic processes in cyanobacteria (including the photosynthesis-deficient case) are not associated with extraordinary evolutionary pressures and thus are processes consistent with putative astrobiological organisms.

  19. Specialized microbial databases for inductive exploration of microbial genome sequences

    Directory of Open Access Journals (Sweden)

    Cabau Cédric

    2005-02-01

    Full Text Available Abstract Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. Methods The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. Results Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore http://bioinfo.hku.hk/genochore.html, a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. Conclusion This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis associated to related organisms for comparison.

  20. Deep sequencing extends the diversity of human papillomaviruses in human skin.

    Science.gov (United States)

    Bzhalava, Davit; Mühr, Laila Sara Arroyo; Lagheden, Camilla; Ekström, Johanna; Forslund, Ola; Dillner, Joakim; Hultin, Emilie

    2014-07-24

    Most viruses in human skin are known to be human papillomaviruses (HPVs). Previous sequencing of skin samples has identified 273 different cutaneous HPV types, including 47 previously unknown types. In the present study, we wished to extend prior studies using deeper sequencing. This deeper sequencing without prior PCR of a pool of 142 whole genome amplified skin lesions identified 23 known HPV types, 3 novel putative HPV types and 4 non-HPV viruses. The complete sequence was obtained for one of the known putative types and almost the complete sequence was obtained for one of the novel putative types. In addition, sequencing of amplimers from HPV consensus PCR of 326 skin lesions detected 385 different HPV types, including 226 previously unknown putative types. In conclusion, metagenomic deep sequencing of human skin samples identified no less than 396 different HPV types in human skin, out of which 229 putative HPV types were previously unknown.

  1. Catalyst support structure, catalyst including the structure, reactor including a catalyst, and methods of forming same

    Science.gov (United States)

    Van Norman, Staci A.; Aston, Victoria J.; Weimer, Alan W.

    2017-05-09

    Structures, catalysts, and reactors suitable for use for a variety of applications, including gas-to-liquid and coal-to-liquid processes and methods of forming the structures, catalysts, and reactors are disclosed. The catalyst material can be deposited onto an inner wall of a microtubular reactor and/or onto porous tungsten support structures using atomic layer deposition techniques.

  2. Application of deep sequence technology in hepatology.

    Science.gov (United States)

    Ninomiya, Masashi; Ueno, Yoshiyuki; Shimosegawa, Tooru

    2014-02-01

    Deep sequencing technologies are currently cutting edge, and are opening fascinating opportunities in biomedicine, producing over 100-times more data compared to the conventional capillary sequencers based on the Sanger method. Next-generation sequencing (NGS) is now generally defined as the sequencing technology that, by employing parallel sequencing processes, producing thousands or millions of sequence reads simultaneously. Since the GS20 was released as the first NGS sequencer on the market by 454 Life Sciences, the competition in the development of the new sequencers has become intense. In this review, we describe the current deep sequencing systems and discuss the application of advanced technologies in the field of hepatology. © 2013 The Japan Society of Hepatology.

  3. Complete Genome Sequence of Escherichia coli Strain WG5

    DEFF Research Database (Denmark)

    Imamovic, Lejla; Misiakou, Maria-Anna; van der Helm, Eric

    2018-01-01

    Escherichia coli strain WG5 is a widely used host for phage detection, including somatic coliphages employed as standard ISO method 10705-1 (2000). Here, we present the complete genome sequence of a commercial E. coli WG5 strain.......Escherichia coli strain WG5 is a widely used host for phage detection, including somatic coliphages employed as standard ISO method 10705-1 (2000). Here, we present the complete genome sequence of a commercial E. coli WG5 strain....

  4. Construction of an integrated database to support genomic sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, W.; Overbeek, R.

