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Sample records for frequency-selective fat-saturation sequences

  1. Detection of optic nerve lesions in optic neuritis using frequency-selective fat-saturation sequences

    International Nuclear Information System (INIS)

    Miller, D.H.; MacManus, D.G.; Bartlett, P.A.; Kapoor, R.; Morrissey, S.P.; Moseley, I.F.

    1993-01-01

    MRI was performed on seven patients with acute optic neuritis, using two sequences which suppress the signal from orbital fat: frequency-selective fat-saturation and inversion recovery with a short inversion time. Lesions were seen on both sequences in all the symptomatic optic nerves studied. (orig.)

  2. Fat-saturated diffusion-weighted imaging with three-dimensional MP-RAGE sequence

    International Nuclear Information System (INIS)

    Numano, Tomokazu; Homma, Kazuhiro; Takahashi, Nobuyuki; Hirose, Takeshi

    2005-01-01

    Image misrepresentation due to chemical shifts can create image artifacts on MR images. Distinguishing the organization and affected area can be difficult due to the chemical shift artifacts. Chemical shift selective (CHESS) is a method of decreasing chemical shift artifacts. In this study we have developed a new sequence for fat-saturated three-dimensional diffusion weighted MR imaging. This imaging was done during in vivo studies using an animal experiment MR imaging system at 2.0 T. In this sequence a preparation phase with a ''CHESS-90 deg RF-Motion Proving Gradient (MPG-180 deg RF-MPG-90 deg RF pulse train) was used to sensitize the magnetization to fat-saturated diffusion. Centric k-space acquisition order is necessary to minimize saturation effects from tissues with short relaxation times. From experimental results obtained with a phantom, the effect of the diffusion weighting and the effect of the fat-saturation were confirmed. From rat experimental results, fat-saturated diffusion weighted image data (0.55 x 0.55 x 0.55 mm 3 : voxel size) were obtained. This sequence was useful for in vivo imaging. (author)

  3. Comparison of the effects of the CHESS sequence and the SPAIR sequence for fat saturation

    Science.gov (United States)

    Dong, Kyung-Rae; Goo, Eun-Hoe; Kweon, Dae-Cheol; Chung, Woon-Kwan; Lee, Jong-Woong

    2013-06-01

    This study compared the abilities of the chemical-shift selective saturation(CHESS) and the spectrally-adiabatic inversion recovery (SPAIR) fat-saturation techniques to resolve the recent problems in fat saturation caused by areas of changing volume such as the head and the neck and by metal artifacts when T1 fat-saturation techniques representing the anatomical images and T2 fat-saturation techniques representing pathological images are used. To compare the abilities of CHESS and SPAIR, we acquired images of the head and the neck and of the pelvis, and we compared the contrast-to-noise ratios (CNRs) and the signal-to-noise ratios (SNRs) of the signals from the flexed body parts. Images were taken of the abdomens, heads and necks, and pelvises of 15 men and 15 women (30 in total). In all scanning techniques, the SNRs and the CNRs were calculated based on a quantitative analysis method with a view to obtaining uniform data. According to the study results, the CNRs of the SPAIR and the CHESS techniques for the pelvis in the T1-weighted image were 55.10 and 67.23, respectively. The SNRs of the SPAIR technique were70.61 for muscle and 15.50 for fat whereas the SNRs of the CHESS technique were 79.23 for muscle and 12.00 for fat. For the pelvis in the T2-weighted image, the CNRs of the SPAIR and the CHESS technique were 12.50 and 16.66, respectively. The SNRs of the SPAIR technique were 16.98 for muscle and 5.14 for fat. In contrast, the SNRs of the CHESS technique were 27.90 for muscle and 11.23 for fat. Consequently, the signal intensity was higher in the CHESS than in the SPAIR technique. Nevertheless, with regard to the clinical usefulness, the image quality was higher in the SPAIR technique than in the CHESS technique.

  4. MR imaging of articular cartilage in the knee. Evaluation of cadaver knee by 3D FLASH sequence with fat saturation

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    Sato, Katsuhiko; Hachiya, Junichi; Matsumura, Joji [Kyorin Univ., Mitaka, Tokyo (Japan). School of Medicine

    1999-06-01

    MR imaging of the articular cartilage of the 24 cadever knees was performed using 3D FLASH sequence with fat saturation. Good correlation was noted between MR findings and either macroscopic or microscopic appearances of the hyaline cartilage. Low signal intensity area without significant thinning of the cartilage was considered to represent the degenerative changes due to relatively early process of osteoarthritis. (author)

  5. Fat-saturated, contrast-enhanced spin echo sequences in magnetic resonance tomographic diagnosis of peritoneal carcinosis

    International Nuclear Information System (INIS)

    Ricke, J.; Hosten, N.; Stroszczynski, C.; Amthauer, H.; Felix, R.; Sehouli, J.; Buchmann, E.; Rieger, J.

    1999-01-01

    Purpose: To evaluate contrast-enhanced, fat-saturated spin echo sequences for the detection of peritoneal carcinosis with MRI. Material and Methods: 61 patients, 35 with and 26 without peritoneal carcinosis, were examined with abdominal MRI. Fat-saturated, T 1 -weighted spin echo sequences were performed before and after administration of Gd-DTPA. In addition, 22 patients with peritoneal carcinosis were examined with contrast-enhanced abdominal CT. Results: 32 of 35 patients with peritoneal carcinosis demonstrated contrast enhancement of the visceral and 30 to 35 enhancement of the parietal peritoneum (91 and 86%, respectively). Wall thickening of the intestine or parietal peritoneum were noted in 21 and 20 of 35 patients (60 and 57%, respectively), ascites in 18 of 35 patients (51%). False positive contrast enhancement of the peritoneum was noted in 4 of 26 patients (15%). In the direct comparison of MRI and CT, 22 of 22 patients versus 7 of 22 patients showed contrast enhancement of the visceral peritoneum (100 and 32%, respectively). For other signs of peritoneal carcinosis (e.g., ascites, peritoneal seedings), no differences in diagnostic reliability were demonstrated. Conclusions: The use of fat-saturated, spin echo sequences facilitates the diagnosis of peritoneal carcinosis by artifact reduction and improved detection of peritoneal contrast enhancement. MRI with fat-saturated sequences was superior to CT. (orig.) [de

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

    Science.gov (United States)

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

    2012-04-01

    To evaluate fat saturated (fs) T2-weighted (w) fast relaxation fast spin echo (FRFSE)-sequences compared to the standard protocol with contrast agent for the evaluation of inflammatory activity in patients with Crohn's Disease (CD). Fourty-eight patients (male, 17; female, 33; mean age, 37 years) with suspicion of inflammatory activity in proven CD who underwent MR enteroclysis (MRE) at 1.5T (GE Healthcare) were retrospectively included. Two blinded radiologists analyzed MRE images for presence and extent of CD lesions and degree of local inflammation for fsT2-w FRFSE and contrast enhanced T1-w images (T2-activity; T1-activity; score, 1-4) in consensus. Furthermore, mural signal intensity (SI) ratios (T2-ratio; T1-ratio) were recorded. Patient based MRE findings were correlated with endoscopic (45 patients), surgical (6 patients), histopathological, and clinical data (CDAI) as a surrogate reference standard. In total, 24 of 48 eligible patients presented with acute inflammatory activity with 123 affected bowel segments. ROC analysis of the total inflammatory score presented an AUC of 0.93 (pT2-activity (T1-activity, AUC 0.63; p=0.019). ROC analysis revealed an AUC of 0.76 (pT2-ratio (T1-ratio, AUC 0.51; p=0.93). General linear regression model revealed T2-activity (p=0.001) and age (p=0.024) as predictive factors of acute bowel inflammation. T2-w FRFSE-sequences can depict CD lesions and help to assess the inflammation activity, even with improved accuracy as compared to contrast-enhanced T1-w sequences. Copyright © 2011 European Crohn's and Colitis Organisation. Published by Elsevier B.V. All rights reserved.

  7. Value of Perineural Edema/Inflammation Detected by Fat Saturation Sequences in Lumbar Magnetic Resonance Imaging of Patients with Unilateral Sciatica

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    Sirvanci, M.; Duran, C. (Dept. of Radiology, Faculty of Medicine, Istanbul Bilim Univ., Istanbul (Turkey)); Kara, B.; Onat, L.; Ulusoy, O.L.; Mutlu, A. (Dept. of Radiology of Florence Nightingale Hospital, Istanbul (Turkey)); Ozturk, E. (Dept. of Radiology, GATA Haydarpasa Teaching Hospital, Istanbul (Turkey)); Karatoprak, O. (Dept. of Orthopeadic Surgery, Kadikoy Florence Nightingale Hospital, Istanbul (Turkey))

    2009-02-15

    Background: Routine lumbar spine magnetic resonance imaging (MRI) may not show any evidence of the cause of sciatica in some cases. The relationship between nerve root compression detected on lumbar MRI and sciatica is also sometimes uncertain. Purpose: To ascertain whether axial (and, when necessary, sagittal and coronal) short-tau inversion recovery or fat-saturated T2-weighted MRI findings can be used to study the level of sciatica in patients with a non-yielding routine MRI examination. Material and Methods: A total of 215 patients with unilateral sciatica underwent MRI. All patients were asked to complete pain drawing forms describing their pain dermatomal distributions. Perineural edema/inflammation corresponding to the pain location indicated by the pain drawings was sought on short-tau inversion recovery or fat-saturated T2-weighted images. Results: Routine MRI findings revealed that 110 of the 215 patients had nerve root compromise related to the patients' symptoms. Routine MRI could not ascertain the cause of these symptoms in the remaining 105 patients. In 31 (29.5%) of these 105 patients, short-tau inversion recovery or fat-saturated T2-weighted magnetic resonance images revealed perineural edema/inflammation surrounding the nerve roots related to the pain locations indicated in the pain drawings. Conclusion: Axial (and, when required, sagittal and coronal) short-tau inversion recovery or fat-saturated T2-weighted magnetic resonance images may be helpful for revealing additional findings in cases of unexplained sciatica in standard magnetic resonance imaging. However, the value of this imaging may be not great enough to justify routine use of these additional sequences to study the level of sciatica

  8. Value of Perineural Edema/Inflammation Detected by Fat Saturation Sequences in Lumbar Magnetic Resonance Imaging of Patients with Unilateral Sciatica

    International Nuclear Information System (INIS)

    Sirvanci, M.; Duran, C.; Kara, B.; Onat, L.; Ulusoy, O.L.; Mutlu, A.; Ozturk, E.; Karatoprak, O.

    2009-01-01

    Background: Routine lumbar spine magnetic resonance imaging (MRI) may not show any evidence of the cause of sciatica in some cases. The relationship between nerve root compression detected on lumbar MRI and sciatica is also sometimes uncertain. Purpose: To ascertain whether axial (and, when necessary, sagittal and coronal) short-tau inversion recovery or fat-saturated T2-weighted MRI findings can be used to study the level of sciatica in patients with a non-yielding routine MRI examination. Material and Methods: A total of 215 patients with unilateral sciatica underwent MRI. All patients were asked to complete pain drawing forms describing their pain dermatomal distributions. Perineural edema/inflammation corresponding to the pain location indicated by the pain drawings was sought on short-tau inversion recovery or fat-saturated T2-weighted images. Results: Routine MRI findings revealed that 110 of the 215 patients had nerve root compromise related to the patients' symptoms. Routine MRI could not ascertain the cause of these symptoms in the remaining 105 patients. In 31 (29.5%) of these 105 patients, short-tau inversion recovery or fat-saturated T2-weighted magnetic resonance images revealed perineural edema/inflammation surrounding the nerve roots related to the pain locations indicated in the pain drawings. Conclusion: Axial (and, when required, sagittal and coronal) short-tau inversion recovery or fat-saturated T2-weighted magnetic resonance images may be helpful for revealing additional findings in cases of unexplained sciatica in standard magnetic resonance imaging. However, the value of this imaging may be not great enough to justify routine use of these additional sequences to study the level of sciatica

  9. The value of fat saturation sequences and contrast medium administration in MRI of degenerative disease of the posterior/perispinal elements of the lumbosacral spine

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    D' Aprile, P. [San Paolo Hospital, Department of Neuroradiology, Bari (Italy); U.O. Radiologia, Sezione di Neuroradiologia, Ospedale ' ' S. Paolo' ' , Via Caposcardicchio, Bari (Italy); Tarantino, A. [San Paolo Hospital, Department of Neuroradiology, Bari (Italy); Jinkins, J.R. [State University of New York, Department of Radiology, Downstate Medical Center, Brooklyn, NY (United States); Brindicci, D. [San Paolo Hospital, Department of Radiology, Bari (Italy)

    2007-02-15

    Degenerative-inflammatory lumbar spinal pathology is one of the most common reasons why individuals seek medical care, and low back pain is the main symptom among those most commonly associated with this pathologic condition. Pain is commonly attributed to degenerative disc disease, particularly herniated discs, but many different spinal and perispinal structures may undergo degenerative-inflammatory phenomena and produce pain: discs, bone, facet joints, ligaments and muscles. In particular, in patients with non-radicular low back pain, this syndrome may arise from changes of the posterior elements/perispinal tissues of the lumbar spine (i.e., the ''posterior vertebral compartment''). They include: facet joint pathology (e.g., osteoarthritis, joint effusion, synovitis and synovial cysts), spondylolysis, spinal/perispinal ligamentous degenerative-inflammatory changes and perispinal muscular changes. It is well known that magnetic resonance is the most sensitive imaging method for the evaluation of spinal degenerative pathology, even in the initial stages of the disease. T2-weighted sequences with fat saturation, and when indicated the use of contrast-enhanced T1-weighted images with fat saturation, permit the visualization of degenerative-inflammatory changes of the posterior elements of the lumbar spine that in most cases would have been overlooked with conventional non-fat suppressed imaging. (orig.)

  10. The value of fat saturation sequences and contrast medium administration in MRI of degenerative disease of the posterior/perispinal elements of the lumbosacral spine

    International Nuclear Information System (INIS)

    D'Aprile, P.; Tarantino, A.; Jinkins, J.R.; Brindicci, D.

    2007-01-01

    Degenerative-inflammatory lumbar spinal pathology is one of the most common reasons why individuals seek medical care, and low back pain is the main symptom among those most commonly associated with this pathologic condition. Pain is commonly attributed to degenerative disc disease, particularly herniated discs, but many different spinal and perispinal structures may undergo degenerative-inflammatory phenomena and produce pain: discs, bone, facet joints, ligaments and muscles. In particular, in patients with non-radicular low back pain, this syndrome may arise from changes of the posterior elements/perispinal tissues of the lumbar spine (i.e., the ''posterior vertebral compartment''). They include: facet joint pathology (e.g., osteoarthritis, joint effusion, synovitis and synovial cysts), spondylolysis, spinal/perispinal ligamentous degenerative-inflammatory changes and perispinal muscular changes. It is well known that magnetic resonance is the most sensitive imaging method for the evaluation of spinal degenerative pathology, even in the initial stages of the disease. T2-weighted sequences with fat saturation, and when indicated the use of contrast-enhanced T1-weighted images with fat saturation, permit the visualization of degenerative-inflammatory changes of the posterior elements of the lumbar spine that in most cases would have been overlooked with conventional non-fat suppressed imaging. (orig.)

  11. Acute bone crises in sickle cell disease: the T1 fat-saturated sequence in differentiation of acute bone infarcts from acute osteomyelitis

    International Nuclear Information System (INIS)

    Jain, R.; Sawhney, S.; Rizvi, S.G.

    2008-01-01

    Aim: To prove the hypothesis that acute bone infarcts in sickle cell disease are caused by sequestration of red blood cells (RBCs) in bone marrow, and to evaluate the unenhanced T1 fat-saturated (fs) sequence in the differentiation of acute bone infarction from acute osteomyelitis in patients with sickle-cell disease. Materials and methods: Two studies were undertaken: an experimental study using in-vitro packed red blood cells and normal volunteers, and a retrospective clinical study of 86 magnetic resonance imaging (MRI) studies. For the experimental study containers of packed RBCs were placed between the knees of four healthy volunteers with a saline bag under the containers as an additional control, and were scanned with the pre-contrast T1-fs sequence. Signal intensity (SI) ratios were obtained for packed RBCs:skeletal muscle and packed RBCs:saline. For the clinical study, the SIs of normal bone marrow, packed RBCs, bone and/or soft-tissue lesions, and normal skeletal muscle of 74 patients (86 MRI studies) were measured using unenhanced, T1 fat-saturated MRI. The ratios of the above SIs to normal skeletal muscle were calculated and subjected to statistical analysis. Results: Fifty-one of 86 MRI studies were included in the final analysis. The ratios of SIs for normal bone marrow, packed red cells, bone infarction, acute osteomyelitis, and soft-tissue lesions associated with bone infarct, compared with normal skeletal muscle were (mean ± SD) 0.9 ± 0.2, 2.1 ± 0.7, 1.7 ± 0.5, 1.0 ± 0.3, and 2.2 ± 0.7, respectively. The difference in the ratio of SIs of bone infarcts and osteomyelitis was significant (p = 0.003). The final diagnoses were bone infarction (n = 50), acute osteomyelitis (n = 1), and co-existent bone infarction and osteomyelitis (n = 2). Seven patients who had suspected osteomyelitis underwent image-guided aspiration. Conclusion: Acute bone infarcts in sickle cell disease are caused by sequestration of red blood cells in the bone marrow. The

  12. Linear signal hyperintensity adjacent to the subchondral bone plate at the knee on T2-weighted fat-saturated sequences: imaging aspects and association with structural lesions

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    Gondim Teixeira, Pedro Augusto; Balaj, Clemence [CHU Hopital Central, Service D' Imagerie Guilloz, Nancy (France); Universite de Lorraine, IADI, UMR S 947, Nancy (France); Marie, Beatrice [CHU Hopital Central, Service d' Anatomo-Pathologie, Nancy (France); Lecocq, Sophie; Louis, Matthias; Blum, Alain [CHU Hopital Central, Service D' Imagerie Guilloz, Nancy (France); Braun, Marc [CHU Hopital Central, Service de Neuroradiologie, Nancy (France)

    2014-11-15

    To describe the association between linear T2 signal abnormalities in the subchondral bone and structural knee lesions. MR studies of patients referred for the evaluation of knee pain were retrospectively evaluated and 133 of these patients presented bone marrow edema pattern (BMEP) (study group) and while 61 did not (control group). The presence of linear anomalies of the subchondral bone on T2-weighted fat-saturated sequences was evaluated. The findings were correlated to the presence of structural knee lesions and to the duration of the patient's symptoms. Histologic analysis of a cadaveric specimen was used for anatomic correlation. Linear T2 hyperintensities at the subchondral bone were present in 41 % of patients with BMEP. None of the patients in the control group presented this sign. When a subchondral linear hyperintensity was present, the prevalence of radial or root tears was high and that of horizontal tears was low (71.4 and 4.8 %, respectively). Sixty-nine percent of the patients with a subchondral insufficiency fracture presented a subchondral linear hyperintensity. It was significantly more prevalent in patients with acute or sub-acute symptoms (p < 0.0001). The studied linear T2 hyperintensity is located at the subchondral spongiosa and can be secondary to local or distant joint injuries. Its presence should evoke acute and sub-acute knee injuries. This sign is closely related to subchondral insufficiency fractures and meniscal tears with a compromise in meniscal function. (orig.)