    1994-11-01

    The central goal of this project is to develop an integrated database to support comparative analysis of genomes including DNA sequence data, protein sequence data, gene expression data and metabolism data. In developing the logic-based system GenoBase, a broader integration of available data was achieved due to assistance from collaborators. Current goals are to easily include new forms of data as they become available and to easily navigate through the ensemble of objects described within the database. This report comments on progress made in these areas.

  5. Diagnostic accuracy of unenhanced, contrast-enhanced perfusion and angiographic MRI sequences for pulmonary embolism diagnosis: results of independent sequence readings

    Energy Technology Data Exchange (ETDEWEB)

    Revel, Marie Pierre [Hopital Europeen Georges Pompidou, APHP, Departments of Radiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); Hotel-Dieu, Service de Radiologie, Paris (France); Sanchez, Olivier; Meyer, Guy [Hopital Europeen Georges Pompidou, APHP, Respiratory and intensive care and, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); INSERM Unite 765, Paris (France); Lefort, Catherine; Couchon, Sophie; Hernigou, Anne; Frija, Guy [Hopital Europeen Georges Pompidou, APHP, Departments of Radiology, Paris (France); Niarra, Ralph [Hopital Europeen Georges Pompidou, APHP, Clinical Epidemiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); Chatellier, Gilles [Hopital Europeen Georges Pompidou, APHP, Clinical Epidemiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); INSERM CIC-EC E4, Paris (France)

    2013-09-15

    To independently evaluate unenhanced, contrast-enhanced perfusion and angiographic MR sequences for pulmonary embolism (PE) diagnosis. Prospective investigation, including 274 patients who underwent perfusion, unenhanced 2D steady-state-free-precession (SSFP) and contrast-enhanced 3D angiographic MR sequences on a 1.5-T unit, in addition to CTA (CT angiography). Two independent readers evaluated each sequence independently in random order. Sensitivity, specificity, predictive values and inter-reader agreement were calculated for each sequence, excluding sequences judged inconclusive. Sensitivity was also calculated according to PE location. Contrast-enhanced angiographic sequences showed the highest sensitivity (82.9 and 89.7 %, reader 1 and reader 2, respectively), specificity (98.5 and 100 %) and agreement (kappa value 0.77). Unenhanced angiographic sequences, although less sensitive overall (68.7 and 76.4 %), were sensitive for the detection of proximal PE (92.7 and 100 %) and showed high specificity (96.1 and 99.1 %) and good agreement (kappa value 0.62). Perfusion sequences showed lower sensitivity (75.0 and 79.3 %), specificity (84.8 and 89.7 %) and agreement (kappa value 0.51), and a negative predictive value of 84.8 % at best. Compared with contrast-enhanced angiographic sequences, unenhanced sequences demonstrate lower sensitivity, except for proximal PE, but high specificity and agreement. The negative predictive value of perfusion sequences was insufficient to safely rule out PE. (orig.)

  6. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    OpenAIRE

    Natanaelsson, Christian; Oskarsson, Mattias CR; Angleby, Helen; Lundeberg, Joakim; Kirkness, Ewen; Savolainen, Peter

    2006-01-01

    Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromo...

  7. The Biomolecule Sequencer Project: Nanopore Sequencing as a Dual-Use Tool for Crew Health and Astrobiology Investigations

    Science.gov (United States)

    John, K. K.; Botkin, D. S.; Burton, A. S.; Castro-Wallace, S. L.; Chaput, J. D.; Dworkin, J. P.; Lehman, N.; Lupisella, M. L.; Mason, C. E.; Smith, D. J.; hide

    2016-01-01

    Human missions to Mars will fundamentally transform how the planet is explored, enabling new scientific discoveries through more sophisticated sample acquisition and processing than can currently be implemented in robotic exploration. The presence of humans also poses new challenges, including ensuring astronaut safety and health and monitoring contamination. Because the capability to transfer materials to Earth will be extremely limited, there is a strong need for in situ diagnostic capabilities. Nucleotide sequencing is a particularly powerful tool because it can be used to: (1) mitigate microbial risks to crew by allowing identification of microbes in water, in air, and on surfaces; (2) identify optimal treatment strategies for infections that arise in crew members; and (3) track how crew members, microbes, and mission-relevant organisms (e.g., farmed plants) respond to conditions on Mars through transcriptomic and genomic changes. Sequencing would also offer benefits for science investigations occurring on the surface of Mars by permitting identification of Earth-derived contamination in samples. If Mars contains indigenous life, and that life is based on nucleic acids or other closely related molecules, sequencing would serve as a critical tool for the characterization of those molecules. Therefore, spaceflight-compatible nucleic acid sequencing would be an important capability for both crew health and astrobiology exploration. Advances in sequencing technology on Earth have been driven largely by needs for higher throughput and read accuracy. Although some reduction in size has been achieved, nearly all commercially available sequencers are not compatible with spaceflight due to size, power, and operational requirements. Exceptions are nanopore-based sequencers that measure changes in current caused by DNA passing through pores; these devices are inherently much smaller and require significantly less power than sequencers using other detection methods

  8. NEW COOLING SEQUENCES FOR OLD WHITE DWARFS

    International Nuclear Information System (INIS)

    Renedo, I.; Althaus, L. G.; GarcIa-Berro, E.; Miller Bertolami, M. M.; Romero, A. D.; Corsico, A. H.; Rohrmann, R. D.

    2010-01-01

    We present full evolutionary calculations appropriate for the study of hydrogen-rich DA white dwarfs. This is done by evolving white dwarf progenitors from the zero-age main sequence, through the core hydrogen-burning phase, the helium-burning phase, and the thermally pulsing asymptotic giant branch phase to the white dwarf stage. Complete evolutionary sequences are computed for a wide range of stellar masses and for two different metallicities, Z = 0.01, which is representative of the solar neighborhood, and Z = 0.001, which is appropriate for the study of old stellar systems, like globular clusters. During the white dwarf cooling stage, we self-consistently compute the phase in which nuclear reactions are still important, the diffusive evolution of the elements in the outer layers and, finally, we also take into account all the relevant energy sources in the deep interior of the white dwarf, such as the release of latent heat and the release of gravitational energy due to carbon-oxygen phase separation upon crystallization. We also provide colors and magnitudes for these sequences, based on a new set of improved non-gray white dwarf model atmospheres, which include the most up-to-date physical inputs like the Lyα quasi-molecular opacity. The calculations are extended down to an effective temperature of 2500 K. Our calculations provide a homogeneous set of evolutionary cooling tracks appropriate for mass and age determinations of old DA white dwarfs and for white dwarf cosmochronology of the different Galactic populations.

  9. Mobius sequence--a Swedish multidiscipline study.

    Science.gov (United States)

    Strömland, Kerstin; Sjögreen, Lotta; Miller, Marilyn; Gillberg, Christopher; Wentz, Elisabet; Johansson, Maria; Nylén, Olle; Danielsson, Aina; Jacobsson, Catharina; Andersson, Jan; Fernell, Elisabeth

    2002-01-01

    Mobius sequence/syndrome is a rare disorder characterized by congenital palsy of the 6th and 7th cranial nerves. Other cranial nerves may be affected, skeletal and orofacial anomalies and mental retardation occur. The aims were to determine the frequency of associated clinical characteristics and to identify any pregnancy or environmental factors in patients with Mobius sequence. A prospective study of 25 Swedes with apparent involvement of the 6th and 7th cranial nerves was performed and 25 patients, 1 month to 55 years old, were examined. Obvious associated systemic anomalies observed included: limb malformations (10), Poland anomaly (2), hypodontia (7), microglossia (6), cleft palate (4), hearing impairment (5) and external ear malformation (1). Pronounced functional abnormalities were observed involving facial expression (16), speech (13), eating and swallowing (12) and difficulty in sucking in infancy (11). Six patients had an autistic syndrome, one an autistic-like condition, and mental retardation was found in all these patients. No common aetiological cause was found but their mothers' pregnancy histories revealed a history of benzodiazepines (1), bleeding during pregnancy (8), spontaneous abortion (7) and chorion villus sampling in the second month of pregnancy (1). In conclusion, many patients had multiple problems with eating and communication resulting from facial palsy, cleft palate and tongue anomalies. Autism and mental retardation was diagnosed in one-third of the patients. Awareness of the wide spectrum of manifestations in Mobius sequence will assist in identification of the associated malformations and functional problems that are often seen and result in better care of the children.