  13. Magnetic resonance imaging of articular cartilage in the knee. Evaluation of 3D-fat-saturation FLASH sequence in normal volunteer and patient with osteoarthritis

    International Nuclear Information System (INIS)

    Sato, Katsuhiko

    1996-01-01

    MR imaging of normal and abnormal articular cartilage of the knee was performed using 3D-fat-saturation FLASH sequence (FSF). Contrast-to-noise ratios between the cartilage and fluid, and cartilage and bone marrow were evaluated respectively in 10 normal volunteers. The optimal imaging parameters were determined as flip angle of 40deg and TE of 10 ms. Good correlation was noted between MR images and macroscopic appearance of the hyaline cartilages in the cadaver knees. Comparison of MR and radiographic findings was made in 39 cases of osteoarthritis. MR was significantly more sensitive than radiography in detecting cartilage abnormalities. In patient with radiographically normal joint spaces, cartilage abnormality was detected by MRI in the medial compartment of 13 cases and the lateral compartment of 19 cases. Signal intensity of joint effusion was sufficiently suppressed and did not hamper evaluation of the cartilages. FSF method was considered as a valuable imaging technique in the evaluation of cartilage abnormalities of the knee. (author)

  14. Magnetic resonance imaging of articular cartilage in the knee. Evaluation of 3D-fat-saturation FLASH sequence in normal volunteer and patient with osteoarthritis

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    Sato, Katsuhiko [Kyorin Univ., Mitaka, Tokyo (Japan). School of Medicine

    1996-07-01

    MR imaging of normal and abnormal articular cartilage of the knee was performed using 3D-fat-saturation FLASH sequence (FSF). Contrast-to-noise ratios between the cartilage and fluid, and cartilage and bone marrow were evaluated respectively in 10 normal volunteers. The optimal imaging parameters were determined as flip angle of 40deg and TE of 10 ms. Good correlation was noted between MR images and macroscopic appearance of the hyaline cartilages in the cadaver knees. Comparison of MR and radiographic findings was made in 39 cases of osteoarthritis. MR was significantly more sensitive than radiography in detecting cartilage abnormalities. In patient with radiographically normal joint spaces, cartilage abnormality was detected by MRI in the medial compartment of 13 cases and the lateral compartment of 19 cases. Signal intensity of joint effusion was sufficiently suppressed and did not hamper evaluation of the cartilages. FSF method was considered as a valuable imaging technique in the evaluation of cartilage abnormalities of the knee. (author)

  15. Detection of optic nerve atrophy following a single episode of unilateral optic neuritis by MRI using a fat-saturated short-echo fast FLAIR sequence

    International Nuclear Information System (INIS)

    Hickman, S.J.; Brex, P.A.; Silver, N.C.; Barker, G.J.; Miller, D.H.; Brierley, C.M.H.; Compston, D.A.S.; Scolding, N.J.; Moseley, I.F.; Plant, G.T.

    2001-01-01

    We describe an MRI technique for quantifying optic nerve atrophy resulting from a single episode of unilateral optic neuritis. We imaged 17 patients, with a median time since onset of optic neuritis of 21 months (range 3-81 months), using a coronal-oblique fat-saturated short-echo fast fluid-attenuated inversion-recovery (sTE fFLAIR) sequence. The mean cross-sectional area of the intraorbital portion of the optic nerves was calculated by a blinded observer from five consecutive 3 mm slices from the orbital apex forwards using a semiautomated contouring technique and compared with data from 16 controls. The mean optic nerve area was 11.2mm 2 in the affected eye of the patients, 12.9mm 2 in the contralateral eye (P = 0.006 compared to the affected eye) and 12.8mm 2 in controls (P = 0.03 compared to the affected eyes). There was a significant negative correlation between disease duration and the size of the affected optic nerve (r = -0.59, P = 0.012). The measurement coefficient of variation was 4.8 %. The sTE fFLAIR sequence enables measurement of optic nerve area with sufficient reproducibility to show optic nerve atrophy following a single episode of unilateral optic neuritis. The correlation of increasing optic nerve atrophy with disease duration would be consistent with ongoing axonal loss in a persistently demyelinated lesion, or Wallerian degeneration following axonal damage during the acute inflammatory phase. (orig.)

  16. 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

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

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    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.

  18. Breast MRI at very short TE (minTE). Image analysis of minTE sequences on non-fat-saturated, subtracted T1-weighted images

    International Nuclear Information System (INIS)

    Wenkel, Evelyn; Janka, Rolf; Kaemmerer, Nadine; Uder, Michael; Hammon, Matthias; Brand, Michael; Hartmann, Arndt

    2017-01-01

    The aim was to evaluate a minimum echo time (minTE) protocol for breast magnetic resonance imaging (MRI) in patients with breast lesions compared to a standard TE (nTE) time protocol. Breasts of 144 women were examined with a 1.5 Tesla MRI scanner. Additionally to the standard gradient-echo sequence with nTE (4.8 ms), a variant with minimum TE (1.2 ms) was used in an interleaved fashion which leads to a better temporal resolution and should reduce the scan time by approximately 50%. Lesion sizes were measured and the signal-to-noise ratio (SNR) as well as the contrast-to-noise ratio (CNR) were calculated. Subjective confidence was evaluated using a 3-point scale before looking at the nTE sequences (1 = very sure that I can identify a lesion and classify it, 2 = quite sure that I can identify a lesion and classify it, 3 = definitely want to see nTE for final assessment) and the subjective image quality of all examinations was evaluated using a four-grade scale (1 = sharp, 2 = slight blur, 3 = moderate blur and 4 = severe blur/not evaluable) for lesion and skin sharpness. Lesion morphology and contrast enhancement were also evaluated. With minTE sequences, no lesion was rated with ''definitely want to see nTE sequences for final assessment''. The difference of the longitudinal and transverse diameter did not differ significantly (p>0.05). With minTE, lesions and skin were rated to be significantly more blurry (p<0.01 for lesions and p<0.05 for skin). There was no difference between both sequences with respect to SNR, CNR, lesion morphology, contrast enhancement and detection of multifocal disease. Dynamic breast MRI with a minTE protocol is feasible without a major loss of information (SNR, CNR, lesion morphology, contrast enhancement and lesion sizes) and the temporal resolution can be increased by a factor of 2 using minTE sequences.

  19. Breast MRI at very short TE (minTE). Image analysis of minTE sequences on non-fat-saturated, subtracted T1-weighted images

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    Wenkel, Evelyn; Janka, Rolf; Kaemmerer, Nadine; Uder, Michael; Hammon, Matthias; Brand, Michael [Univ. Hospital Erlangen (Germany). Dept. of Radiology; Geppert, Christian [Siemens Healthcare GmbH, Erlangen (Germany); Hartmann, Arndt [Univ. Hospital Erlangen (Germany). Dept. of Pathology

    2017-02-15

    The aim was to evaluate a minimum echo time (minTE) protocol for breast magnetic resonance imaging (MRI) in patients with breast lesions compared to a standard TE (nTE) time protocol. Breasts of 144 women were examined with a 1.5 Tesla MRI scanner. Additionally to the standard gradient-echo sequence with nTE (4.8 ms), a variant with minimum TE (1.2 ms) was used in an interleaved fashion which leads to a better temporal resolution and should reduce the scan time by approximately 50%. Lesion sizes were measured and the signal-to-noise ratio (SNR) as well as the contrast-to-noise ratio (CNR) were calculated. Subjective confidence was evaluated using a 3-point scale before looking at the nTE sequences (1 = very sure that I can identify a lesion and classify it, 2 = quite sure that I can identify a lesion and classify it, 3 = definitely want to see nTE for final assessment) and the subjective image quality of all examinations was evaluated using a four-grade scale (1 = sharp, 2 = slight blur, 3 = moderate blur and 4 = severe blur/not evaluable) for lesion and skin sharpness. Lesion morphology and contrast enhancement were also evaluated. With minTE sequences, no lesion was rated with ''definitely want to see nTE sequences for final assessment''. The difference of the longitudinal and transverse diameter did not differ significantly (p>0.05). With minTE, lesions and skin were rated to be significantly more blurry (p<0.01 for lesions and p<0.05 for skin). There was no difference between both sequences with respect to SNR, CNR, lesion morphology, contrast enhancement and detection of multifocal disease. Dynamic breast MRI with a minTE protocol is feasible without a major loss of information (SNR, CNR, lesion morphology, contrast enhancement and lesion sizes) and the temporal resolution can be increased by a factor of 2 using minTE sequences.

  20. Magnetic resonance imaging of pelvic entheses - a systematic comparison between short tau inversion recovery (STIR) and T1-weighted, contrast-enhanced, fat-saturated sequences

    International Nuclear Information System (INIS)

    Klang, Eyal; Aharoni, Dvora; Rimon, Uri; Eshed, Iris; Hermann, Kay-Geert; Herman, Amir; Shazar, Nachshon

    2014-01-01

    To assess the contribution of contrast material in detecting and evaluating enthesitis of pelvic entheses by MRI. Sixty-seven hip or pelvic 1.5-T MRIs (30:37 male:female, mean age: 53 years) were retrospectively evaluated for the presence of hamstring and gluteus medius (GM) enthesitis by two readers (a resident and an experienced radiologist). Short tau inversion recovery (STIR) and T1-weighted pre- and post-contrast (T1+Gd) images were evaluated by each reader at two sessions. A consensus reading of two senior radiologists was regarded as the gold standard. Clinical data was retrieved from patients' referral form and medical files. Cohen's kappa was used for intra- and inter-observer agreement calculation. Diagnostic properties were calculated against the gold standard reading. A total of 228 entheses were evaluated. Gold standard analysis diagnosed 83 (36 %) enthesitis lesions. Intra-reader reliability for the experienced reader was significantly (p = 0.0001) higher in the T1+Gd images compared to the STIR images (hamstring: k = 0.84/0.45, GM: k = 0.84/0.47). Sensitivity and specificity increased from 0.74/0.8 to 0.87/0.9 in the STIR images and T1+Gd sequences. Intra-reader reliability for the inexperienced reader was lower (p > 0.05). Evidence showing that contrast material improves the reliability, sensitivity, and specificity of detecting enthesitis supports its use in this setting. (orig.)

  1. Fat-saturated post gadolinium T1 imaging of the brain in multiple sclerosis

    International Nuclear Information System (INIS)

    Al-Saeed, Osama; Sheikh, Mehraj; Ismail, Mohammed; Athyal, Reji

    2011-01-01

    Background Magnetic resonance imaging (MRI) is of vital importance in the diagnosis and follow-up of patients with multiple sclerosis (MS). Imaging sequences better demonstrating enhancing lesions can help in detecting active MS plaques. Purpose To evaluate the role of fat-saturated gadolinium-enhanced T1-weighted (T1W) images of the brain in MS and to assess the benefit of performing this additional sequence in the detection of enhancing lesions. Material and Methods In a prospective study over a six-month period, 70 consecutive patients with clinically diagnosed MS were enrolled. These constituted 14 male and 56 female patients between the ages of 21 and 44 years. All the patients underwent brain MRIs on a 1.5 Tesla Magnet. Gadolinium-enhanced T1 images with and without fat saturation were compared and results were recorded and analyzed using a conspicuity score and McNemar test. Results There were a total of 157 lesions detected in 70 patients on post-contrast T1W fat-saturated images compared with 139 lesions seen on the post-contrast T1W fast spin-echo (FSE) images. This was because 18 of the lesions (11.5%) were only seen on the fat-saturated images. In addition, 15 lesions were more conspicuous on the fat saturation sequence (9.5%). The total conspicuity score obtained, including all the lesions, was 2.24 +/-0.60 (SD). Using the two-tailed McNemar test for quantitative analysis, the P value obtained was <0.0001. Conclusion T1W fat-saturated gadolinium-enhanced images show better lesion enhancement than T1W images without fat saturation

  2. Magnetic Resonance Imaging in degenerative disease of the lumbar spine: Fat Saturation technique and contrast medium.

    Science.gov (United States)

    D'Aprile, Paola; Nasuto, Michelangelo; Tarantino, Alfredo; Cornacchia, Samantha; Guglielmi, Giuseppe; Jinkins, J Randy

    2018-01-19

    To examine both anterior and posterior elements of the lumbar spine in patients with low back pain using MRI T2-weighted sequences with Fat Saturation (FS) and contrast enhanced T1-weighted sequences with FS. Two thousand eight hundred and twenty (2820) patients (1628 male, 1192 female, mean age 54) presenting low back pain underwent MRI standard examination (Sagittal T1w TSE and T2w TSE, axial T1 SE) with the addition of sagittal and axial T2w Fat Sat (FS) sequences. Among all the patients, 987 (35%) have been studied adding Contrast Enhanced (CE) T1w FS sequences after administration of contrast medium. Among 987 patients studied with contrast medium, we found: active-inflammatory intervertebral osteochondrosis in 646 (65%) patients; degenerative-inflammatory changes in facet joints (facet joint effusion, synovitis, synovial cysts) in 462 (47%); spondylolysis in 69 (7%); degenerative-inflammatory changes of the flava, interspinous and supraspinous ligaments in 245 (25%); inflammatory changes of posterior perispinal muscles in 84 (8%) patients. In patients with suspected no-disc-related low back pain, the implementation of T2w FS and CE T1w FS sequences to the standard MR protocol could allow a better identification of degenerative-inflammatory changes more likely associated to the pain.

  3. Studies on diagnosis of endometriosis by magnetic resonance imaging by means of fat saturation techniques

    International Nuclear Information System (INIS)

    Okada, Saori

    1995-01-01

    It is difficult to distinguish a small endometrial implant from adipose tissue by magnetic resonance imaging (MRI). I assessed the usefulness of fat saturated MRI in detecting small endometrial implants by comparing it with conventional MRI. Seventy-four patients with clinically suspected endometriosis were referred for MRI. In every patient, laparoscopy or laparotomy was performed. MRI was performed with a 1.5 T superconducting magnet with spin echo T1, T2 and fat saturated T1 weighted images. Surgery revealed a normal pelvis in 6 patients, endometriosis in 65, and cystic lesions in three others. With fat saturated MRI, overall sensitivity, specificity, positive predictive value and negative predictive value were 87.7%, 66.7%, 95.0% and 42.9%, respectively. At surgery, 160 pigmented lesions of endometriosis were detected. Conventional MRI permitted identification of almost all ovarian endometriomas >10 mm in diameter, as with fat saturated MRI. With conventional MRI, 18 endometrial implant lesions <10 mm in diameter were detected. Including those detected by fat saturated MRI, altogether 42 lesions were detected. Conventional MRI demonstrated only 3 lesions among the 48 blueberry spots, but the additional fat saturated MRI technique increased the detection rate to 21 out of 48. Fat saturated MRI can therefore be used for detecting small endometrial implants. (author)

  4. Studies on diagnosis of endometriosis by magnetic resonance imaging by means of fat saturation techniques

    Energy Technology Data Exchange (ETDEWEB)

    Okada, Saori [Shimane Medical Univ., Izumo (Japan)

    1995-03-01

    It is difficult to distinguish a small endometrial implant from adipose tissue by magnetic resonance imaging (MRI). I assessed the usefulness of fat saturated MRI in detecting small endometrial implants by comparing it with conventional MRI. Seventy-four patients with clinically suspected endometriosis were referred for MRI. In every patient, laparoscopy or laparotomy was performed. MRI was performed with a 1.5 T superconducting magnet with spin echo T1, T2 and fat saturated T1 weighted images. Surgery revealed a normal pelvis in 6 patients, endometriosis in 65, and cystic lesions in three others. With fat saturated MRI, overall sensitivity, specificity, positive predictive value and negative predictive value were 87.7%, 66.7%, 95.0% and 42.9%, respectively. At surgery, 160 pigmented lesions of endometriosis were detected. Conventional MRI permitted identification of almost all ovarian endometriomas >10 mm in diameter, as with fat saturated MRI. With conventional MRI, 18 endometrial implant lesions <10 mm in diameter were detected. Including those detected by fat saturated MRI, altogether 42 lesions were detected. Conventional MRI demonstrated only 3 lesions among the 48 blueberry spots, but the additional fat saturated MRI technique increased the detection rate to 21 out of 48. Fat saturated MRI can therefore be used for detecting small endometrial implants. (author).

  5. Lumbosacral lipoma : gadolinium-enhanced fat saturation T1 weighted MR image is necessary?

    International Nuclear Information System (INIS)

    Yoon, Man Won; Kim, Hyun Chul; Chung, Tae Woong; Seo, Jeong Jin; Chung, Gwang Woo; Kim, Yun Hyeon; Kim, Jae Kyu; Park, Jin Gyoon; Kang, Heoung Keun

    1999-01-01

    To evaluate the usefulness of contrast-enhanced fat saturation T1-weighted imaging for the evaluation of spinal lipoma, compared with clinical symptoms and surgical findings. Ten patients with lipomyelomeningocele, confirmed by surgery, were included in this study. In all cases, conventional spin echo T1-and T2-weighted MR imaging, and contrast-enhanced fat saturation T1-weighted imaging was performed to evaluate clinical symptoms, the position of the conus medullaris, the presence of cord tethering, and associated anomalies, and to compare the relative usefulness of the techniques. All ten patients were suffering from lipomyelomeningocele without filum terminale fibrolipoma or intradural lipoma. All cases were associated with cord tethering. As associated anomalies, there were seven cases of syringomyelia without hydrocephalus or anorectal anomaly. To evaluate the position of the spinal conus and the presence of cord tethering, conventional T1-weighted imaging was more useful than the contrast-enhanced fat saturation equivalent. In patients with early-stage spinal lipoma, MRI is useful for evaluation of the causes and position of cord tethering and associated anomalies Our results suggest that contrast-enhanced fat saturation T1-weighted images do not provide additional information concerning spinal lipoma, and that for the diagnosis of this condition, conventional T1 and T2-weighted images are more useful than those obtained by contrast-enhanced fat saturation T1-weighted imaging

  6. Frequency selective bolometers

    DEFF Research Database (Denmark)

    Kowitt, M.S.; Fixsen, D.J.; Goldin, A.

    1996-01-01

    We propose a concept for radiometry in the millimeter, the submillimeter, and the far-IR spectral regions, the frequency selective bolometer (FSB). This system uses a bolometer as a coupled element of a tuned quasi-optical interference filter in which the absorption, the transmission......-dimensional transmission-line model. Instruments based on FSB technology should have several advantages over current multiband bolometric radiometers including smaller and more compact cryogenic optics; reduced demands on cryostat size and weight, high coupling efficiency, minimum constraints on the geometry in the focal...

  7. MR imaging of osteonecrosis using frequency selective chemical shift sequences; Neue Aspekte in der MR-Diagnostik der Osteonekrose: Selektive Fett/Wasser-Bildgebung

    Energy Technology Data Exchange (ETDEWEB)

    Duda, S H [Abt. fuer Radiologische Diagnostik, Tuebingen Univ. (Germany); Laniado, M [Abt. fuer Radiologische Diagnostik, Tuebingen Univ. (Germany); Schick, F [Inst. fuer Physik, Tuebingen Univ. (Germany)

    1994-12-31

    The MR appearance of osteonecrosis was assessed on selective fat- and water images to further evaluate the nature of double-line sign. Conventional T1- and T2-weighted SE and frequency selective chemical shift images of eight patients with avascular necrosis of the femoral head and three patients with bone infarcts were retrospectively reviewed. Eight of 11 patients showed a double-line sign on T2-weighted SE images. In these cases, correlation with selective water images revealed that a chemical shift artifact contributed to appearance and location of the hyperintense line. The authors conclude that chemical shift imaging improves our understanding of the nature of the double-line sign. (orig.) [Deutsch] Das MR-tomographische Erscheinungsbild der Osteonekrose auf selektiven Fett- und Wasserbildern wurde analysiert, um das in der Literatur beschriebene Doppellinienzeichen naeher zu untersuchen. Hierfuer wurden sowohl die herkoemmlichen T1- und T2-gewichteten Spin-Echo-Sequenzen herangezogen, als auch frequenzselektive Bilder, die aufgrund chemischer Verschiebung gewonnen wurden (1,5 T). Es wurden die Untersuchungen von acht Patienten mit avaskulaerer Hueftkopfnekrose und von drei Patienten mit Knocheninfarkten retrospektiv ausgewertet. Acht von 11 Patienten zeigten ein Doppellinienzeichen auf den T2-gewichteten Bildern. Die Korrelation mit den selektiven Wasserbildern ergab, dass durch chemische Verschiebung bedingte Artefakte das Erscheinungsbild und den Ort der hyperintensen Linie beeinflussten. Die Bildgebung mit Hilfe der chemischen Verschiebung verbessert unser Verstaendnis der MRT-Charakteristika der Osteonekrose. (orig.)

  8. Reducing calories, fat, saturated fat, and sodium in restaurant menu items: Effects on consumer acceptance.

    Science.gov (United States)

    Patel, Anjali A; Lopez, Nanette V; Lawless, Harry T; Njike, Valentine; Beleche, Mariana; Katz, David L

    2016-12-01

    To assess consumer acceptance of reductions of calories, fat, saturated fat, and sodium to current restaurant recipes. Twenty-four menu items, from six restaurant chains, were slightly modified and moderately modified by reducing targeted ingredients. Restaurant customers (n = 1,838) were recruited for a taste test and were blinded to the recipe version as well as the purpose of the study. Overall consumer acceptance was measured using a 9-point hedonic (like/dislike) scale, likelihood to purchase scale, Just-About-Right (JAR) 5-point scale, penalty analysis, and alienation analysis. Overall, modified recipes of 19 menu items were scored similar to (or better than) their respective current versions. Eleven menu items were found to be acceptable in the slightly modified recipe version, and eight menu items were found to be acceptable in the moderately modified recipe version. Acceptable ingredient modifications resulted in a reduction of up to 26% in calories and a reduction of up to 31% in sodium per serving. The majority of restaurant menu items with small reductions of calories, fat, saturated fat, and sodium were acceptable. Given the frequency of eating foods away from home, these reductions could be effective in creating dietary improvements for restaurant diners. © 2016 The Obesity Society.