  10. Flexible taxonomic assignment of ambiguous sequencing reads

    Directory of Open Access Journals (Sweden)

    Jansson Jesper

    2011-01-01

    Full Text Available Abstract Background To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it. Results We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed. Conclusions The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results.

  11. The pig X and Y Chromosomes: structure, sequence, and evolution.

    Science.gov (United States)

    Skinner, Benjamin M; Sargent, Carole A; Churcher, Carol; Hunt, Toby; Herrero, Javier; Loveland, Jane E; Dunn, Matt; Louzada, Sandra; Fu, Beiyuan; Chow, William; Gilbert, James; Austin-Guest, Siobhan; Beal, Kathryn; Carvalho-Silva, Denise; Cheng, William; Gordon, Daria; Grafham, Darren; Hardy, Matt; Harley, Jo; Hauser, Heidi; Howden, Philip; Howe, Kerstin; Lachani, Kim; Ellis, Peter J I; Kelly, Daniel; Kerry, Giselle; Kerwin, James; Ng, Bee Ling; Threadgold, Glen; Wileman, Thomas; Wood, Jonathan M D; Yang, Fengtang; Harrow, Jen; Affara, Nabeel A; Tyler-Smith, Chris

    2016-01-01

    We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution. © 2016 Skinner et al.; Published by Cold Spring Harbor Laboratory Press.

  12. Exploring the relationship between sequence similarity and accurate phylogenetic trees.

    Science.gov (United States)

    Cantarel, Brandi L; Morrison, Hilary G; Pearson, William

    2006-11-01

    We have characterized the relationship between accurate phylogenetic reconstruction and sequence similarity, testing whether high levels of sequence similarity can consistently produce accurate evolutionary trees. We generated protein families with known phylogenies using a modified version of the PAML/EVOLVER program that produces insertions and deletions as well as substitutions. Protein families were evolved over a range of 100-400 point accepted mutations; at these distances 63% of the families shared significant sequence similarity. Protein families were evolved using balanced and unbalanced trees, with ancient or recent radiations. In families sharing statistically significant similarity, about 60% of multiple sequence alignments were 95% identical to true alignments. To compare recovered topologies with true topologies, we used a score that reflects the fraction of clades that were correctly clustered. As expected, the accuracy of the phylogenies was greatest in the least divergent families. About 88% of phylogenies clustered over 80% of clades in families that shared significant sequence similarity, using Bayesian, parsimony, distance, and maximum likelihood methods. However, for protein families with short ancient branches (ancient radiation), only 30% of the most divergent (but statistically significant) families produced accurate phylogenies, and only about 70% of the second most highly conserved families, with median expectation values better than 10(-60), produced accurate trees. These values represent upper bounds on expected tree accuracy for sequences with a simple divergence history; proteins from 700 Giardia families, with a similar range of sequence similarities but considerably more gaps, produced much less accurate trees. For our simulated insertions and deletions, correct multiple sequence alignments did not perform much better than those produced by T-COFFEE, and including sequences with expressed sequence tag-like sequencing errors did not

  13. Launch Lock Assemblies Including Axial Gap Amplification Devices and Spacecraft Isolation Systems Including the Same

    Science.gov (United States)