  9. The evaluation of fat saturation fast spin-echo T2W1 for patients with acute spinal trauma

    International Nuclear Information System (INIS)

    Kim, Sung Gyu; Lee, Chang Jun; Lee, Myung Joon; Kang, Ik Won; Yoo, Jeong Hyun

    2002-01-01

    To determine the usefulness of fat saturation fast spin-echo T2W1 for patients with mild acute trauma of the spine. Between July 1998 and June 2002, 36 patients with acute spinal trauma underwent MRI within four months of injury. One, whose clinal symptoms indicated neurological paralysis, was excluded form our study. A superconductive 1.0-T MRI scanner was used, and conventional T1W1, T2W1, and additional fat-saturation fast spin-echo T2W1 were performed. Two radiologists compared conventional T2-weighted sagittal imaging and fat-saturation T2-weighted sagittal imaging in terms of the extension of increased high signal intensities in soft tissue and vertebral bodies, bone marrow signal change, disk herniation, and signal change of the disk. The detection rate of focal high signal intensities in soft tissue and bone marrow was significantly higher at fat-saturation fast spin-echo T2W1 than at conventional T2W1. Fat-saturation fast spin-echo T2W1 is useful for the evaluation of patients with mild acute spinal trauma without neurological impairment

  10. Binaural frequency selectivity in humans.

    Science.gov (United States)

    Verhey, Jesko L; van de Par, Steven

    2018-01-23

    Several behavioural studies in humans have shown that listening to sounds with two ears that is binaural hearing, provides the human auditory system with extra information on the sound source that is not available when sounds are only perceived through one ear that is monaurally. Binaural processing involves the analysis of phase and level differences between the two ear signals. As monaural cochlea processing (in each ear) precedes the neural stages responsible for binaural processing properties it is reasonable to assume that properties of the cochlea may also be observed in binaural processing. A main characteristic of cochlea processing is its frequency selectivity. In psychoacoustics, there is an ongoing discussion on the frequency selectivity of the binaural auditory system. While some psychoacoustic experiments seem to indicate poorer frequency selectivity of the binaural system than that of the monaural processing others seem to indicate the same frequency selectivity for monaural and binaural processing. This study provides an overview of these seemingly controversial results and the different explanations that were provided to account for the different results. © 2018 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

  11. The evaluation of fat saturation fast spin-echo T2WI for patients with acute spinal trauma

    International Nuclear Information System (INIS)

    Kim, Sung Gyu; Lee, Chang Jun; Lee, Myung Joon; Kang, Ik Won; Yoo, Jeong Hyun

    2002-01-01

    To determine the usefulness of fat saturation fast spin-echo T2WI for patients with mild acute trauma of the spine. Between July 1998 and June 2002, 36 patients with acute spinal trauma underwent MRI within four months of injury. One, whose clinal symptoms indicated neurological paralysis, was excluded form our study. A superconductive 1.0-T MRI scanner was used, and conventional T1W1, T2W1, and additional fat-saturation fast spin-echo T2W1 were performed. Two radiologists compared conventional T2-weighted sagittal imaging and fat-saturation T2-weighted sagittal imaging in terms of the extension of increased high signal intensities in soft tissue and vertebral bodies, bone marrow signal change, disk herniation, and signal change of the disk. The detection rate of focal high signal intensities in soft tissue and bone marrow was significantly higher at fat-saturation fast spin-echo T2W1 is useful the evaluation of patients with mild acute spinal trauma without neurological impairment

  12. Metastatic spinal tumor. Assessment with fat-saturation T1-weighted MR imaging

    International Nuclear Information System (INIS)

    Kasai, Toshifumi; Sugimura, Kazuro; Uchida, Nobue; Kawamitsu, Hideaki; Komatsu, Akio; Okui, Shouji; Kimino, Katsuji.

    1994-01-01

    The purpose of this study was to compare conventional T1-weighted imaging (T1-WI) and chemical shift fat-saturation T1-weighted imaging (fat-sat T1-WI) by a diagnosis of the bone metastases. Thirty-two patients (143 vertebrae) with non-neoplastic lesions (normal group) and 32 patients (82 vertebrae) with spinal metastases (metastatic group) were evaluated using both images. The signal intensity (SI) distribution of both groups regarding T1-WI provided various patterns, and the SI measurements were not significantly different between the two groups ; however, the metastases which were mixed, showed a low SI. Regarding fat-sat T1-WI, all non-neoplastic lesions had a low-intensity homogeneous appearance ; however, the metastases were mixed to a high SI. The SI measurement data of the metastatic group was significantly higher than that of the normal group. In conclusion, fat-sat T1-WI was useful for evaluating the vertebral metastases. When fat-sat T1-WI demonstrated a mixed to high SI in patients suspected of having vertebral metastasis, Gd-DTPA enhancement was thought to be the problem. (author)

  13. Change in T2-Fat Saturation MRI Correlates With Outcome in Cervical Cancer Patients

    International Nuclear Information System (INIS)

    Ma, Daniel J.; Zhu Jianming; Grigsby, Perry W.

    2011-01-01

    Purpose: To compare pretreatment and midtreatment tumor intensity as measured by T2 fat-saturation (T2-FS) MRI and its association with treatment response in cervical cancer patients. Methods and Materials: Weekly MRI scans were performed for brachytherapy planning on 23 consecutive patients with clinical Stage IB1 to IIIB cervical cancer treated with definitive chemoradiotherapy. These scans were performed on a 1.5-T clinical scanner using a specialized pelvic coil. Mean signal intensity from T2-FS imaging was calculated for each tumor voxel. Average tumor intensity and tumor volume were recorded pre- and midtreatment (at Weeks 0 and 4). All patients subsequently underwent routine follow-up, including periodic clinical examinations and fluorodeoxyglucose–positron emission tomography imaging. Results: Mean follow-up for surviving patients was 14.5 months. Mean tumor volume at presentation was 49.6 cc, and mean midtreatment tumor volume was 16.0 cc. There was no correlation between initial tumor volume and pretreatment signal intensity (r = 0.44), nor was there a correlation between pre- or midtreatment tumor volume with disease-free survival (p = 0.18, p = 0.08 respectively.) However, having at least a 30% drop in signal intensity from pretreatment to midtreatment was correlated with having disease resolution on posttreatment fluorodeoxyglucose–positron emission tomography imaging (p = 0.05) and with disease-free survival (p = 0.03.) Estimated disease-free survival at 22 months was 100% for patients with at least a 30% drop in tumor signal intensity compared with 33% for patients above this selected threshold (p = 0.004). Conclusions: Longitudinal changes in T2-FS tumor intensity during chemoradiation correlated with disease-free survival in cervical cancer patients. Persistently high midtreatment tumor intensities correlated with a high risk of treatment failure, whereas large decreases in tumor intensity correlated with a favorable outcome.

  14. Evaluation of shoulder pathology: three-dimensional enhanced T1 high-resolution isotropic volume excitation MR vs two-dimensional fast spin echo T2 fat saturation MR.

    Science.gov (United States)

    Park, H J; Lee, S Y; Kim, M S; Choi, S H; Chung, E C; Kook, S H; Kim, E

    2015-03-01

    To evaluate the diagnostic accuracy of three-dimensional (3D) enhanced T1 high-resolution isotropic volume excitation (eTHRIVE) shoulder MR for the detection of rotator cuff tears, labral lesions and calcific tendonitis of the rotator cuff in comparison with two-dimensional (2D) fast spin echo T2 fat saturation (FS) MR. This retrospective study included 73 patients who underwent shoulder MRI using the eTHRIVE technique. Shoulder MR images were interpreted separately by two radiologists. They evaluated anatomic identification and image quality of the shoulder joint on routine MRI sequences (axial and oblique coronal T2 FS images) and compared them with the reformatted eTHRIVE images. The images were scored on a four-point scale (0, poor; 1, questionable; 2, adequate; 3, excellent) according to the degree of homogeneous and sufficient fat saturation to penetrate bone and soft tissue, visualization of the glenoid labrum and distinction of the supraspinatus tendon (SST). The diagnostic accuracy of eTHRIVE images compared with routine MRI sequences was evaluated in the setting of rotator cuff tears, glenoid labral injuries and calcific tendonitis of the SST. Fat saturation scores for eTHRIVE were significantly higher than those of the T2 FS for both radiologists. The sensitivity and accuracy of the T2 FS in diagnosing rotor cuff tears were >90%, whereas sensitivity and accuracy of the eTHRIVE method were significantly lower. The sensitivity, specificity and accuracy of both images in diagnosing labral injuries and calcific tendonitis were similar and showed no significant differences. The specificity of both images for the diagnosis of labral injuries and calcific tendonitis was higher than the sensitivities. The accuracy of 3D eTHRIVE imaging was comparable to that of 2D FSE T2 FS for the diagnosis of glenoid labral injury and calcific tendonitis of SST. The 3D eTHRIVE technique was superior to 2D FSE T2 FS in terms of fat saturation. Overall, 3D eTHRIVE was inferior

  15. Comparison of axial T1 spin-echo and T1 fat-saturation magnetic resonance imaging techniques in the diagnosis of chondromalacia patellae.

    Science.gov (United States)

    Vanarthos, W J; Pope, T L; Monu, J U

    1994-12-01

    To test the diagnostic value of T1 spin-echo and T1 fat-saturated magnetic resonance images (MRIs), we reviewed axial T1-weighted images with and without fat saturation in 20 patients with clinically suspected chondromalacia of the patella. All scans were obtained on 1.5-MR units. The scans were randomly ordered and reviewed independently at different times by two radiologists without knowledge of the arthroscopy results. The sensitivity of the individual techniques for detecting grade 3 or 4 chondromalacia patellae was 92% for fat-saturated axial T1-weighted images alone, and 67% for axial T1-weighted images without fat saturation. The sensitivity of the combined techniques was 100% for grades 3 and 4 and 90% for all grades (0 to 4). Chondromalacia patellae is diagnosed more accurately by using T1 fat saturation than by using T1 spin-echo images. With a combination of the two techniques, accuracy is 90% to 100%.

  16. Frequency selectivity at very low centre frequencies

    DEFF Research Database (Denmark)

    Orellana, Carlos Andrés Jurado; Pedersen, Christian Sejer; Marquardt, Torsten

    2010-01-01

    measurements based on OAE suppression techniques and notched-noise masking data psychophysically measured for centre frequencies in the range 50-125 Hz, this study examines how individual differences in frequency selectivity, as well as in masking, may occur at very low CFs due to individual differences...

  17. Optic nerve sheath diameter on fat-saturated T2-weighted orbital MR imaging reflects intracranial pressure

    International Nuclear Information System (INIS)

    Watanabe, Arata; Kinouchi, Hiroyuki; Horikoshi, Toru; Uchida, Mikito; Sakatsume, Satoshi

    2009-01-01

    Although dilated optic nerve sheath (ONS) is observed in the setting of increased intracranial pressure (ICP) such as idiopathic intracranial hypertension or hydrocephalus, the relationship between ONS diameter and ICP is unclear. We analyzed the relationship between subdural pressure measured during surgery in patients with chronic subdural fluid collections and ONS diameter measured on MR images. Orbital thin slice fat-saturated MR images were obtained within 24 hours before surgery and ONS diameters were measured just behind the optic globe. Subdural pressure was measured using a manometer before opening the dura mater during surgery. Significant correlation was found between the ONS diameter and subdural pressure (y=0.0618x+4.8219. y: ONS diameter (mm), x: subdural pressure (cmH 2 O), correlation coefficient: 0.505). The ONS diameter before surgery (6.1±0.7 mm) was significantly reduced after surgery (4.8±0.9 mm, p=0.003). Increased ONS diameter on MR images is a strong indicator of increased ICP we propose 6 mm as the normal limit of diameter just behind the eyeball because this value corresponds to the upper normal limit of ICP of around 20 cmH 2 O with above mentioned approximate curve. (author)

  18. Frequency Selective Surface for Structural Health Monitoring

    Science.gov (United States)

    Norlyana Azemi, Saidatul; Mustaffa, Farzana Hazira Wan; Faizal Jamlos, Mohd; Abdullah Al-Hadi, Azremi; Soh, Ping Jack

    2018-03-01

    Structural health monitoring (SHM) technologies have attained attention to monitor civil structures. SHM sensor systems have been used in various civil structures such as bridges, buildings, tunnels and so on. However the previous sensor for SHM is wired and encounter with problem to cover large areas. Therefore, wireless sensor was introduced for SHM to reduce network connecting problem. Wireless sensors for Structural Health monitoring are new technology and have many advantages to overcome the drawback of conventional and wired sensor. This project proposed passive wireless SHM sensor using frequency selective surface (FSS) as an alternative to conventional sensors. The electromagnetic wave characteristic of FSS will change by geometrical changes of FSS due to mechanical strain or structural failure. The changes feature is used as a sensing function without any connecting wires. Two type of design which are circular ring and square loop along with the transmission and reflection characteristics of SHM using FSS were discussed in this project. A simulation process has shown that incident angle characteristics can be use as a data for SHM application.

  19. Fat suppression MR imaging of sellar and parasellar lesions. The usefulness of the fat-saturation (FATSAT) technique

    International Nuclear Information System (INIS)

    Isoda, Haruo; Masui, Takayuki; Mochizuki, Takao; Ushimi, Takashi; Takahashi, Motoichiro; Kaneko, Masao; Ohta, Atsuko; Shirakawa, Toyomi; Takizawa, Osamu.

    1994-01-01

    The purpose of this study was to investigate the utility of fat suppression T 1 -weighted MR images using a frequency-selective presaturation pulse when evaluating the pituitary gland and parasellar lesions. Conventional spin echo T 1 weighted images and fat suppression spin echo T 1 -weighted images were obtained in twenty-three patients with clinically suspected pituitary gland diseases or parasellar lesions using a 1.5T superconductive MR imager with a head coil. Both conventional T 1 -weighted images and fat suppression T 1 -weighted images of the pituitary anterior lobe, posterior lobe, pituitary stalk and pituitary tumors were compared by two radiologists. The visibility of the anterior lobe, posterior lobe, pituitary stalk and pituitary tumors on fat suppression T 1 -weighted images was equal to or better than that on conventional T 1 -weighted images. After the intravenous administration of Gd-DTPA, both imaging methods showed little difference in the visibility of the posterior lobe and pituitary stalk. In conclusion, fat suppression T 1 -weighted images using a frequency-selective presaturation pulse can be useful in evaluating the pituitary gland and parasellar lesions. (author)

  20. Diffusion-weighted imaging of the rat pelvis using 3D water-excitation MP-RAGE MR sequence

    International Nuclear Information System (INIS)

    Numano, Tomokazu; Homma, Kazuhiro; Hyodo, Koji; Nitta, Naotaka; Iwasaki, Nobuaki

    2008-01-01

    We developed a novel technique for fat-saturated, 3-dimensional (3D) diffusion-weighted (DW) magnetic resonance (MR) imaging sequencing based upon the 3D magnetization-prepared, rapid gradient-echo (3D-MP-RAGE) method. We saturated fat using 2 techniques, chemical shift selective (CHESS; FatSat)-3D-DWI sequence versus water excitation (WE)-3D-DWI method, then compared the 2 sequences in terms of degree of fat suppression. In preparing the FatSat-3D-DWI sequence, we used a ''CHESS-90deg radiofrequency (RF)-motion probing gradient (MPG)-180deg RFMPG-90deg RF'' pulse-train, to sensitize the magnetization to fat-saturated diffusion. In contrast, in the WE-3D-DWI sequence, we selected a RAGE-excitation pulse with a binominal-pulse 1-1 or 1-2-1 for water-excited (fat-saturated) diffusion imaging. Experimental results in a phantom confirmed the effects of diffusion weighting and of fat saturation. Fat saturation was much better in the WE-3D-DWI sequence than the CHESS-3D-DWI sequence. From results from animal (rat pelvis) experiments using WE-3D-DWI, we obtained fat-saturated DWI. This sequence was useful for in vivo imaging. (author)

  1. MRI of the lumbar spine. Technical aspect. T2-weighted fat saturation coronal dynamic MRI of the lumbar spine

    International Nuclear Information System (INIS)

    Clarisse, J.; Francke, J.P.; Leclet, H.; Bourgeois, Ph.; Chastanet, P.; Cotten, A.

    1998-01-01

    Assess the feasibility of 'dynamic' MRI of the lumbar spine and study the parameters of a single MRI sequence favorable for simultaneous imaging of the meningeal space and the epidural and foraminal venous system. Favor a decline in the number of sacco-radiculograms. Clinical assessment in the following circumstances: discordant clinical and and radiographic findings, difficulty in interpreting single or multiple disc-root conflicts, preoperative work-up in cases of narrow or stenotic lumbar canal. Dynamic MRI of the lumbar spine is possible if the hypothesis that the hyper-lordosis obtained in the supine position creates an anatomic and radiographic situation identical to the hyper-lordosis induced by the upright position is accepted. The 'radiculo-phlebographic' sequence gives images of the root sheaths and the epidural, foraminal and extra-foraminal veins simultaneously, particularly in the coronal plane. (authors)

  2. IDEAL 3D spoiled gradient echo of the articular cartilage of the knee on 3.0 T MRI: a comparison with conventional 3.0 T fast spin-echo T2 fat saturation image.

    Science.gov (United States)

    Han, Chul Hee; Park, Hee Jin; Lee, So Yeon; Chung, Eun Chul; Choi, Seon Hyeong; Yun, Ji Sup; Rho, Myung Ho

    2015-12-01

    Many two-dimensional (2D) morphologic cartilage imaging sequences have disadvantages such as long acquisition time, inadequate spatial resolution, suboptimal tissue contrast, and image degradation secondary to artifacts. IDEAL imaging can overcome these disadvantages. To compare sound-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and quality of two different methods of imaging that include IDEAL 3D SPGR and 3.0-T FSE T2 fat saturation (FS) imaging and to evaluate the utility of IDEAL 3D SPGR for knee joint imaging. SNR and CNR of the patellar and femoral cartilages were measured and calculated. Two radiologists performed subjective scoring of all images for three measures: general image quality, FS, and cartilage evaluation. SNR and CNR values were compared by paired Student's t-tests. Mean SNRs of patellar and femoral cartilages were 90% and 66% higher, respectively, for IDEAL 3D SPGR. CNRs of patellar cartilages and joint fluids were 2.4 times higher for FSE T2 FS, and CNR between the femoral cartilage and joint fluid was 2.2 times higher for FSE T2 FS. General image quality and FS were superior using FSE T2 FS compared to those of IDEAL 3D SPGR imaging according to both readers, while cartilage evaluation was superior using IDEAL 3D SPGR. Additionally, cartilage injuries were more prominent in IDEAL 3D SPGR than in FSE T2FS according to both readers. IDEAL 3D SPGR images show excellent visualization of patellar and femoral cartilages in 3.0 T and can compensate for the weaknesses of FSE T2 FS in the evaluation of cartilage injuries. © The Foundation Acta Radiologica 2014.

  3. Influence of amplitude-related perfusion parameters in the parotid glands by non-fat-saturated dynamic contrast-enhanced magnetic resonance imaging

    International Nuclear Information System (INIS)

    Chiu, Su-Chin; Cheng, Cheng-Chieh; Chang, Hing-Chiu; Chung, Hsiao-Wen; Chiu, Hui-Chu; Liu, Yi-Jui; Hsu, Hsian-He; Juan, Chun-Jung

    2016-01-01

    Purpose: To verify whether quantification of parotid perfusion is affected by fat signals on non-fat-saturated (NFS) dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and whether the influence of fat is reduced with fat saturation (FS). Methods: This study consisted of three parts. First, a retrospective study analyzed DCE-MRI data previously acquired on different patients using NFS (n = 18) or FS (n = 18) scans. Second, a phantom study simulated the signal enhancements in the presence of gadolinium contrast agent at six concentrations and three fat contents. Finally, a prospective study recruited nine healthy volunteers to investigate the influence of fat suppression on perfusion quantification on the same subjects. Parotid perfusion parameters were derived from NFS and FS DCE-MRI data using both pharmacokinetic model analysis and semiquantitative parametric analysis. T tests and linear regression analysis were used for statistical analysis with correction for multiple comparisons. Results: NFS scans showed lower amplitude-related parameters, including parameter A, peak enhancement (PE), and slope than FS scans in the patients (all with P < 0.0167). The relative signal enhancement in the phantoms was proportional to the dose of contrast agent and was lower in NFS scans than in FS scans. The volunteer study showed lower parameter A (6.75 ± 2.38 a.u.), PE (42.12% ± 14.87%), and slope (1.43% ± 0.54% s"−"1) in NFS scans as compared to 17.63 ± 8.56 a.u., 104.22% ± 25.15%, and 9.68% ± 1.67% s"−"1, respectively, in FS scans (all with P < 0.005). These amplitude-related parameters were negatively associated with the fat content in NFS scans only (all with P < 0.05). Conclusions: On NFS DCE-MRI, quantification of parotid perfusion is adversely affected by the presence of fat signals for all amplitude-related parameters. The influence could be reduced on FS scans.

  4. Influence of amplitude-related perfusion parameters in the parotid glands by non-fat-saturated dynamic contrast-enhanced magnetic resonance imaging

    Energy Technology Data Exchange (ETDEWEB)

    Chiu, Su-Chin [Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan, Republic of China and Department of Radiology, Tri-Service General Hospital, Taipei 114, Taiwan (China); Cheng, Cheng-Chieh [Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115 (United States); Chang, Hing-Chiu [Department of Diagnostic Radiology, The University of Hong Kong (Hong Kong); Chung, Hsiao-Wen [Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan (China); Department of Radiology, Tri-Service General Hospital, Taipei 114, Taiwan (China); Department of Radiology, National Defense Medical Center, Taipei 114, Taiwan (China); Chiu, Hui-Chu [Ph.D. Program of Technology Management, Chung Hua University, Hsinchu 300, Taiwan (China); Liu, Yi-Jui [Department of Automatic Control Engineering, Feng-Chia University, Taichung 407, Taiwan (China); Hsu, Hsian-He; Juan, Chun-Jung, E-mail: peterjuancj@yahoo.com.tw [Department of Radiology, Tri-Service General Hospital, Taipei 114, Taiwan and Department of Radiology, National Defense Medical Center, Taipei 114, Taiwan (China)

    2016-04-15

    Purpose: To verify whether quantification of parotid perfusion is affected by fat signals on non-fat-saturated (NFS) dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and whether the influence of fat is reduced with fat saturation (FS). Methods: This study consisted of three parts. First, a retrospective study analyzed DCE-MRI data previously acquired on different patients using NFS (n = 18) or FS (n = 18) scans. Second, a phantom study simulated the signal enhancements in the presence of gadolinium contrast agent at six concentrations and three fat contents. Finally, a prospective study recruited nine healthy volunteers to investigate the influence of fat suppression on perfusion quantification on the same subjects. Parotid perfusion parameters were derived from NFS and FS DCE-MRI data using both pharmacokinetic model analysis and semiquantitative parametric analysis. T tests and linear regression analysis were used for statistical analysis with correction for multiple comparisons. Results: NFS scans showed lower amplitude-related parameters, including parameter A, peak enhancement (PE), and slope than FS scans in the patients (all with P < 0.0167). The relative signal enhancement in the phantoms was proportional to the dose of contrast agent and was lower in NFS scans than in FS scans. The volunteer study showed lower parameter A (6.75 ± 2.38 a.u.), PE (42.12% ± 14.87%), and slope (1.43% ± 0.54% s{sup −1}) in NFS scans as compared to 17.63 ± 8.56 a.u., 104.22% ± 25.15%, and 9.68% ± 1.67% s{sup −1}, respectively, in FS scans (all with P < 0.005). These amplitude-related parameters were negatively associated with the fat content in NFS scans only (all with P < 0.05). Conclusions: On NFS DCE-MRI, quantification of parotid perfusion is adversely affected by the presence of fat signals for all amplitude-related parameters. The influence could be reduced on FS scans.

  5. Combination of fat saturation and variable bandwidth imaging to increase signal-to-noise ratio and decrease motion artifacts for body MR imaging at high field

    International Nuclear Information System (INIS)

    Chew, W.M.

    1989-01-01

    The signal-to-noise ratio (SNR) of the MR imaging examination is a critical component of the quality of the image. Standard methods to increase SNR include signal averaging with multiple excitations, at the expense of imaging time (which on T2-weighted images could be quite significant), or increasing pixel volume by manipulation of field of view, matrix size, and/or section thickness, all at the expense of resolution. Another available method to increase SNR is to reduce the bandwidth of the receiver, which increases SNR by the square root of the amount of the reduction. The penalty imposed on high-field-strength MR examinations of the body is an unacceptable increase in chemical shift artifact. However, presaturating the fat resonance eliminates the chemical shift artifact. Thus, a combination of imaging techniques, fat suppression, and decreased bandwidth imaging can produce images free of chemical shift artifact with increased SNR and no penalty in resolution or imaging time. Early studies also show a reduction in motion artifact when fat saturation is used. This paper reports MR imaging performed with a 1.5-T Signa imager. With this technique, T2-weighted images (2,500/20/80 [repetition time msec/echo time msec/inversion time msec]) illustrating the increase in SNR and T1-weighted images (600/20) demonstrating a decrease in motion artifact are shown

  6. Frequency selective tunable spin wave channeling in the magnonic network

    Energy Technology Data Exchange (ETDEWEB)

    Sadovnikov, A. V., E-mail: sadovnikovav@gmail.com; Nikitov, S. A. [Laboratory “Metamaterials,” Saratov State University, Saratov 410012 (Russian Federation); Kotel' nikov Institute of Radioengineering and Electronics, Russian Academy of Sciences, Moscow 125009 (Russian Federation); Beginin, E. N.; Odincov, S. A.; Sheshukova, S. E.; Sharaevskii, Yu. P. [Laboratory “Metamaterials,” Saratov State University, Saratov 410012 (Russian Federation); Stognij, A. I. [Scientific-Practical Materials Research Center, National Academy of Sciences of Belarus, 220072 Minsk (Belarus)

    2016-04-25

    Using the space-resolved Brillouin light scattering spectroscopy, we study the frequency and wavenumber selective spin-wave channeling. We demonstrate the frequency selective collimation of spin-wave in an array of magnonic waveguides, formed between the adjacent magnonic crystals on the surface of yttrium iron garnet film. We show the control over spin-wave propagation length by the orientation of an in-plane bias magnetic field. Fabricated array of magnonic crystal can be used as a magnonic platform for multidirectional frequency selective signal processing applications in magnonic networks.

  7. Frequency selective surfaces integrated with phased array antennas

    NARCIS (Netherlands)

    Monni, S.

    2005-01-01

    Frequency Selective Surfaces (FSS's) are periodic arrays of patches and/or slots etched on a metal plate, having frequency and angular ??ltering properties. The FSS response to an excitation (for example a plane wave) is characterized in terms of its re ection and transmission coe??cient, and

  8. Consequences of peripheral frequency selectivity for nonsimultaneous masking

    NARCIS (Netherlands)

    Duifhuis, H.

    1973-01-01

    The frequency selectivity of the peripheral ear (e.g., at the VIIIth nerve level) is so acute that onset and offset transients in responses to short signals produce a nonnegligible extension of the signal duration. Thus, peripheral excitation patterns produced by signals which were separated in time

  9. Characteristics of spectro-temporal modulation frequency selectivity in humans.

    Science.gov (United States)

    Oetjen, Arne; Verhey, Jesko L

    2017-03-01

    There is increasing evidence that the auditory system shows frequency selectivity for spectro-temporal modulations. A recent study of the authors has shown spectro-temporal modulation masking patterns that were in agreement with the hypothesis of spectro-temporal modulation filters in the human auditory system [Oetjen and Verhey (2015). J. Acoust. Soc. Am. 137(2), 714-723]. In the present study, that experimental data and additional data were used to model this spectro-temporal frequency selectivity. The additional data were collected to investigate to what extent the spectro-temporal modulation-frequency selectivity results from a combination of a purely temporal amplitude-modulation filter and a purely spectral amplitude-modulation filter. In contrast to the previous study, thresholds were measured for masker and target modulations with opposite directions, i.e., an upward pointing target modulation and a downward pointing masker modulation. The comparison of this data set with previous corresponding data with the same direction from target and masker modulations indicate that a specific spectro-temporal modulation filter is required to simulate all aspects of spectro-temporal modulation frequency selectivity. A model using a modified Gabor filter with a purely temporal and a purely spectral filter predicts the spectro-temporal modulation masking data.

  10. Cavity-soliton laser with frequency-selective feedback

    International Nuclear Information System (INIS)

    Scroggie, A. J.; Firth, W. J.; Oppo, G.-L.

    2009-01-01

    We present a coupled-cavity model of a laser with frequency-selective feedback, and use it to analyze and explain the existence of stationary and dynamic spatial solitons in the device. Particular features of soliton addressing in this system are discussed. We demonstrate the advantages of our model with respect to the common Lang-Kobayashi approximation.

  11. Frequency Selective Surfaces for extended Bandwidth backing reflector functions

    NARCIS (Netherlands)

    Pasian, M.; Neto, A.; Monni, S.; Ettorre, M.; Gerini, G.

    2008-01-01

    This paper deals with the use of Frequency Selective Surfaces (FSS) to increase the Efficiency × Bandwidth product in Ultra-Wide Band (UWB) antenna arrays whose efficiency is limited by the front-to-back ratio. If the backing reflector is realized in one metal plane solution its location will be

  12. Pulsed magnetization transfer contrast MRI by a sequence with water selective excitation

    Energy Technology Data Exchange (ETDEWEB)

    Schick, F. [Univ. of Tuebingen (Germany)

    1996-01-01

    A water selective SE imaging sequence was developed providing suitable properties for the assessment of magnetization transfer (MT) effects in tissues with considerable amounts of fat. The sequence with water selective excitation and slice selective refocusing combines the following features: The RIF exposure on the macromolecular protons is relatively low for single slice imaging without MT prepulses, since no additional pulses for fat saturation are necessary. Water selection by frequency selective excitation diminishes faults in the subtraction of images recorded with and without MT prepulses (which might arise from movements). High differences in the signal amplitudes from hyaline cartilage and muscle tissue were obtained comparing images recorded with irradiation of the series of prepulses for MT and those lacking MT prepulses. Utilizations of the described water selective approach for the assessment of MT effects in lesions of cartilage and bone are demonstrated. MT saturation was also examined in muscles with fatty degeneration of patients suffering from progressive muscular dystrophy. The described technique allows determination of MT effects with good precision in a single slice, especially in regions with dominating fat signals. 22 refs., 5 figs.

  13. Equivalence of Linear MMSE Detection in DS-CDMA and MC-CDMA Systems over Time and Frequency Selective Channels

    Directory of Open Access Journals (Sweden)

    Tamer A. Kadous

    2003-01-01

    Full Text Available The goal of this paper is to compare the performance of the linear minimum mean square error (MMSE detector for a class of code division multiple access (CDMA systems in time and frequency selective channels. Specifically, we consider direct sequence (DS-CDMA, multicarrier (MC-CDMA, and the MC-DS-CDMA systems. Two key tools are used in our development. First, a general time-frequency framework that includes the different CDMA systems as special cases. Second, the duality between time and frequency domains that is used to derive equivalences between the different CDMA systems operating over purely frequency selective and purely time selective channels. We then combine the insights obtained from these special cases to assess the performance of CDMA systems over time and frequency selective channels. We provide sufficient conditions for the codes employed by the CDMA systems for the equivalences to hold. Numerical results are presented to illustrate the results.

  14. Distributive estimation of frequency selective channels for massive MIMO systems

    KAUST Repository

    Zaib, Alam

    2015-12-28

    We consider frequency selective channel estimation in the uplink of massive MIMO-OFDM systems, where our major concern is complexity. A low complexity distributed LMMSE algorithm is proposed that attains near optimal channel impulse response (CIR) estimates from noisy observations at receive antenna array. In proposed method, every antenna estimates the CIRs of its neighborhood followed by recursive sharing of estimates with immediate neighbors. At each step, every antenna calculates the weighted average of shared estimates which converges to near optimal LMMSE solution. The simulation results validate the near optimal performance of proposed algorithm in terms of mean square error (MSE). © 2015 EURASIP.

  15. Analysis of Various Frequency Selective Shielding Glass by FDTD method

    OpenAIRE

    笠嶋, 善憲; Kasashima, Yoshinori

    2012-01-01

    A frequency Selective shielding (FSS) glass is a print of many same size antennas on a sheet of glass, and it has high shielding properties for one specific frequency. This time, the author analyzed characteristics of various FSSs whose antenna types are different by FDTD method. The antenna types are cross dipole, circular loop, square loop, circular patch, and square patch. As the result, the FSSs can be composed of the various types of the antennas, and the FSSs have broad-band shielding c...

  16. Frequency selective bolometer development at Argonne National Laboratory

    Science.gov (United States)

    Datesman, Aaron; Pearson, John; Wang, Gensheng; Yefremenko, Volodymyr; Divan, Ralu; Downes, Thomas; Chang, Clarence; McMahon, Jeff; Meyer, Stephan; Carlstrom, John; Logan, Daniel; Perera, Thushara; Wilson, Grant; Novosad, Valentyn

    2008-07-01

    We discuss the development, at Argonne National Laboratory, of a four-pixel camera suitable for photometry of distant dusty galaxies located by Spitzer and SCUBA, and for study of other millimeter-wave sources such as ultra-luminous infrared galaxies, the Sunyaev-Zeldovich (SZ) effect in clusters, and galactic dust. Utilizing Frequency Selective Bolometers (FSBs) with superconducting Transition-Edge Sensors (TESs), each of the camera's four pixels is sensitive to four colors, with frequency bands centered approximately at 150, 220, 270, and 360 GHz. The current generation of these devices utilizes proximity effect superconducting bilayers of Mo/Au or Ti/Au for TESs, along with frequency selective circuitry on membranes of silicon nitride 1 cm across and 1 micron thick. The operational properties of these devices are determined by this circuitry, along with thermal control structures etched into the membranes. These etched structures do not perforate the membrane, so that the device is both comparatively robust mechanically and carefully tailored in terms of its thermal transport properties. In this paper, we report on development of the superconducting bilayer TES technology and characterization of the FSB stacks. This includes the use of new materials, the design and testing of thermal control structures, the introduction of desirable thermal properties using buried layers of crystalline silicon underneath the membrane, detector stability control, and optical and thermal test results. The scientific motivation, FSB design, FSB fabrication, and measurement results are discussed.

  17. Effect of efferent activation on binaural frequency selectivity.

    Science.gov (United States)

    Verhey, Jesko L; Kordus, Monika; Drga, Vit; Yasin, Ifat

    2017-07-01

    Binaural notched-noise experiments indicate a reduced frequency selectivity of the binaural system compared to monaural processing. The present study investigates how auditory efferent activation (via the medial olivocochlear system) affects binaural frequency selectivity in normal-hearing listeners. Thresholds were measured for a 1-kHz signal embedded in a diotic notched-noise masker for various notch widths. The signal was either presented in phase (diotic) or in antiphase (dichotic), gated with the noise. Stimulus duration was 25 ms, in order to avoid efferent activation due to the masker or the signal. A bandpass-filtered noise precursor was presented prior to the masker and signal stimuli to activate the efferent system. The silent interval between the precursor and the masker-signal complex was 50 ms. For comparison, thresholds for detectability of the masked signal were also measured in a baseline condition without the precursor and, in addition, without the masker. On average, the results of the baseline condition indicate an effectively wider binaural filter, as expected. For both signal phases, the addition of the precursor results in effectively wider filters, which is in agreement with the hypothesis that cochlear gain is reduced due to the presence of the precursor. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Mechanical stress-controlled tunable active frequency-selective surface

    Science.gov (United States)

    Huang, Bo-Cin; Hong, Jian-Wei; Lo, Cheng-Yao

    2017-01-01

    This study proposes a tunable active frequency-selective surface (AFSS) realized by mechanically expanding or contracting a split-ring resonator (SRR) array. The proposed AFSS transfers mechanical stress from its elastic substrate to the top of the SRR, thereby achieving electromagnetic (EM) modulation without the need for an additional external power supply, meeting the requirements for the target application: the invisibility cloak. The operating mechanism of the proposed AFSS differs from those of other AFSSs, supporting modulations in arbitrary frequencies in the target range. The proposed stress-controlled or strain-induced EM modulation proves the existence of an identical and linear relationship between the strain gradient and the frequency shift, implying its suitability for other EM modulation ranges and applications.

  19. Nanoparticle array based optical frequency selective surfaces: theory and design.

    Science.gov (United States)

    Saeidi, Chiya; van der Weide, Daniel

    2013-07-01

    We demonstrate a synthesis procedure for designing a bandstop optical frequency selective surface (FSS) composed of nanoparticle (NP) elements. The proposed FSS uses two-dimensional (2-D) periodic arrays of NPs with subwavelength unit-cell dimensions. We derive equivalent circuit for a nanoparticle array (NPA) using the closed-form solution for a 2-D NPA excited by a plane wave in the limit of the dipole approximation, which includes contribution from both individual and collective plasmon modes. Using the extracted equivalent circuit, we demonstrate synthesis of an optical FSS using cascaded NPA layers as coupled resonators, which we validate with both circuit model and full-wave simulation for a third-order Butterworth bandstop prototype.

  20. Frequency selective surfaces based high performance microstrip antenna

    CERN Document Server

    Narayan, Shiv; Jha, Rakesh Mohan

    2016-01-01

    This book focuses on performance enhancement of printed antennas using frequency selective surfaces (FSS) technology. The growing demand of stealth technology in strategic areas requires high-performance low-RCS (radar cross section) antennas. Such requirements may be accomplished by incorporating FSS into the antenna structure either in its ground plane or as the superstrate, due to the filter characteristics of FSS structure. In view of this, a novel approach based on FSS technology is presented in this book to enhance the performance of printed antennas including out-of-band structural RCS reduction. In this endeavor, the EM design of microstrip patch antennas (MPA) loaded with FSS-based (i) high impedance surface (HIS) ground plane, and (ii) the superstrates are discussed in detail. The EM analysis of proposed FSS-based antenna structures have been carried out using transmission line analogy, in combination with the reciprocity theorem. Further, various types of novel FSS structures are considered in desi...

  1. Optically transparent frequency selective surfaces on flexible thin plastic substrates

    Energy Technology Data Exchange (ETDEWEB)

    Dewani, Aliya A., E-mail: a.ashraf@griffith.edu.au; O’Keefe, Steven G.; Thiel, David V.; Galehdar, Amir [School Of Electrical Engineering, Griffith University, Brisbane, 4111 (Australia)

    2015-02-15

    A novel 2D simple low cost frequency selective surface was screen printed on thin (0.21 mm), flexible transparent plastic substrate (relative permittivity 3.2). It was designed, fabricated and tested in the frequency range 10-20 GHz. The plane wave transmission and reflection coefficients agreed with numerical modelling. The effective permittivity and thickness of the backing sheet has a significant effect on the frequency characteristics. The stop band frequency reduced from 15GHz (no backing) to 12.5GHz with polycarbonate. The plastic substrate thickness beyond 1.8mm has minimal effect on the resonant frequency. While the inner element spacing controls the stop-band frequency, the substrate thickness controls the bandwidth. The screen printing technique provided a simple, low cost FSS fabrication method to produce flexible, conformal, optically transparent and bio-degradable FSS structures which can find their use in electromagnetic shielding and filtering applications in radomes, reflector antennas, beam splitters and polarizers.

  2. Optically transparent frequency selective surfaces on flexible thin plastic substrates

    Science.gov (United States)

    Dewani, Aliya A.; O'Keefe, Steven G.; Thiel, David V.; Galehdar, Amir

    2015-02-01

    A novel 2D simple low cost frequency selective surface was screen printed on thin (0.21 mm), flexible transparent plastic substrate (relative permittivity 3.2). It was designed, fabricated and tested in the frequency range 10-20 GHz. The plane wave transmission and reflection coefficients agreed with numerical modelling. The effective permittivity and thickness of the backing sheet has a significant effect on the frequency characteristics. The stop band frequency reduced from 15GHz (no backing) to 12.5GHz with polycarbonate. The plastic substrate thickness beyond 1.8mm has minimal effect on the resonant frequency. While the inner element spacing controls the stop-band frequency, the substrate thickness controls the bandwidth. The screen printing technique provided a simple, low cost FSS fabrication method to produce flexible, conformal, optically transparent and bio-degradable FSS structures which can find their use in electromagnetic shielding and filtering applications in radomes, reflector antennas, beam splitters and polarizers.

  3. Design of Nonuniform Filter Bank Transceivers for Frequency Selective Channels

    Directory of Open Access Journals (Sweden)

    Yuan-Pei Lin

    2007-01-01

    Full Text Available In recent years, there has been considerable interest in the theory and design of filter bank transceivers due to their superior frequency response. In many applications, it is desired to have transceivers that can support multiple services with different incoming data rates and different quality-of-service requirements. To meet these requirements, we can either do resource allocation or design transceivers with a nonuniform bandwidth partition. In this paper, we propose a method for the design of nonuniform filter bank transceivers for frequency selective channels. Both frequency response and signal-to-interference ratio (SIR can be incorporated in the transceiver design. Moreover, the technique can be extended to the case of nonuniform filter bank transceivers with rational sampling factors. Simulation results show that nonuniform filter bank transceivers with good filter responses as well as high SIR can be obtained by the proposed design method.