    Barber, Tim Daniel (Inventor); Hindle, Timothy (Inventor); Young, Ken (Inventor); Davis, Torey (Inventor)

    2014-01-01

    Embodiments of a launch lock assembly are provided, as are embodiments of a spacecraft isolation system including one or more launch lock assemblies. In one embodiment, the launch lock assembly includes first and second mount pieces, a releasable clamp device, and an axial gap amplification device. The releasable clamp device normally maintains the first and second mount pieces in clamped engagement; and, when actuated, releases the first and second mount pieces from clamped engagement to allow relative axial motion there between. The axial gap amplification device normally residing in a blocking position wherein the gap amplification device obstructs relative axial motion between the first and second mount pieces. The axial gap amplification device moves into a non-blocking position when the first and second mount pieces are released from clamped engagement to increase the range of axial motion between the first and second mount pieces.

  14. Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments

    OpenAIRE

    McCormick, Kevin P; Willmann, Matthew R; Meyers, Blake C

    2011-01-01

    Prior to the advent of new, deep sequencing methods, small RNA (sRNA) discovery was dependent on Sanger sequencing, which was time-consuming and limited knowledge to only the most abundant sRNA. The innovation of large-scale, next-generation sequencing has exponentially increased knowledge of the biology, diversity and abundance of sRNA populations. In this review, we discuss issues involved in the design of sRNA sequencing experiments, including choosing a sequencing platform, inherent biase...

  15. Recent applications of DNA sequencing technologies in food, nutrition and agriculture.

    Science.gov (United States)

    Liu, George E

    2011-09-01

    Next-generation DNA sequencing technologies are able to produce millions of short sequence reads in a highthroughput, cost-effective fashion. The emergence of these technologies has not only facilitated genome sequencing but also changed the landscape of life sciences. This review surveys their recent applications in food, nutrition and agriculture ranging from whole-genome sequencing and resequencing, RNA-seq and ChIP-seq, structural, functional and comparative genomics to metagenomics and epigenetics. We already began to witness broad impacts of these DNA sequencing technologies for solving the complex biological problems in food, nutrition and agriculture. In this article, recent patent-based information is also included.

  16. Refining borders of genome-rearrangements including repetitions.

    Science.gov (United States)

    Arjona-Medina, J A; Trelles, O

    2016-10-25

    DNA rearrangement events have been widely studied in comparative genomic for many years. The importance of these events resides not only in the study about relatedness among different species, but also to determine the mechanisms behind evolution. Although there are many methods to identify genome-rearrangements (GR), the refinement of their borders has become a huge challenge. Until now no accepted method exists to achieve accurate fine-tuning: i.e. the notion of breakpoint (BP) is still an open issue, and despite repeated regions are vital to understand evolution they are not taken into account in most of the GR detection and refinement methods. We propose a method to refine the borders of GR including repeated regions. Instead of removing these repetitions to facilitate computation, we take advantage of them using a consensus alignment sequence of the repeated region in between two blocks. Using the concept of identity vectors for Synteny Blocks (SB) and repetitions, a Finite State Machine is designed to detect transition points in the difference between such vectors. The method does not force the BP to be a region or a point but depends on the alignment transitions within the SBs and repetitions. The accurate definition of the borders of SB and repeated genomic regions and consequently the detection of BP might help to understand the evolutionary model of species. In this manuscript we present a new proposal for such a refinement. Features of the SBs borders and BPs are different and fit with what is expected. SBs with more diversity in annotations and BPs short and richer in DNA replication and stress response, which are strongly linked with rearrangements.

  17. Refining borders of genome-rearrangements including repetitions

    Directory of Open Access Journals (Sweden)

    JA Arjona-Medina

    2016-10-01

    Full Text Available Abstract Background DNA rearrangement events have been widely studied in comparative genomic for many years. The importance of these events resides not only in the study about relatedness among different species, but also to determine the mechanisms behind evolution. Although there are many methods to identify genome-rearrang