  4. Tunable antenna radome based on graphene frequency selective surface

    Science.gov (United States)

    Qu, Meijun; Rao, Menglou; Li, Shufang; Deng, Li

    2017-09-01

    In this paper, a graphene-based frequency selective surface (FSS) is proposed. The proposed FSS exhibits a tunable bandpass filtering characteristic due to the alterable conductivity of the graphene strips which is controlled by chemical potential. Based on the reconfigurable bandpass property of the proposed FSS, a cylindrical antenna radome is designed using the FSS unit cells. A conventional omnidirectional dipole can realize a two-beam directional pattern when it is placed into the proposed antenna radome. Forward and backward endfire radiations of the dipole loaded with the radome is realized by properly adjusting the chemical potential. The proposed antenna radome is extremely promising for beam-scanning in terahertz and mid-infrared plasmonic devices and systems when the gain of a conventional antenna needs to be enhanced.

  5. Dual-band frequency selective surface with large band separation and stable performance

    Science.gov (United States)

    Zhou, Hang; Qu, Shao-Bo; Peng, Wei-Dong; Lin, Bao-Qin; Wang, Jia-Fu; Ma, Hua; Zhang, Jie-Qiu; Bai, Peng; Wang, Xu-Hua; Xu, Zhuo

    2012-05-01

    A new technique of designing a dual-band frequency selective surface with large band separation is presented. This technique is based on a delicately designed topology of L- and Ku-band microwave filters. The two band-pass responses are generated by a capacitively-loaded square-loop frequency selective surface and an aperture-coupled frequency selective surface, respectively. A Faraday cage is located between the two frequency selective surface structures to eliminate undesired couplings. Based on this technique, a dual-band frequency selective surface with large band separation is designed, which possesses large band separation, high selectivity, and stable performance under various incident angles and different polarizations.

  6. Optically transparent frequency selective surfaces on flexible thin plastic substrates

    Directory of Open Access Journals (Sweden)

    Aliya A. Dewani

    2015-02-01

    Full Text Available A novel 2D simple low cost frequency selective surface was screen printed on thin (0.21 mm, flexible transparent plastic substrate (relative permittivity 3.2. It was designed, fabricated and tested in the frequency range 10-20 GHz. The plane wave transmission and reflection coefficients agreed with numerical modelling. The effective permittivity and thickness of the backing sheet has a significant effect on the frequency characteristics. The stop band frequency reduced from 15GHz (no backing to 12.5GHz with polycarbonate. The plastic substrate thickness beyond 1.8mm has minimal effect on the resonant frequency. While the inner element spacing controls the stop-band frequency, the substrate thickness controls the bandwidth. The screen printing technique provided a simple, low cost FSS fabrication method to produce flexible, conformal, optically transparent and bio-degradable FSS structures which can find their use in electromagnetic shielding and filtering applications in radomes, reflector antennas, beam splitters and polarizers.

  7. Spectro-temporal modulation masking patterns reveal frequency selectivity.

    Science.gov (United States)

    Oetjen, Arne; Verhey, Jesko L

    2015-02-01

    The present study investigated the possibility that the human auditory system demonstrates frequency selectivity to spectro-temporal amplitude modulations. Threshold modulation depth for detecting sinusoidal spectro-temporal modulations was measured using a generalized masked threshold pattern paradigm with narrowband masker modulations. Four target spectro-temporal modulations were examined, differing in their temporal and spectral modulation frequencies: a temporal modulation of -8, 8, or 16 Hz combined with a spectral modulation of 1 cycle/octave and a temporal modulation of 4 Hz combined with a spectral modulation of 0.5 cycles/octave. The temporal center frequencies of the masker modulation ranged from 0.25 to 4 times the target temporal modulation. The spectral masker-modulation center-frequencies were 0, 0.5, 1, 1.5, and 2 times the target spectral modulation. For all target modulations, the pattern of average thresholds for the eight normal-hearing listeners was consistent with the hypothesis of a spectro-temporal modulation filter. Such a pattern of modulation-frequency sensitivity was predicted on the basis of psychoacoustical data for purely temporal amplitude modulations and purely spectral amplitude modulations. An analysis of separability indicates that, for the present data set, selectivity in the spectro-temporal modulation domain can be described by a combination of a purely spectral and a purely temporal modulation filter function.

  8. Generation of radio vortex beams with designable polarization using anisotropic frequency selective surface

    Science.gov (United States)

    Yang, Jin; Zhang, Cheng; Ma, Hui Feng; Zhao, Jie; Dai, Jun Yan; Yuan, Wei; Yang, Liu Xi; Cheng, Qiang; Cui, Tie Jun

    2018-05-01

    We propose a strategy to convert a linearly polarized wave from a single point source to an orbital angular momentum (OAM) wave by arbitrary polarization via an anisotropic frequency selective surface (FSS) in the microwave frequency. By tailoring the geometries of FSS elements, reflection-phases in x and y polarizations are engineered and encoded independently, which allows us to design the eventual polarization state of the generated OAM vortex beam by elaborately selecting individual coding sequences for each polarization. Two types of FSSs are designed and experimentally characterized to demonstrate the capability of OAM generation with circular and linear polarizations, respectively, showing excellent performance in a wide bandwidth from 14 to 16 GHz. This method provides opportunities for polarization multiplexing in microwave OAM communication systems.

  9. Substrate integrated ferrite phase shifters and active frequency selective surfaces

    International Nuclear Information System (INIS)

    Cahill, B.M.

    2002-01-01

    There are two distinct parts to this thesis; the first investigates the use of ferrite tiles in the construction of printed phase shifting transmission lines, culminating in the design of two compact electromagnetic controlled beam steered patch and slot antenna arrays. The second part investigates the use of active frequency selective surfaces (AFSS), which are later used to cover a uPVC constructed enclosure. Field intensity measurements are taken from within the enclosure to determine the dynamic screening effectiveness. Trans Tech G-350 Ferrite is investigated to determine its application in printed microstrip and stripline phase shifting transmission lines. 50-Ohm transmission lines are constructed using the ferrite tile and interfaced to Rogers RT Duroid 5870 substrate. Scattering parameter measurements are made under the application of variable magnetic fields to the ferrite. Later, two types of planar microwave beam steering antennas are constructed. The first uses the ferrites integrated into the Duroid as microstrip lines with 3 patch antennas as the radiating elements. The second uses stripline transmission lines, with slot antennas as the radiating sources etched into the ground plane of the triplate. Beam steering is achieved by the application of an external electromagnet. An AFSS is constructed by the interposition of PIN diodes into a dipole FSS array. Transmission response measurements are then made for various angles of electromagnetic wave incidence. Two states of operation exist: when a current is passed through the diodes and when the diodes are switched off. These two states form a high pass and band stop space filter respectively. An enclosure covered with the AFSS is constructed and externally illuminated in the range 2.0 - 2.8GHz. A probe antenna inside the enclosure positioned at various locations through out the volume is used to establish the effective screening action of the AFSS in 3 dimensional space. (author)

  10. Dual-band frequency selective surface with large band separation and stable performance

    International Nuclear Information System (INIS)

    Zhou Hang; Qu Shao-Bo; Lin Bao-Qin; Wang Jia-Fu; Ma Hua; Zhang Jie-Qiu; Peng Wei-Dong; Bai Peng; Wang Xu-Hua; Xu Zhuo

    2012-01-01

    A new technique of designing a dual-band frequency selective surface with large band separation is presented. This technique is based on a delicately designed topology of L- and Ku-band microwave filters. The two band-pass responses are generated by a capacitively-loaded square-loop frequency selective surface and an aperture-coupled frequency selective surface, respectively. A Faraday cage is located between the two frequency selective surface structures to eliminate undesired couplings. Based on this technique, a dual-band frequency selective surface with large band separation is designed, which possesses large band separation, high selectivity, and stable performance under various incident angles and different polarizations. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

  11. Application of high Tc superconductors as frequency selective surfaces: Experiment and theory

    International Nuclear Information System (INIS)

    Dawei Zhang; Yahya Rahmat-Samii; Fetterman, H.R.

    1993-01-01

    YBa 2 Cu 3 O 7-x and Tl 2 CaBa 2 Cu 2 O 8 high temperature superconducting thin films were utilized to fabricate frequency selective surfaces (FSS) at millimeter-wave frequencies (75--110 GHz). An analytical/numerical model was applied, using a Floquet expansion and the Method of Moments, to analyze bandstop superconducting frequency selective surfaces. Experimental results were compared with the model, and showed a good agreement with resonant frequency prediction with an accuracy of better than 1%. The use of the superconducting frequency selective surfaces as quasi-optical millimeter-wave bandpass filters was also demonstrated

  12. Multisource full waveform inversion of marine streamer data with frequency selection

    KAUST Repository

    Huang, Yunsong; Schuster, Gerard T.

    2013-01-01

    Multisource migration with frequency selection is now extended to multisource full waveform inversion (FWI) of supergathers for marine streamer data. There are three advantages of this approach compared to conventional FWI for marine streamer data. 1. The multisource FWI method with frequency selection is computationally more efficient than conventional FWI. 2. A supergather requires more than an order of magnitude less storage than the the original data. 3. Frequency selection overcomes the acquisition mismatch between the observed data and the simulated multisource supergathers for marine data. This mismatch problem has prevented the efficient application of FWI to marine geometries in the space-time domain. Preliminary result of applying multisource FWI with frequency selection to a synthetic marine data set suggests it is at least four times more efficient than standard FWI.

  13. Full Waveform Inversion with Multisource Frequency Selection of Marine Streamer Data

    KAUST Repository

    Huang, Yunsong; Schuster, Gerard T.

    2017-01-01

    The theory and practice of multisource full waveform inversion of marine supergathers are described with a frequency-selection strategy. The key enabling property of frequency selection is that it eliminates the crosstalk among sources, thus overcoming the aperture mismatch of marine multisource inversion. Tests on multisource full waveform inversion of synthetic marine data and Gulf of Mexico data show speedups of 4× and 8×, respectively, compared to conventional full waveform inversion.

  14. Full Waveform Inversion with Multisource Frequency Selection of Marine Streamer Data

    KAUST Repository

    Huang, Yunsong

    2017-10-27

    The theory and practice of multisource full waveform inversion of marine supergathers are described with a frequency-selection strategy. The key enabling property of frequency selection is that it eliminates the crosstalk among sources, thus overcoming the aperture mismatch of marine multisource inversion. Tests on multisource full waveform inversion of synthetic marine data and Gulf of Mexico data show speedups of 4× and 8×, respectively, compared to conventional full waveform inversion.

  15. Spatial Tuning of a RF Frequency Selective Surface through Origami (Postprint)

    Science.gov (United States)

    2016-05-12

    computational tools to systematically predict optimal folds. 15. SUBJECT TERMS origami, frequency selective surface, tuning, radio frequency 16...experimental study and motivates the development of computational tools to systematically predict optimal fold patterns for targeted frequency response...folding motions. The precise mapping of origami presents a novel method to spatially tune radio frequency (RF) devices, including adaptive antennas

  16. Secured Communication over Frequency-Selective Fading Channels: A Practical Vandermonde Precoding

    Directory of Open Access Journals (Sweden)

    Mari Kobayashi

    2009-01-01

    Full Text Available We study the frequency-selective broadcast channel with confidential messages (BCC where the transmitter sends a confidential message to receiver 1 and a common message to receivers 1 and 2. In the case of a block transmission of N symbols followed by a guard interval of L symbols, the frequency-selective channel can be modeled as a N×(N+L Toeplitz matrix. For this special type of multiple-input multiple-output channels, we propose a practical Vandermonde precoding that projects the confidential messages in the null space of the channel seen by receiver 2 while superposing the common message. For this scheme, we provide the achievable rate region and characterize the optimal covariance for some special cases of interest. Interestingly, the proposed scheme can be applied to other multiuser scenarios such as the K+1-user frequency-selective BCC with K confidential messages and the two-user frequency-selective BCC with two confidential messages. For each scenario, we provide the secrecy degree of freedom (s.d.o.f. region of the corresponding channel and prove the optimality of the Vandermonde precoding. One of the appealing features of the proposed scheme is that it does not require any specific secrecy encoding technique but can be applied on top of any existing powerful encoding schemes.

  17. Secured Communication over Frequency-Selective Fading Channels: A Practical Vandermonde Precoding

    Directory of Open Access Journals (Sweden)

    Debbah Mérouane

    2009-01-01

    Full Text Available We study the frequency-selective broadcast channel with confidential messages (BCC where the transmitter sends a confidential message to receiver 1 and a common message to receivers 1 and 2. In the case of a block transmission of symbols followed by a guard interval of symbols, the frequency-selective channel can be modeled as a Toeplitz matrix. For this special type of multiple-input multiple-output channels, we propose a practical Vandermonde precoding that projects the confidential messages in the null space of the channel seen by receiver 2 while superposing the common message. For this scheme, we provide the achievable rate region and characterize the optimal covariance for some special cases of interest. Interestingly, the proposed scheme can be applied to other multiuser scenarios such as the -user frequency-selective BCC with confidential messages and the two-user frequency-selective BCC with two confidential messages. For each scenario, we provide the secrecy degree of freedom (s.d.o.f. region of the corresponding channel and prove the optimality of the Vandermonde precoding. One of the appealing features of the proposed scheme is that it does not require any specific secrecy encoding technique but can be applied on top of any existing powerful encoding schemes.

  18. Frequency Selective Properties of Coaxial Transmission Lines Loaded with Combined Artificial Inclusions

    Directory of Open Access Journals (Sweden)

    Francisco Falcone

    2014-01-01

    Full Text Available The properties of a modified coaxial transmission line by periodic inclusions will be discussed. The introduction of split ring resonators, conductor stubs, air gaps, and combination of these gives rise to new frequency selective properties, such as stopband or passband behavior, observable in planar as well as volumetric metamaterial structures. These results envisage new potential applications and implementation of devices in coaxial transmission line technology.

  19. A study of the impact of frequency selectivity on link adaptive wireless LAN systems

    OpenAIRE

    Armour, SMD; Doufexi, A; Nix, AR; Bull, DR

    2002-01-01

    Wireless local area networks (WLANs) supporting broadband multimedia communication are being developed and standardized around the world. The HIPERLAN/2, 802.11a and HiSWANa standards provide channel adaptive data rates between 6 and 54 Mbps in the 5GHz radio band. The link adaptation mechanism is not specified in the standards. In this paper the performance of the HIPERLAN/2 system is evaluated in terms of throughput in a range of test channels with different degrees of frequency selectivity...

  20. Least-squares reverse time migration of marine data with frequency-selection encoding

    KAUST Repository

    Dai, Wei

    2013-08-20

    The phase-encoding technique can sometimes increase the efficiency of the least-squares reverse time migration (LSRTM) by more than one order of magnitude. However, traditional random encoding functions require all the encoded shots to share the same receiver locations, thus limiting the usage to seismic surveys with a fixed spread geometry. We implement a frequency-selection encoding strategy that accommodates data with a marine streamer geometry. The encoding functions are delta functions in the frequency domain, so that all the en- coded shots have unique non-overlapping frequency content, and the receivers can distinguish the wavefield from each shot with a unique frequency band. Since the encoding functions are orthogonal to each other, there will be no crosstalk between different shots during modeling and migration. With the frequency-selection encoding method, the computational efficiency of LSRTM is increased so that its cost is compara- ble to conventional RTM for both the Marmousi2 model and a marine data set recorded in the Gulf of Mexico. With more iterations, the LSRTM image quality is further improved. We conclude that LSRTM with frequency-selection is an efficient migration method that can sometimes produce more focused images than conventional RTM.

  1. Mechanical frequency selectivity of an artificial basilar membrane using a beam array with narrow supports

    International Nuclear Information System (INIS)

    Kim, Sangwon; Jang, Jongmoon; Choi, Hongsoo; Song, Won Joon; Jang, Jeong Hun

    2013-01-01

    The study presented in this paper assessed the frequency selectivity of an artificial basilar membrane (ABM) constructed using a piezoelectric beam array with narrow supports. Three ABM samples were constructed. Each ABM contained 16 beams with various lengths in a one-dimensional array. To experimentally assess the frequency selectivity of the ABM, mechanical vibration induced either by an electrical or an acoustic stimulus was measured with a scanning laser-Doppler vibrometer. The electro-mechanical and acousto-mechanical transfer functions were defined for the same purpose. The tonotopy of each beam array was visualized by post-processing the experimental results. Finite element analyses were conducted to numerically compute the resonance frequencies, identify the associated vibrational modes, and evaluate the harmonic responses of the beams. The influence of the residual stresses existing in the beams was reflected in the geometric models by introducing three different levels of arc-shaped lateral deformations in the beams. The harmonic analyses revealed that each beam of the ABM samples presented independent band-pass characteristics. The experiments and simulations commonly showed a frequency selectivity of the fabricated ABMs in the range of 2–20 kHz. Therefore, the device is suitable for development of a totally implantable artificial cochlea, implementing a mechanical frequency analyzer. This work is part of research to develop a prototype of a totally implantable artificial cochlea. (paper)

  2. Least-squares reverse time migration of marine data with frequency-selection encoding

    KAUST Repository

    Dai, Wei

    2013-06-24

    The phase-encoding technique can sometimes increase the efficiency of the least-squares reverse time migration (LSRTM) by more than one order of magnitude. However, traditional random encoding functions require all the encoded shots to share the same receiver locations, thus limiting the usage to seismic surveys with a fixed spread geometry. We implement a frequency-selection encoding strategy that accommodates data with a marine streamer geometry. The encoding functions are delta functions in the frequency domain, so that all the encoded shots have unique nonoverlapping frequency content, and the receivers can distinguish the wavefield from each shot with a unique frequency band. Because the encoding functions are orthogonal to each other, there will be no crosstalk between different shots during modeling and migration. With the frequency-selection encoding method, the computational efficiency of LSRTM is increased so that its cost is comparable to conventional RTM for the Marmousi2 model and a marine data set recorded in the Gulf of Mexico. With more iterations, the LSRTM image quality is further improved by suppressing migration artifacts, balancing reflector amplitudes, and enhancing the spatial resolution. We conclude that LSRTM with frequency-selection is an efficient migration method that can sometimes produce more focused images than conventional RTM. © 2013 Society of Exploration Geophysicists.

  3. Temperature dependency of cupular mechanics and hair cell frequency selectivity in the fish canal lateral line organ

    NARCIS (Netherlands)

    Wiersinga-Post, JEC; van Netten, SM

    2000-01-01

    The mechanical frequency selectivity of the cupula located in the supraorbital lateral line canal and the frequency selectivity of the hair cells driven by the cupula were measured simultaneously in vivo. Laser interferometry was used to measure cupular mechanics and extracellular receptor

  4. Analysis of Broad-band Frequency Selective Shielding Glass by FDTD method

    OpenAIRE

    笠嶋, 善憲; Kasashima, Yoshinori

    2010-01-01

    A frequency Selective shielding (FSS) glass is a print of many same size antennas on a sheet of glass, and it has high shielding properties for one specific frequency. In the past, the author analyzed theoretically the characteristics of the FSS, as a large scale array antenna. The FSS has narrow-band shielding characteristics. This time, the author analyzed accurately the characteristics of a FSS glass being a print of many same size dipole antennas on a sheet of glass by FDTD method. As the...

  5. Cooperative Orthogonal Space-Time-Frequency Block Codes over a MIMO-OFDM Frequency Selective Channel

    Directory of Open Access Journals (Sweden)

    M. Rezaei

    2016-03-01

    Full Text Available In this paper, a cooperative algorithm to improve the orthogonal space-timefrequency block codes (OSTFBC in frequency selective channels for 2*1, 2*2, 4*1, 4*2 MIMO-OFDM systems, is presented. The algorithm of three node, a source node, a relay node and a destination node is formed, and is implemented in two stages. During the first stage, the destination and the relay antennas receive the symbols sent by the source antennas. The destination node and the relay node obtain the decision variables employing time-space-frequency decoding process by the received signals. During the second stage, the relay node transmits decision variables to the destination node. Due to the increasing diversity in the proposed algorithm, decision variables in the destination node are increased to improve system performance. The bit error rate of the proposed algorithm at high SNR is estimated by considering the BPSK modulation. The simulation results show that cooperative orthogonal space-time-frequency block coding, improves system performance and reduces the BER in a frequency selective channel.

  6. Spatial Frequency Selectivity Is Impaired in Dopamine D2 Receptor Knockout Mice

    Science.gov (United States)

    Souza, Bruno Oliveira Ferreira; Abou Rjeili, Mira; Quintana, Clémentine; Beaulieu, Jean M.; Casanova, Christian

    2018-01-01

    Dopamine is a neurotransmitter implicated in several brain functions, including vision. In the present study, we investigated the impacts of the lack of D2 dopamine receptors on the structure and function of the primary visual cortex (V1) of D2-KO mice using optical imaging of intrinsic signals. Retinotopic maps were generated in order to measure anatomo-functional parameters such as V1 shape, cortical magnification factor, scatter, and ocular dominance. Contrast sensitivity and spatial frequency selectivity (SF) functions were computed from responses to drifting gratings. When compared to control mice, none of the parameters of the retinotopic maps were affected by D2 receptor loss of function. While the contrast sensitivity function of D2-KO mice did not differ from their wild-type counterparts, SF selectivity function was significantly affected as the optimal SF and the high cut-off frequency (p D2-KO than in WT mice. These findings show that the lack of function of D2 dopamine receptors had no influence on cortical structure whereas it had a significant impact on the spatial frequency selectivity and high cut-off. Taken together, our results suggest that D2 receptors play a specific role on the processing of spatial features in early visual cortex while they do not seem to participate in its development. PMID:29379422

  7. Frequency-Selective Attention in Auditory Scenes Recruits Frequency Representations Throughout Human Superior Temporal Cortex.

    Science.gov (United States)

    Riecke, Lars; Peters, Judith C; Valente, Giancarlo; Kemper, Valentin G; Formisano, Elia; Sorger, Bettina

    2017-05-01

    A sound of interest may be tracked amid other salient sounds by focusing attention on its characteristic features including its frequency. Functional magnetic resonance imaging findings have indicated that frequency representations in human primary auditory cortex (AC) contribute to this feat. However, attentional modulations were examined at relatively low spatial and spectral resolutions, and frequency-selective contributions outside the primary AC could not be established. To address these issues, we compared blood oxygenation level-dependent (BOLD) responses in the superior temporal cortex of human listeners while they identified single frequencies versus listened selectively for various frequencies within a multifrequency scene. Using best-frequency mapping, we observed that the detailed spatial layout of attention-induced BOLD response enhancements in primary AC follows the tonotopy of stimulus-driven frequency representations-analogous to the "spotlight" of attention enhancing visuospatial representations in retinotopic visual cortex. Moreover, using an algorithm trained to discriminate stimulus-driven frequency representations, we could successfully decode the focus of frequency-selective attention from listeners' BOLD response patterns in nonprimary AC. Our results indicate that the human brain facilitates selective listening to a frequency of interest in a scene by reinforcing the fine-grained activity pattern throughout the entire superior temporal cortex that would be evoked if that frequency was present alone. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  8. Video error concealment using block matching and frequency selective extrapolation algorithms

    Science.gov (United States)

    P. K., Rajani; Khaparde, Arti

    2017-06-01

    Error Concealment (EC) is a technique at the decoder side to hide the transmission errors. It is done by analyzing the spatial or temporal information from available video frames. It is very important to recover distorted video because they are used for various applications such as video-telephone, video-conference, TV, DVD, internet video streaming, video games etc .Retransmission-based and resilient-based methods, are also used for error removal. But these methods add delay and redundant data. So error concealment is the best option for error hiding. In this paper, the error concealment methods such as Block Matching error concealment algorithm is compared with Frequency Selective Extrapolation algorithm. Both the works are based on concealment of manually error video frames as input. The parameter used for objective quality measurement was PSNR (Peak Signal to Noise Ratio) and SSIM(Structural Similarity Index). The original video frames along with error video frames are compared with both the Error concealment algorithms. According to simulation results, Frequency Selective Extrapolation is showing better quality measures such as 48% improved PSNR and 94% increased SSIM than Block Matching Algorithm.

  9. Improved CT-detection of acute bowel ischemia using frequency selective non-linear image blending.

    Science.gov (United States)

    Schneeweiss, Sven; Esser, Michael; Thaiss, Wolfgang; Boesmueller, Hans; Ditt, Hendrik; Nikolau, Konstantin; Horger, Marius

    2017-07-01

    Computed tomography (CT) as a fast and reliable diagnostic technique is the imaging modality of choice for acute bowel ischemia. However, diagnostic is often difficult mainly due to low attenuation differences between ischemic and perfused segments. To compare the diagnostic efficacy of a new post-processing tool based on frequency selective non-linear blending with that of conventional linear contrast-enhanced CT (CECT) image blending for the detection of bowel ischemia. Twenty-seven consecutive patients (19 women; mean age = 73.7 years, age range = 50-94 years) with acute bowel ischemia were scanned using multidetector CT (120 kV; 100-200 mAs). Pre-contrast and portal venous scans (65-70 s delay) were acquired. All patients underwent surgery for acute bowel ischemia and intraoperative diagnosis as well as histologic evaluation of explanted bowel segments was considered "gold standard." First, two radiologists read the conventional CECT images in which linear blending was adapted for optimal contrast, and second (three weeks later) the frequency selective non-linear blending (F-NLB) image. Attenuation values were compared, both in the involved and non-involved bowel segments creating ratios between unenhanced and CECT. The mean attenuation difference between ischemic and non-ischemic wall in the portal venous scan was 69.54 HU (reader 2 = 69.01 HU) higher for F-NLB compared with conventional CECT. Also, the attenuation ratio between contrast-enhanced and pre-contrast CT data for the non-ischemic walls showed significantly higher values for the F-NLB image (CECT: reader 1 = 2.11 (reader 2 = 3.36), F-NLB: reader 1 = 4.46 (reader 2 = 4.98)]. Sensitivity in detecting ischemic areas increased significantly for both readers using F-NLB (CECT: reader 1/2 = 53%/65% versus F-NLB: reader 1/2 = 62%/75%). Frequency selective non-linear blending improves detection of bowel ischemia compared with conventional CECT by increasing

  10. All-dielectric metamaterial frequency selective surface based on spatial arrangement ceramic resonators

    Science.gov (United States)

    Li, Liyang; Wang, Jun; Feng, Mingde; Ma, Hua; Wang, Jiafu; Du, Hongliang; Qu, Shaobo

    In this paper, we demonstrate a method of designing all-dielectric metamaterial frequency selective surface (FSS) with ceramic resonators in spatial arrangement. Compared with the traditional way, spatial arrangement provides a flexible way to handle the permutation and combination of different ceramic resonators. With this method, the resonance response can be adjusted easily to achieve pass/stop band effects. As an example, a stop band spatial arrangement all-dielectric metamaterial FSS is designed. Its working band is in 11.65-12.23GHz. By adjusting permittivity and geometrical parameters of ceramic resonators, we can easily modulate the resonances, band pass or band stop characteristic, as well as the working band.

  11. A Comparison Between Jerusalem Cross and Square Patch Frequency Selective Surfaces for Low Profile Antenna Applications

    Science.gov (United States)

    Cure, David; Weller, Thomas; Miranda, Felix A.

    2011-01-01

    In this paper, a comparison between Jerusalem Cross (JC) and Square Patch (SP) based Frequency Selected Surfaces (FSS) for low profile antenna applications is presented. The comparison is aimed at understanding the performance of low profile antennas backed by high impedance surfaces. In particular, an end loaded planar open sleeve dipole (ELPOSD) antenna is examined due to the various parameters within its configuration, offering significant design flexibility and a wide operating bandwidth. Measured data of the antennas demonstrate that increasing the number of unit cells improves the fractional bandwidth. The antenna bandwidth increased from 0.8% to 1.8% and from 0.8% to 2.7% for the JC and SP structures, respectively. The number of unit cells was increased from 48 to 80 for the JC-FSS and from 24 to 48 for the SP-FSS.

  12. A novel reduced-complexity group detection structure in MIMO frequency selective fading channels

    KAUST Repository

    Qaraqe, Khalid A.; Ahimian, Nariman R.; Alouini, Mohamed-Slim

    2010-01-01

    In this paper a novel reduced complexity detection method named modified symbol flipping method is introduced and its advantages on reducing the burden of the calculations at the receiver compared to the optimum maximum likelihood detection method on multiple input- multiple output frequency selective fading channels are explained. The initial concept of the symbol flipping method is derived from a preliminary detection scheme named bit flipping which was introduced in [1]. The detection structure employed in this paper is ing, detection, and cancellation. On the detection stage, the proposed method is employed and the results are compared to the group maximum likelihood detection scheme proposed in [2]. Simulation results show that a 6 dB performance gain can be achieved at the expense of a slight increase in complexity in comparison with the conventional symbol flipping scheme. © 2010 Crown.

  13. Passive Frequency Selective Surface Array as a Diffuser for Destroying Millimeter Wave Coherence

    Directory of Open Access Journals (Sweden)

    Saiful Islam

    2008-01-01

    Full Text Available This paper presents the design, construction, and testing of grounded frequency selective surface (FSS array as a diffuser for destroying millimeter wave coherence which is used to eliminate speckle in active millimeter wave imaging. To create stochastically independent illumination patterns, we proposed a diffuser based on random-phase distributions obtained by changing the incident frequency. The random-phase diffuser was obtained by mixing up the phase relations between the cells of a deterministic function (e.g., beam splitter. The slot length of FSS is the main design parameter used to optimize the phase shifting properties of the array. The critical parameters of the diffuser array design, such as phase relation with slot lengths, losses, and bandwidth, are discussed. We designed the FSS arrays with finite integral technique (FIT, fabricated by etching technique, and characterized the S-parameters with a free-space MVNA, and measured the radiation patterns with a BWO in motorized setup.

  14. A novel reduced-complexity group detection structure in MIMO frequency selective fading channels

    KAUST Repository

    Qaraqe, Khalid A.

    2010-09-01

    In this paper a novel reduced complexity detection method named modified symbol flipping method is introduced and its advantages on reducing the burden of the calculations at the receiver compared to the optimum maximum likelihood detection method on multiple input- multiple output frequency selective fading channels are explained. The initial concept of the symbol flipping method is derived from a preliminary detection scheme named bit flipping which was introduced in [1]. The detection structure employed in this paper is ing, detection, and cancellation. On the detection stage, the proposed method is employed and the results are compared to the group maximum likelihood detection scheme proposed in [2]. Simulation results show that a 6 dB performance gain can be achieved at the expense of a slight increase in complexity in comparison with the conventional symbol flipping scheme. © 2010 Crown.

  15. Fine-structure processing, frequency selectivity and speech perception in hearing-impaired listeners

    DEFF Research Database (Denmark)

    Strelcyk, Olaf; Dau, Torsten

    2008-01-01

    Hearing-impaired people often experience great difficulty with speech communication when background noise is present, even if reduced audibility has been compensated for. Other impairment factors must be involved. In order to minimize confounding effects, the subjects participating in this study...... consisted of groups with homogeneous, symmetric audiograms. The perceptual listening experiments assessed the intelligibility of full-spectrum as well as low-pass filtered speech in the presence of stationary and fluctuating interferers, the individual's frequency selectivity and the integrity of temporal...... modulation were obtained. In addition, these binaural and monaural thresholds were measured in a stationary background noise in order to assess the persistence of the fine-structure processing to interfering noise. Apart from elevated speech reception thresholds, the hearing impaired listeners showed poorer...

  16. Analytical Solution for Elliptical Cloaks Based on The Frequency Selective Surface

    Directory of Open Access Journals (Sweden)

    E. Ghasemi Mizuji

    2015-01-01

    Full Text Available In this paper the elliptical dielectric cylinder which is covered with FSS cloak is considered. Frequency selective surface cloak which Alu named it mantle cloak is one of the recent techniques for cloaking. In this method an appropriate FSS can act as cloaking device for suppressing  the scattering of object  in the desired frequency. With using this method the dimension of the cloaks is extremely reduced. By this proposed structure, the RCS of elliptical cylinder  is reduced about 10-20 dB and designed cloak has an appropriate performance.  The analytical solution for the wave in each layer is presented and with using simulation, the electric field and the scattering pattern has been drawn.

  17. Low-Complexity Iterative Receiver for Space-Time Coded Signals over Frequency Selective Channels

    Directory of Open Access Journals (Sweden)

    Mohamed Siala

    2002-05-01

    Full Text Available We propose a low-complexity turbo-detector scheme for frequency selective multiple-input multiple-output channels. The detection part of the receiver is based on a List-type MAP equalizer which is a state-reduction algorithm of the MAP algorithm using per-survivor technique. This alternative achieves a good tradeoff between performance and complexity provided a small amount of the channel is neglected. In order to induce the good performance of this equalizer, we propose to use a whitened matched filter (WMF which leads to a white-noise “minimum phase” channel model. Simulation results show that the use of the WMF yields significant improvement, particularly over severe channels. Thanks to the iterative turbo processing (detection and decoding are iterated several times, the performance loss due to the use of the suboptimum List-type equalizer is recovered.

  18. On the application of frequency selective common mode feedback for multifrequency EIT.

    Science.gov (United States)

    Langlois, Peter J; Wu, Yu; Bayford, Richard H; Demosthenous, Andreas

    2015-06-01

    Common mode voltages are frequently a problem in electrical impedance tomography (EIT) and other bioimpedance applications. To reduce their amplitude common mode feedback is employed. Formalised analyses of both current and voltage feedback is presented in this paper for current drives. Common mode effects due to imbalances caused by the current drives, the electrode connections to the body load and the introduction of the body impedance to ground are considered. Frequency selective narrowband common mode feedback previously proposed to provide feedback stability is examined. As a step towards multifrequency applications the use of narrowband feedback is experimentally demonstrated for two simultaneous current drives. Measured results using standard available components show a reduction of 62 dB for current feedback and 31 dB for voltage feedback. Frequencies ranged from 50 kHz to 1 MHz.

  19. Frequency Selective Non-Linear Blending to Improve Image Quality in Liver CT.

    Science.gov (United States)

    Bongers, M N; Bier, G; Kloth, C; Schabel, C; Fritz, J; Nikolaou, K; Horger, M

    2016-12-01

    Purpose: To evaluate the effects of a new frequency selective non-linear blending (NLB) algorithm on the contrast resolution of liver CT with low intravascular concentration of iodine contrast. Materials and Methods: Our local ethics committee approved this retrospective study. The informed consent requirement was waived. CT exams of 25 patients (60 % female, mean age: 65 ± 16 years of age) with late phase CT scans of the liver were included as a model for poor intrahepatic vascular contrast enhancement. Optimal post-processing settings to enhance the contrast of hepatic vessels were determined. Outcome variables included signal-to-noise (SNR) and contrast-to-noise ratios (CNR) of hepatic vessels and SNR of liver parenchyma of standard and post-processed images. Image quality was quantified by two independent readers using Likert scales. Results: The post-processing settings for the visualization of hepatic vasculature were optimal at a center of 115HU, delta of 25HU, and slope of 5. Image noise was statistically indifferent between standard and post-processed images. The CNR between the hepatic vasculature (HV) and liver parenchyma could be significantly increased for liver veins (CNR Standard 1.62 ± 1.10, CNR NLB 3.6 ± 2.94, p = 0.0002) and portal veins (CNR Standard 1.31 ± 0.85, CNR NLB 2.42 ± 3.03, p = 0.046). The SNR of liver parenchyma was significantly higher on post-processed images (SNR NLB 11.26 ± 3.16, SNR Standard 8.85 ± 2.27, p = 0.008). The overall image quality and depiction of HV were significantly higher on post-processed images (NLB DHV : 4 [3 - 4.75], S tandardDHV : 2 [1.3 - 2.5], p = algorithm increases the contrast resolution of liver CT and can improve the visibility of the hepatic vasculature in the setting of a low contrast ratio between vessels and the parenchyma. Key Points: • Using the new frequency selective non-linear blending algorithm is feasible in contrast

  20. Frequency selective non-linear blending to improve image quality in liver CT

    International Nuclear Information System (INIS)

    Bongers, M.N.; Bier, G.; Kloth, C.; Schabel, C.; Nikolaou, K.; Horger, M.; Fritz, J.

    2016-01-01

    To evaluate the effects of a new frequency selective non-linear blending (NLB) algorithm on the contrast resolution of liver CT with low intravascular concentration of iodine contrast. Our local ethics committee approved this retrospective study. The informed consent requirement was waived. CT exams of 25 patients (60% female, mean age: 65±16 years of age) with late phase CT scans of the liver were included as a model for poor intrahepatic vascular contrast enhancement. Optimal post-processing settings to enhance the contrast of hepatic vessels were determined. Outcome variables included signal-to-noise (SNR) and contrast-to-noise ratios (CNR) of hepatic vessels and SNR of liver parenchyma of standard and post-processed images. Image quality was quantified by two independent readers using Likert scales. The post-processing settings for the visualization of hepatic vasculature were optimal at a center of 115HU, delta of 25HU, and slope of 5. Image noise was statistically indifferent between standard and post-processed images. The CNR between the hepatic vasculature (HV) and liver parenchyma could be significantly increased for liver veins (CNR Standard 1.62±1.10, CNR NLB 3.6±2.94, p=0.0002) and portal veins (CNR Standard 1.31±0.85, CNR NLB 2.42±3.03, p=0.046). The SNR of liver parenchyma was significantly higher on post-processed images (SNR NLB 11.26±3.16, SNR Standard 8.85± 2.27, p=0.008). The overall image quality and depiction of HV were significantly higher on post-processed images (NLB DHV : 4 [3-4.75], S tandardDHV : 2 [1.3-2.5], p=<0.0001; NLBIQ : 4 [4-4], StandardIQ : 2 [2-3], p=<0.0001). The use of a frequency selective non-linear blending algorithm increases the contrast resolution of liver CT and can improve the visibility of the hepatic vasculature in the setting of a low contrast ratio between vessels and the parenchyma.

  1. Frequency selective non-linear blending to improve image quality in liver CT

    Energy Technology Data Exchange (ETDEWEB)

    Bongers, M.N.; Bier, G.; Kloth, C.; Schabel, C.; Nikolaou, K.; Horger, M. [University Hospital of Tuebingen (Germany). Dept. of Diagnostic and Interventional Radiology; Fritz, J. [Johns Hopkins University School of Medicine, Baltimore, MD (United States). Russell H. Morgan Dept. of Radiology and Radiological Science

    2016-12-15

    To evaluate the effects of a new frequency selective non-linear blending (NLB) algorithm on the contrast resolution of liver CT with low intravascular concentration of iodine contrast. Our local ethics committee approved this retrospective study. The informed consent requirement was waived. CT exams of 25 patients (60% female, mean age: 65±16 years of age) with late phase CT scans of the liver were included as a model for poor intrahepatic vascular contrast enhancement. Optimal post-processing settings to enhance the contrast of hepatic vessels were determined. Outcome variables included signal-to-noise (SNR) and contrast-to-noise ratios (CNR) of hepatic vessels and SNR of liver parenchyma of standard and post-processed images. Image quality was quantified by two independent readers using Likert scales. The post-processing settings for the visualization of hepatic vasculature were optimal at a center of 115HU, delta of 25HU, and slope of 5. Image noise was statistically indifferent between standard and post-processed images. The CNR between the hepatic vasculature (HV) and liver parenchyma could be significantly increased for liver veins (CNR{sub Standard} 1.62±1.10, CNR{sub NLB} 3.6±2.94, p=0.0002) and portal veins (CNR{sub Standard} 1.31±0.85, CNR{sub NLB} 2.42±3.03, p=0.046). The SNR of liver parenchyma was significantly higher on post-processed images (SNR{sub NLB} 11.26±3.16, SNR{sub Standard} 8.85± 2.27, p=0.008). The overall image quality and depiction of HV were significantly higher on post-processed images (NLB{sub DHV}: 4 [3-4.75], S{sub tandardDHV}: 2 [1.3-2.5], p=<0.0001; {sub NLBIQ}: 4 [4-4], {sub StandardIQ}: 2 [2-3], p=<0.0001). The use of a frequency selective non-linear blending algorithm increases the contrast resolution of liver CT and can improve the visibility of the hepatic vasculature in the setting of a low contrast ratio between vessels and the parenchyma.

  2. Frequency selective surface based passive wireless sensor for structural health monitoring

    International Nuclear Information System (INIS)

    Jang, Sang-Dong; Kang, Byung-Woo; Kim, Jaehwan

    2013-01-01

    Wireless sensor networks or ubiquitous sensor networks are a promising technology giving useful information to people. In particular, the chipless passive wireless sensor is one of the most important developments in wireless sensor technology because it is compact and does not need a battery or chip for the sensor operation. So it has many possibilities for use in various types of sensor system with economical efficiency and robustness in harsh environmental conditions. This sensor uses an electromagnetic resonance frequency or phase angle shift associated with a geometrical change of the sensor tag or an impedance change of the sensor. In this paper, a chipless passive wireless structural health monitoring (SHM) sensor is made using a frequency selective surface (FSS). The cross type FSS is introduced, and its SHM principle is explained. The electromagnetic characteristics of the FSS are simulated in terms of transmission and reflection coefficients using simulation software, and an experimental verification is conducted. The electromagnetic characteristic change of the FSS in the presence of mechanical strain or a structural crack is investigated by means of simulation and experiment. Since large-area structures can be covered by deploying FSS, it is possible to detect the location of any cracks. (paper)

  3. Wideband RCS Reduction of Microstrip Array Antenna Based on Absorptive Frequency Selective Surface and Microstrip Resonators

    Directory of Open Access Journals (Sweden)

    Jingjing Xue

    2017-01-01

    Full Text Available An approach for wideband radar cross section (RCS reduction of a microstrip array antenna is presented and discussed. The scheme is based on the microstrip resonators and absorptive frequency selective surface (AFSS with a wideband absorptive property over the low band 1.9–7.5 GHz and a transmission characteristic at high frequency 11.05 GHz. The AFSS is designed to realize the out-of-band RCS reduction and preserve the radiation performance simultaneously, and it is placed above the antenna with the operating frequency of 11.05 GHz. Moreover, the microstrip resonators are loaded to obtain the in-band RCS reduction. As a result, a significant RCS reduction from 1.5 GHz to 13 GHz for both types of polarization has been accomplished. Compared with the reference antenna, the simulated results exhibit that the monostatic RCS of the proposed array antenna in x- and y-polarization can be reduced as much as 17.6 dB and 21.5 dB, respectively. And the measured results agree well with the simulated ones.

  4. Analysis and applications of a frequency selective surface via a random distribution method

    International Nuclear Information System (INIS)

    Xie Shao-Yi; Huang Jing-Jian; Yuan Nai-Chang; Liu Li-Guo

    2014-01-01

    A novel frequency selective surface (FSS) for reducing radar cross section (RCS) is proposed in this paper. This FSS is based on the random distribution method, so it can be called random surface. In this paper, the stacked patches serving as periodic elements are employed for RCS reduction. Previous work has demonstrated the efficiency by utilizing the microstrip patches, especially for the reflectarray. First, the relevant theory of the method is described. Then a sample of a three-layer variable-sized stacked patch random surface with a dimension of 260 mm×260 mm is simulated, fabricated, and measured in order to demonstrate the validity of the proposed design. For the normal incidence, the 8-dB RCS reduction can be achieved both by the simulation and the measurement in 8 GHz–13 GHz. The oblique incidence of 30° is also investigated, in which the 7-dB RCS reduction can be obtained in a frequency range of 8 GHz–14 GHz. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  5. Blind CP-OFDM and ZP-OFDM Parameter Estimation in Frequency Selective Channels

    Directory of Open Access Journals (Sweden)

    Vincent Le Nir

    2009-01-01

    Full Text Available A cognitive radio system needs accurate knowledge of the radio spectrum it operates in. Blind modulation recognition techniques have been proposed to discriminate between single-carrier and multicarrier modulations and to estimate their parameters. Some powerful techniques use autocorrelation- and cyclic autocorrelation-based features of the transmitted signal applying to OFDM signals using a Cyclic Prefix time guard interval (CP-OFDM. In this paper, we propose a blind parameter estimation technique based on a power autocorrelation feature applying to OFDM signals using a Zero Padding time guard interval (ZP-OFDM which in particular excludes the use of the autocorrelation- and cyclic autocorrelation-based techniques. The proposed technique leads to an efficient estimation of the symbol duration and zero padding duration in frequency selective channels, and is insensitive to receiver phase and frequency offsets. Simulation results are given for WiMAX and WiMedia signals using realistic Stanford University Interim (SUI and Ultra-Wideband (UWB IEEE 802.15.4a channel models, respectively.

  6. Ferrite Film Loaded Frequency Selective Metamaterials for Sub-GHz Applications

    Directory of Open Access Journals (Sweden)

    Bo Gao

    2016-12-01

    Full Text Available Electromagnetic metamaterials are constructed with sub-wavelength structures that exhibit particular electromagnetic properties under a certain frequency range. Because the form-factor of the substructures has to be comparable to the wavelength of the operating frequency, few papers have discussed the metamaterials under GHz frequency. In this paper, we developed an innovative method to reduce the resonant frequency of metamaterals. By integrating the meta-structures with ferrite materials of higher permeability, the cell size of the meta-structure can be scaled down. This paper describes the methodology, design, and development of low-profile GHz ferrite loaded metamaterials. A ferrite film with a permeability of 20 could reduce the resonant frequency of metamaterials by up to 50%. A prototype has been fabricated and the measurement data align well with the simulation results. Because of the lowered operational frequency, the proposed ferrite loaded metamaterials offer more flexibility for various sub-GHz microwave applications, such as cloaks, absorbers, and frequency selective surfaces.

  7. A reconfigurable frequency-selective surface for dual-mode multi-band filtering applications

    Science.gov (United States)

    Majidzadeh, Maryam; Ghobadi, Changiz; Nourinia, Javad

    2017-03-01

    A reconfigurable single-layer frequency-selective surface (FSS) with dual-mode multi-band modes of operation is presented. The proposed structure is printed on a compact 10 × 10 mm2 FR4 substrate with the thickness of 1.6 mm. A simple square loop is printed on the front side while another one along with two defected vertical arms is deployed on the backside. To realise the reconfiguration, two pin diodes are embedded on the backside square loop. Suitable insertion of conductive elements along with pin diodes yields in dual-mode multi-band rejection of applicable in service frequency ranges. The first operating mode due to diodes' 'ON' state provides rejection of 2.4 GHz WLAN in 2-3 GHz, 5.2/5.8 GHz WLAN and X band in 5-12 GHz, and a part of Ku band in 13.9-16 GHz. In diodes 'OFF' state, the FSS blocks WLAN in 4-7.3 GHz, X band in 8-12.7 GHz as well as part of Ku band in 13.7-16.7 GHz. As well, high attenuation of incident waves is observed by a high shielding effectiveness (SE) in the blocked frequency bands. Also, a stable behaviour against different polarisations and angles of incidence is obtained. Comprehensive studies are conducted on a fabricated prototype to assess its performance from which encouraging results are obtained.

  8. Diversity Techniques for Single-Carrier Packet Retransmissions over Frequency-Selective Channels

    Directory of Open Access Journals (Sweden)

    Assimi Abdel-Nasser

    2009-01-01

    Full Text Available In data packet communication systems over multipath frequency-selective channels, hybrid automatic repeat request (HARQ protocols are usually used in order to ensure data reliability. For single-carrier packet transmission in slow fading environment, an identical retransmission of the same packet, due to a decoding failure, does not fully exploit the available time diversity in retransmission-based HARQ protocols. In this paper, we compare two transmit diversity techniques, namely, cyclic frequency-shift diversity and bit-interleaving diversity. Both techniques can be integrated in the HARQ scheme in order to improve the performance of the joint detector. Their performance in terms of pairwise error probability is investigated using maximum likelihood detection and decoding. The impact of the channel memory and the modulation order on the performance gain is emphasized. In practice, we use low complexity linear filter-based equalization which can be efficiently implemented in the frequency domain. The use of iterative equalization and decoding is also considered. The performance gain in terms of frame error rate and data throughput is evaluated by numerical simulations.

  9. Iterative MMSE Detection for MIMO/BLAST DS-CDMA Systems in Frequency Selective Fading Channels - Achieving High Performance in Fully Loaded Systems

    Science.gov (United States)

    Silva, João Carlos; Souto, Nuno; Cercas, Francisco; Dinis, Rui

    A MMSE (Minimum Mean Square Error) DS-CDMA (Direct Sequence-Code Division Multiple Access) receiver coupled with a low-complexity iterative interference suppression algorithm was devised for a MIMO/BLAST (Multiple Input, Multiple Output / Bell Laboratories Layered Space Time) system in order to improve system performance, considering frequency selective fading channels. The scheme is compared against the simple MMSE receiver, for both QPSK and 16QAM modulations, under SISO (Single Input, Single Output) and MIMO systems, the latter with 2Tx by 2Rx and 4Tx by 4Rx (MIMO order 2 and 4 respectively) antennas. To assess its performance in an existing system, the uncoded UMTS HSDPA (High Speed Downlink Packet Access) standard was considered.

  10. Optimized Irregular Low-Density Parity-Check Codes for Multicarrier Modulations over Frequency-Selective Channels

    Directory of Open Access Journals (Sweden)

    Valérian Mannoni

    2004-09-01

    Full Text Available This paper deals with optimized channel coding for OFDM transmissions (COFDM over frequency-selective channels using irregular low-density parity-check (LDPC codes. Firstly, we introduce a new characterization of the LDPC code irregularity called “irregularity profile.” Then, using this parameterization, we derive a new criterion based on the minimization of the transmission bit error probability to design an irregular LDPC code suited to the frequency selectivity of the channel. The optimization of this criterion is done using the Gaussian approximation technique. Simulations illustrate the good performance of our approach for different transmission channels.

  11. MRI of the lumbar spine. Technical aspect. T2-weighted fat saturation coronal dynamic MRI of the lumbar spine; IRM du rachis lombaire. Aspects techniques. Coupe coronales en T2 et saturation de graisse IRM dynamique du rachis lombaire

    Energy Technology Data Exchange (ETDEWEB)

    Clarisse, J; Francke, J P; Leclet, H; Bourgeois, Ph; Chastanet, P; Cotten, A [Hopital Roger Salengro, 59 - Lille (France)

    1998-06-01

    Assess the feasibility of `dynamic` MRI of the lumbar spine and study the parameters of a single MRI sequence favorable for simultaneous imaging of the meningeal space and the epidural and foraminal venous system. Favor a decline in the number of sacco-radiculograms. Clinical assessment in the following circumstances: discordant clinical and and radiographic findings, difficulty in interpreting single or multiple disc-root conflicts, preoperative work-up in cases of narrow or stenotic lumbar canal. Dynamic MRI of the lumbar spine is possible if the hypothesis that the hyper-lordosis obtained in the supine position creates an anatomic and radiographic situation identical to the hyper-lordosis induced by the upright position is accepted. The `radiculo-phlebographic` sequence gives images of the root sheaths and the epidural, foraminal and extra-foraminal veins simultaneously, particularly in the coronal plane. (authors)

  12. Least-squares Migration and Full Waveform Inversion with Multisource Frequency Selection

    KAUST Repository

    Huang, Yunsong

    2013-09-01

    Multisource Least-Squares Migration (LSM) of phase-encoded supergathers has shown great promise in reducing the computational cost of conventional migration. But for the marine acquisition geometry this approach faces the challenge of erroneous misfit due to the mismatch between the limited number of live traces/shot recorded in the field and the pervasive number of traces generated by the finite-difference modeling method. To tackle this mismatch problem, I present a frequency selection strategy with LSM of supergathers. The key idea is, at each LSM iteration, to assign a unique frequency band to each shot gather, so that the spectral overlap among those shots—and therefore their crosstallk—is zero. Consequently, each receiver can unambiguously identify and then discount the superfluous sources—those that are not associated with the receiver in marine acquisition. To compare with standard migration, I apply the proposed method to 2D SEG/EAGE salt model and obtain better resolved images computed at about 1/8 the cost; results for 3D SEG/EAGE salt model, with Ocean Bottom Seismometer (OBS) survey, show a speedup of 40×. This strategy is next extended to multisource Full Waveform Inversion (FWI) of supergathers for marine streamer data, with the same advantages of computational efficiency and storage savings. In the Finite-Difference Time-Domain (FDTD) method, to mitigate spectral leakage due to delayed onsets of sine waves detected at receivers, I double the simulation time and retain only the second half of the simulated records. To compare with standard FWI, I apply the proposed method to 2D velocity model of SEG/EAGE salt and to Gulf Of Mexico (GOM) field data, and obtain a speedup of about 4× and 8×. Formulas are then derived for the resolution limits of various constituent wavepaths pertaining to FWI: diving waves, primary reflections, diffractions, and multiple reflections. They suggest that inverting multiples can provide some low and intermediate

  13. A study on change in the center frequency depending on the fat content and on change in the fat saturation image with the use of a self-manufactured phantom depending on the center frequency adjustment method in an MRI breast scan

    Science.gov (United States)

    Kim, Chang-Bok; Dong, Kyung-Rae; Gho, Hee-Jin; Chung, Woon-Kwan; Joo, Kyu-Ji; Kim, Young-Jae

    2013-12-01

    This study examined the changes in the center frequency according to the fat content the using a self-manufactured phantom. In addition, the change in the fat saturation image according to when the center frequency was applied automatically or adjusted manually was analyzed to determine the importance of a manual adjustment of the center frequency. Distilled water and animal fat were solidified in a 10-ml syringe to manufacture nine phantoms for each condition (18 in total). A MR scanner at 1.5 Tesla was used to obtain a T1-weighted three dimensional fast low-angle shot (T1 3D FLASH) dynamic fat saturation image according to the spectral attenuated inversion recovery(SPAIR) method. The images obtained were classified into the following before analyzing the center frequencies for each image: Test A (image where fat was not saturated), Test B (image where fat was saturated in an automatic adjustment of the center frequency), and Test C (image where fat was saturated in a manual adjustment of the center frequency). The signal intensity (SI) values of water, fat and background were measured to calculate the signal to noise ratio (SNR) before examining the difference in the SNRs of water and fat (SNR difference = water SNR — fat SNR). The mean center frequency in Tests A, B and C was 63.631179 MHz when the fat content was 70% or lower. The mean center frequency for Tests A and B was 63.631002 MHz when the fat content was 80% or higher, which was 226 Hz lower than that for Test C (63.631228 MHz). The water SIs of Tests A, B and C with increasing fat content showed a pattern of change similar to that of the fat SIs of Tests A and C. On the other hand, the fat SI of Test B was similar to that of Test A when the fat content was 80%, which showed a large difference in change. The water SNRs of Tests A, B and C, and the fat SNR and SNR differences of Tests A and C showed similar changes according to the fat content. The difference between the fat SNR and the SNR of Test B

  14. Metal artefact suppression at 3 T MRI: comparison of MAVRIC-SL with conventional fast spin echo sequences in patients with Hip joint arthroplasty

    International Nuclear Information System (INIS)

    Kretzschmar, Martin; Nardo, Lorenzo; Han, Misung M.; Heilmeier, Ursula; Sam, Craig; Joseph, Gabby B.; Krug, Roland; Link, Thomas M.; Koch, Kevin M.

    2015-01-01

    The aim of our study was to evaluate the clinical feasibility and diagnostic value of a new MRI metal artefact reduction pulse sequence called MAVRIC-SL in a 3 T MRI environment. Two MAVRIC-SL sequences obtained in 61 patients with symptomatic total hip replacement were compared with standard FSE-STIR sequences optimized for imaging around metal. Artefact size was measured on the slice of greatest extent. Image quality, fat saturation, image distortion, visibility of anatomical structures, and detectability of joint abnormalities were visually assessed and graded on qualitative scales. Differences between MAVRIC-SL and FSE sequences were tested with the Wilcoxon signed-rank test. MAVRIC-SL sequences at 3 T showed significantly smaller metal artefacts compared to FSE-STIR sequences (p < 0.0001). The general image quality of MAVRIC-SL sequences was reduced with regard to spatial resolution, noise and contrast (p = 0.001), and fat saturation (p < 0.0001). The reduction of artefact size and image distortion significantly improved visualization of joint anatomy (p < 0.0001) and diagnostic confidence regarding implant-associated abnormalities (p = 0.0075 to <0.0001). Although the image quality of MAVRIC-SL sequences is limited at 3 T, its clinical application is feasible and provides important additional diagnostic information for the workup of patients with symptomatic hip replacement through substantially reduced metal artefacts. (orig.)

  15. Metal artefact suppression at 3 T MRI: comparison of MAVRIC-SL with conventional fast spin echo sequences in patients with Hip joint arthroplasty

    Energy Technology Data Exchange (ETDEWEB)

    Kretzschmar, Martin; Nardo, Lorenzo; Han, Misung M.; Heilmeier, Ursula; Sam, Craig; Joseph, Gabby B.; Krug, Roland; Link, Thomas M. [University of California San Francisco, Musculoskeletal Quantitative Imaging Research Group, Department of Radiology and Biomedical Imaging, San Francisco, CA (United States); Koch, Kevin M. [Medical Collage of Wisconsin, Departments of Biophysics and Radiology, Milwaukee, WI (United States)

    2015-08-15

    The aim of our study was to evaluate the clinical feasibility and diagnostic value of a new MRI metal artefact reduction pulse sequence called MAVRIC-SL in a 3 T MRI environment. Two MAVRIC-SL sequences obtained in 61 patients with symptomatic total hip replacement were compared with standard FSE-STIR sequences optimized for imaging around metal. Artefact size was measured on the slice of greatest extent. Image quality, fat saturation, image distortion, visibility of anatomical structures, and detectability of joint abnormalities were visually assessed and graded on qualitative scales. Differences between MAVRIC-SL and FSE sequences were tested with the Wilcoxon signed-rank test. MAVRIC-SL sequences at 3 T showed significantly smaller metal artefacts compared to FSE-STIR sequences (p < 0.0001). The general image quality of MAVRIC-SL sequences was reduced with regard to spatial resolution, noise and contrast (p = 0.001), and fat saturation (p < 0.0001). The reduction of artefact size and image distortion significantly improved visualization of joint anatomy (p < 0.0001) and diagnostic confidence regarding implant-associated abnormalities (p = 0.0075 to <0.0001). Although the image quality of MAVRIC-SL sequences is limited at 3 T, its clinical application is feasible and provides important additional diagnostic information for the workup of patients with symptomatic hip replacement through substantially reduced metal artefacts. (orig.)

  16. Channel and delay estimation for base-station–based cooperative communications in frequency-selective fading channels

    Directory of Open Access Journals (Sweden)

    Hongjun Xu

    2011-07-01

    Full Text Available A channel and delay estimation algorithm for both positive and negative delay, based on the distributed Alamouti scheme, has been recently discussed for base-station–based asynchronous cooperative systems in frequency-flat fading channels. This paper extends the algorithm, the maximum likelihood estimator, to work in frequency-selective fading channels. The minimum mean square error (MMSE performance of channel estimation for both packet schemes and normal schemes is discussed in this paper. The symbol error rate (SER performance of equalisation and detection for both time-reversal space-time block code (STBC and single-carrier STBC is also discussed in this paper. The MMSE simulation results demonstrated the superior performance of the packet scheme over the normal scheme with an improvement in performance of up to 6 dB when feedback was used in the frequency-selective channel at a MSE of 3 x 10–2. The SER simulation results showed that, although both the normal and packet schemes achieved similar diversity orders, the packet scheme demonstrated a 1 dB coding gain over the normal scheme at a SER of 10–5. Finally, the SER simulations showed that the frequency-selective fading system outperformed the frequency-flat fading system.

  17. Inkjet printed paper based frequency selective surfaces and skin mounted RFID tags : the interrelation between silver nanoparticle ink, paper substrate and low temperature sintering technique

    NARCIS (Netherlands)

    Sanchez-Romaquera, V.; Wïnscher, S.; Turki, B.M.; Abbel, R.J.; Barbosa, S.; Tate, D.J.; Oyeka, D.; Batchelor, J.C.; Parker, E.A.; Schubert, U.S.; Yeates, S.G.

    2015-01-01

    Inkjet printing of functional frequency selective surfaces (FSS) and radio frequency identification (RFID) tags on commercial paper substrates using silver nanoparticle inks sintered using low temperature thermal, plasma and photonic techniques is reported. Printed and sintered FSS devices

  18. An iterative detection method of MIMO over spatial correlated frequency selective channel: using list sphere decoding for simplification

    Science.gov (United States)

    Shi, Zhiping; Yan, Bing

    2010-08-01

    In multiple-input multiple-output(MIMO) wireless systems, combining good channel codes(e.g., Non-binary Repeat Accumulate codes) with adaptive turbo equalization is a good option to get better performance and lower complexity under Spatial Correlated Frequency Selective(SCFS) Channel. The key of this method is after joint antennas MMSE detection (JAD/MMSE) based on interruption cancelling using soft information, considering the detection result as an output of a Gaussian equivalent flat fading channel, and performing maximum likelihood detection(ML) to get more correct estimated result. But the using of ML brings great complexity increase, which is not allowed. In this paper, a low complexity method called list sphere decoding is introduced and applied to replace the ML in order to simplify the adaptive iterative turbo equalization system.

  19. Wide-range frequency selectivity in an acoustic sensor fabricated using a microbeam array with non-uniform thickness

    International Nuclear Information System (INIS)

    Shintaku, Hirofumi; Kotera, Hidetoshi; Kobayashi, Takayuki; Zusho, Kazuki; Kawano, Satoyuki

    2013-01-01

    In this study, we have demonstrated the fabrication of a microbeam array (MBA) with various thicknesses and investigated the suitability it for an acoustic sensor with wide-range frequency selectivity. For this, an MBA composed of 64 beams, with thicknesses varying from 2.99–142 µm, was fabricated by using single gray-scale lithography and a thick negative photoresist. The vibration of the beams in air was measured using a laser Doppler vibrometer; the resonant frequencies of the beams were measured to be from 11.5 to 290 kHz. Lastly, the frequency range of the MBA with non-uniform thickness was 10.9 times that of the MBA with uniform thickness. (paper)

  20. Design of a Novel Miniaturized Frequency Selective Surface Based on 2.5-Dimensional Jerusalem Cross for 5G Applications

    Directory of Open Access Journals (Sweden)

    Peng Zhao

    2018-01-01

    Full Text Available A compact frequency selective surface (FSS for 5G applications has been designed based on 2.5-dimensional Jerusalem cross. The proposed element consists of two main parts: the successive segments of the metal traces placed alternately on the two surfaces of the substrate and the vertical vias connecting traces. Compared with previous published two-dimensional miniaturized elements, the transmission curves indicate a significant size reduction (1/26 wavelengths at the resonant frequency and exhibit good angular and polarization stabilities. Furthermore, a general equivalent circuit model is established to provide direct physical insight into the operating principle of this FSS. A prototype of the proposed FSS has been fabricated and measured, and the results validate this design.

  1. Design, Fabrication and Characterization of MIM Diodes and Frequency Selective Thermal Emitters for Solar Energy Harvesting and Detection Devices

    Science.gov (United States)

    Sharma, Saumya

    could be achieved in this case. These long chain polymeric molecules exhibit a two-dimensional molecular assembly thereby reducing the tunneling distance between the metal electrodes on either side of the insulating layer. Rectification ratios as high as 450:1 at +/-200mV were obtained for an MIM diode configuration of Ni-LB films of Arachidic Acid films-(Au/Pd). The bandwidth of the incident radiation that can be used by this rectenna assembly is limited to 9.5% of 30THz or +/-1.5THz from the center frequency based on the antenna designs which were proposed for this research. This bandwidth constraint has led to research in the field of frequency selective emitters capable of providing a narrowband emission around 30THz. Several grating structures were fabricated in the form of Ni-Si periodic arrays, in a cleanroom environment using photolithography, sputtering and deep reactive ion etching. These frequency selective samples were characterized with the help of focusing optics, monochromators and HgCdTe detectors. The results obtained from the emission spectra were utilized to calibrate a simulation model with Computer Simulation Technology (CST) which uses numerous robust solving techniques, such as the finite element method, in order to obtain the optical parameters for the model. Thereafter, a thorough analysis of the different dimensional and material parameters was performed, to understand their dependence on the emissivity of the selective emitter. Further research on the frequency selectivity of the periodic nano-disk or nano-hole array led to the temperature dependence of the simulated spectra, because the material parameters, such as refractive index or drude model collision frequency, vary with temperature. Thus, the design of frequency selective absorbers/emitters was found to be significantly affected with temperature range of operation of these structures.

  2. An ultrathin wide-band planar metamaterial absorber based on a fractal frequency selective surface and resistive film

    International Nuclear Information System (INIS)

    Fan Yue-Nong; Cheng Yong-Zhi; Nie Yan; Wang Xian; Gong Rong-Zhou

    2013-01-01

    We propose an ultrathin wide-band metamaterial absorber (MA) based on a Minkowski (MIK) fractal frequency selective surface and resistive film. This absorber consists of a periodic arrangement of dielectric substrates sandwiched with an MIK fractal loop structure electric resonator and a resistive film. The finite element method is used to simulate and analyze the absorption of the MA. Compared with the MA-backed copper film, the designed MA-backed resistive film exhibits an absorption of 90% at a frequency region of 2 GHz–20 GHz. The power loss density distribution of the MA is further illustrated to explain the mechanism of the proposed MA. Simulated absorptions at different incidence cases indicate that this absorber is polarization-insensitive and wide-angled. Finally, further simulated results indicate that the surface resistance of the resistive film and the dielectric constant of the substrate can affect the absorbing property of the MA. This absorber may be used in many military fields

  3. Space-Time Joint Interference Cancellation Using Fuzzy-Inference-Based Adaptive Filtering Techniques in Frequency-Selective Multipath Channels

    Science.gov (United States)

    Hu, Chia-Chang; Lin, Hsuan-Yu; Chen, Yu-Fan; Wen, Jyh-Horng

    2006-12-01

    An adaptive minimum mean-square error (MMSE) array receiver based on the fuzzy-logic recursive least-squares (RLS) algorithm is developed for asynchronous DS-CDMA interference suppression in the presence of frequency-selective multipath fading. This receiver employs a fuzzy-logic control mechanism to perform the nonlinear mapping of the squared error and squared error variation, denoted by ([InlineEquation not available: see fulltext.],[InlineEquation not available: see fulltext.]), into a forgetting factor[InlineEquation not available: see fulltext.]. For the real-time applicability, a computationally efficient version of the proposed receiver is derived based on the least-mean-square (LMS) algorithm using the fuzzy-inference-controlled step-size[InlineEquation not available: see fulltext.]. This receiver is capable of providing both fast convergence/tracking capability as well as small steady-state misadjustment as compared with conventional LMS- and RLS-based MMSE DS-CDMA receivers. Simulations show that the fuzzy-logic LMS and RLS algorithms outperform, respectively, other variable step-size LMS (VSS-LMS) and variable forgetting factor RLS (VFF-RLS) algorithms at least 3 dB and 1.5 dB in bit-error-rate (BER) for multipath fading channels.

  4. Space-Time Joint Interference Cancellation Using Fuzzy-Inference-Based Adaptive Filtering Techniques in Frequency-Selective Multipath Channels

    Directory of Open Access Journals (Sweden)

    Chen Yu-Fan

    2006-01-01

    Full Text Available An adaptive minimum mean-square error (MMSE array receiver based on the fuzzy-logic recursive least-squares (RLS algorithm is developed for asynchronous DS-CDMA interference suppression in the presence of frequency-selective multipath fading. This receiver employs a fuzzy-logic control mechanism to perform the nonlinear mapping of the squared error and squared error variation, denoted by ( , , into a forgetting factor . For the real-time applicability, a computationally efficient version of the proposed receiver is derived based on the least-mean-square (LMS algorithm using the fuzzy-inference-controlled step-size . This receiver is capable of providing both fast convergence/tracking capability as well as small steady-state misadjustment as compared with conventional LMS- and RLS-based MMSE DS-CDMA receivers. Simulations show that the fuzzy-logic LMS and RLS algorithms outperform, respectively, other variable step-size LMS (VSS-LMS and variable forgetting factor RLS (VFF-RLS algorithms at least 3 dB and 1.5 dB in bit-error-rate (BER for multipath fading channels.

  5. Effect of photonic crystal and frequency selective surface implementation on gain enhancement in the microstrip patch antenna at terahertz frequency

    Energy Technology Data Exchange (ETDEWEB)

    Nejati, Ameneh, E-mail: ameneh.nejati@gmail.com [Department of Electrical Engineering, Science and Research Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of); Sadeghzadeh, Ramezan Ali [Faculty of Electrical and Computer Engineering, K.N Toosi University of Technology, Tehran (Iran, Islamic Republic of); Geran, Fatemeh [Faculty of Electrical and Computer Engineering, Shahid Rajaee Teacher Training University, Tehran (Iran, Islamic Republic of)

    2014-09-15

    In this paper, microstrip patch antenna with frequency selective surface (FSS) and photonic band gap (PBG) structures in the frequency range of 0.5–0.7 THz is presented for wireless communications. Proposed patch antenna is designed on a substrate with uniform and non-uniform PBG structures. Here, the effects of substrate thickness, various radii and arrangement of holes on antenna resonance in both PBG forms are studied. Near zero characteristic on uniform and non-uniform PBG substrate is compared and the results show that along with increase in hole radius, antenna operating frequency and bandwidth are increased. Also, the FSS structure is designed as a perfect absorber. Finally, by using FSS and PBG structures simultaneously, gain enhancement, increase in directivity and pattern shaping are studied at THz field. The antenna gain in final structure is increased by 2 dBi (32%) in comparison to simple form and Half-Power beam width is reduced from 100°×80° in simple form to 72°×48° by using FSS and PBG. All simulations and designs are done by Ansoft HFSS and CST Microwave Studio simulation tools with different full wave methods.

  6. Utility of fat-suppressed sequences in differentiation of aggressive vs typical asymptomatic haemangioma of the spine.

    Science.gov (United States)

    Nabavizadeh, Seyed Ali; Mamourian, Alexander; Schmitt, James E; Cloran, Francis; Vossough, Arastoo; Pukenas, Bryan; Loevner, Laurie A; Mohan, Suyash

    2016-01-01

    While haemangiomas are common benign vascular lesions involving the spine, some behave in an aggressive fashion. We investigated the utility of fat-suppressed sequences to differentiate between benign and aggressive vertebral haemangiomas. Patients with the diagnosis of aggressive vertebral haemangioma and available short tau inversion-recovery or T2 fat saturation sequence were included in the study. 11 patients with typical asymptomatic vertebral body haemangiomas were selected as the control group. Region of interest signal intensity (SI) analysis of the entire haemangioma as well as the portion of each haemangioma with highest signal on fat-saturation sequences was performed and normalized to a reference normal vertebral body. A total of 8 patients with aggressive vertebral haemangioma and 11 patients with asymptomatic typical vertebral haemangioma were included. There was a significant difference between total normalized mean SI ratio (3.14 vs 1.48, p = 0.0002), total normalized maximum SI ratio (5.72 vs 2.55, p = 0.0003), brightest normalized mean SI ratio (4.28 vs 1.72, p 88%) and specificity (>82%). In addition to the conventional imaging features such as vertebral expansion and presence of extravertebral component, quantitative evaluation of fat-suppression sequences is also another imaging feature that can differentiate aggressive haemangioma and typical asymptomatic haemangioma. The use of quantitative fat-suppressed MRI in vertebral haemangiomas is demonstrated. Quantitative fat-suppressed MRI can have a role in confirming the diagnosis of aggressive haemangiomas. In addition, this application can be further investigated in future studies to predict aggressiveness of vertebral haemangiomas in early stages.

  7. MR colonography with fecal tagging: comparison between 2D turbo FLASH and 3D FLASH sequences

    International Nuclear Information System (INIS)

    Papanikolaou, Nickolas; Grammatikakis, John; Maris, Thomas; Prassopoulos, Panos; Gourtsoyiannis, Nicholas; Lauenstein, Thomas

    2003-01-01

    The objective of this study was to compare inversion recovery turbo 2D fast low-angle shot (FLASH) and 3D FLASH sequences for fecal-tagged MR colonography studies. Fifteen consecutive patients with indications for colonoscopy underwent MR colonography with fecal tagging. An inversion recovery turbo-FLASH sequence was applied and compared in terms of artifacts presence, efficiency for masking residual stool, and colonic wall conspicuity with a fat-saturated 3D FLASH sequence. Both sequences were acquired following administration of paramagnetic contrast agent. Contrast-to-noise ratio and relative contrast between colonic wall and lumen were calculated and compared for both sequences. Turbo 2D FLASH provided fewer artifacts, higher efficiency for masking the residual stool, and colonic wall conspicuity equivalent to 3D FLASH. An inversion time of 10 ms provided homogeneously low signal intensity of the colonic lumen. Contrast to noise between colonic wall and lumen was significantly higher in the 3D FLASH images, whereas differences in relative contrast were not statistically significant. An optimized inversion-recovery 2D turbo-FLASH sequence provides better fecal tagging results and should be added to the 3D FLASH sequence when designing dark-lumen MR colonography examination protocols. (orig.)

  8. Elimination of motion and pulsation artifacts using BLADE sequences in shoulder MR imaging

    International Nuclear Information System (INIS)

    Lavdas, E.; Zaloni, E.; Vlychou, M.; Vassiou, K.; Fezoulidis, I.; Tsagkalis, A.; Dailiana, Z.

    2015-01-01

    To evaluate the ability of proton-density with fat-suppression BLADE (proprietary name for periodically rotated overlapping parallel lines with enhanced reconstruction in MR systems from Siemens Healthcare, PDFS BLADE) and turbo inversion recovery magnitude-BLADE (TIRM BLADE) sequences to reduce motion and pulsation artifacts in shoulder magnetic resonance examinations. Forty-one consecutive patients who had been routinely scanned for shoulder examination participated in the study. The following pairs of sequences with and without BLADE were compared: (a) Oblique coronal proton-density sequence with fat saturation of 25 patients and (b) oblique sagittal T2 TIRM-weighed sequence of 20 patients. Qualitative analysis was performed by two experienced radiologists. Image motion and pulsation artifacts were also evaluated. In oblique coronal PDFS BLADE sequences, motion artifacts have been significantly eliminated, even in five cases of non-diagnostic value with conventional imaging. Similarly, in oblique sagittal T2 TIRM BLADE sequences, image quality has been improved, even in six cases of non-diagnostic value with conventional imaging. Furthermore, flow artifacts have been improved in more than 80% of all the cases. The use of BLADE sequences is recommended in shoulder imaging, especially in uncooperative patients because it effectively eliminates motion and pulsation artifacts. (orig.)

  9. Study of MR sequence in detecting hyaline cartilage defects of the knee joint

    International Nuclear Information System (INIS)

    Li Songbai; He Cuiju; Sun Wenge; Li Chunkui; Qi Xixun; Li Yanliang; Xu Ke; Bai Xizhuang; Wu Zhenhua

    2003-01-01

    Objective: To evaluate the value of various MR imaging sequences for detecting hyaline cartilage defects. Methods: Ten animal models of cartilage defect were established in 5 pig knees. 5 knees were examined with nine different MR sequences. The signal noise ratio of cartilage and contrast noise ratio were calculated and compared between cartilage and adjacent tissue. Measurement of the defect depth and width on the imaging was correlated with the actual measurement before imaging. 23 patients with hyaline cartilage defects of the knee were evaluated with MR imaging. All these patients underwent subsequent arthroscopy. MR imaging protocol included the selected sequences in the experimental study. Results: The cartilage SNR was better in FSE PD, FS 3D FSPGR, and FS FSE PD sequences. CNR between cartilage and subcartilaginous bone was best in FS 3D FSPGR and FS FSE PD sequences. CNR between cartilage and joint fluid was best in FS 3D FSPGR and FS FSE T 2 WI sequences. CNR between cartilage and meniscus and ligament was best in FS 3D FSPGR, FS FSE PD, SE T 1 WI, and IR TI700 sequences. CNR between cartilage and fat was best in FS 3D FSPGR and SE T 1 WI sequences. The width and depth correlation was best in IR TI700 sequence, which showed the statistical significance (P 2 WI sequence, 68%, 99%, and 0.74, respectively with IR TI700 sequence. Conclusion: The sensitivity of FS 3D FSPGR sequence in detecting hyaline cartilage defect is the highest. T 1 WI of spin echo sequence and T 2 WI/PDWI of fast spin-echo with fat saturation should be the standard sequence in the examination of knee joint. T 1 WI of IR sequence has potential clinical value for cartilage examination

  10. Automated two-point dixon screening for the evaluation of hepatic steatosis and siderosis: comparison with R2*-relaxometry and chemical shift-based sequences

    Energy Technology Data Exchange (ETDEWEB)

    Henninger, B.; Rauch, S.; Schocke, M.; Jaschke, W.; Kremser, C. [Medical University of Innsbruck, Department of Radiology, Innsbruck (Austria); Zoller, H. [Medical University of Innsbruck, Department of Internal Medicine, Innsbruck (Austria); Kannengiesser, S. [Siemens AG, Healthcare Sector, MR Applications Development, Erlangen (Germany); Zhong, X. [Siemens Healthcare, MR R and D Collaborations, Atlanta, GA (United States); Reiter, G. [Siemens AG, Healthcare Sector, MR R and D Collaborations, Graz (Austria)

    2015-05-01

    To evaluate the automated two-point Dixon screening sequence for the detection and estimated quantification of hepatic iron and fat compared with standard sequences as a reference. One hundred and two patients with suspected diffuse liver disease were included in this prospective study. The following MRI protocol was used: 3D-T1-weighted opposed- and in-phase gradient echo with two-point Dixon reconstruction and dual-ratio signal discrimination algorithm (''screening'' sequence); fat-saturated, multi-gradient-echo sequence with 12 echoes; gradient-echo T1 FLASH opposed- and in-phase. Bland-Altman plots were generated and correlation coefficients were calculated to compare the sequences. The screening sequence diagnosed fat in 33, iron in 35 and a combination of both in 4 patients. Correlation between R2* values of the screening sequence and the standard relaxometry was excellent (r = 0.988). A slightly lower correlation (r = 0.978) was found between the fat fraction of the screening sequence and the standard sequence. Bland-Altman revealed systematically lower R2* values obtained from the screening sequence and higher fat fraction values obtained with the standard sequence with a rather high variability in agreement. The screening sequence is a promising method with fast diagnosis of the predominant liver disease. It is capable of estimating the amount of hepatic fat and iron comparable to standard methods. (orig.)

  11. Automated two-point dixon screening for the evaluation of hepatic steatosis and siderosis: comparison with R2*-relaxometry and chemical shift-based sequences

    International Nuclear Information System (INIS)

    Henninger, B.; Rauch, S.; Schocke, M.; Jaschke, W.; Kremser, C.; Zoller, H.; Kannengiesser, S.; Zhong, X.; Reiter, G.

    2015-01-01

    To evaluate the automated two-point Dixon screening sequence for the detection and estimated quantification of hepatic iron and fat compared with standard sequences as a reference. One hundred and two patients with suspected diffuse liver disease were included in this prospective study. The following MRI protocol was used: 3D-T1-weighted opposed- and in-phase gradient echo with two-point Dixon reconstruction and dual-ratio signal discrimination algorithm (''screening'' sequence); fat-saturated, multi-gradient-echo sequence with 12 echoes; gradient-echo T1 FLASH opposed- and in-phase. Bland-Altman plots were generated and correlation coefficients were calculated to compare the sequences. The screening sequence diagnosed fat in 33, iron in 35 and a combination of both in 4 patients. Correlation between R2* values of the screening sequence and the standard relaxometry was excellent (r = 0.988). A slightly lower correlation (r = 0.978) was found between the fat fraction of the screening sequence and the standard sequence. Bland-Altman revealed systematically lower R2* values obtained from the screening sequence and higher fat fraction values obtained with the standard sequence with a rather high variability in agreement. The screening sequence is a promising method with fast diagnosis of the predominant liver disease. It is capable of estimating the amount of hepatic fat and iron comparable to standard methods. (orig.)

  12. Frequency selectivity in pulse responses of Pt/poly(3-hexylthiophene-2,5-diyl/polyethylene oxide +Li+/Pt hetero-junction.

    Directory of Open Access Journals (Sweden)

    Fei Zeng

    Full Text Available Pt/poly(3-hexylthiophene-2,5-diyl/polyethylene oxide + Li+/Pt hetero junctions were fabricated, and their pulse responses were studied. The direct current characteristics were not symmetric in the sweeping range of ±2 V. Negative differential resistance appeared in the input range of 0 to 2 V because of de-doping (or reduction in the side with the semiconductor layer. The device responded stably to a train of pulses with a fixed frequency. The inverse current after a pulse was related to the back-migrated ions. Importantly, the weight calculated based on the inverse current strength, was depressed during low-frequency stimulations but was potentiated during high-frequency stimulations when pulses were positive. Therefore, frequency selectivity was first observed in a semiconducting polymer/electrolyte hetero junction. Detailed analysis of the pulse response showed that the input frequency could modulate the timing of ion doping, de-doping, and re-doping at the semiconducting polymer/electrolyte interface, which then resulted in the frequency selectivity. Our study suggests that the simple redox process in semiconducting polymers can be modulated and used in signal handling or the simulation of bio-learning.

  13. Performance Analysis of the IEEE 802.11A WLAN Standard Optimum and Sub-Optimum Receiver in Frequency-Selective, Slowly Fading Nakagami Channels with AWGN and Pulsed Noise Jamming

    National Research Council Canada - National Science Library

    Kalogrias, Christos

    2004-01-01

    ... 802.11a wireless local area network (WLAN) standard receiver when the signal is transmitted over a frequency selective, slow fading Nakagami channel in a worst case, pulse-noise jamming environment...

  14. Frequency-selective near-field radiative heat transfer between photonic crystal slabs: a computational approach for arbitrary geometries and materials.

    Science.gov (United States)

    Rodriguez, Alejandro W; Ilic, Ognjen; Bermel, Peter; Celanovic, Ivan; Joannopoulos, John D; Soljačić, Marin; Johnson, Steven G

    2011-09-09

    We demonstrate the possibility of achieving enhanced frequency-selective near-field radiative heat transfer between patterned (photonic-crystal) slabs at designable frequencies and separations, exploiting a general numerical approach for computing heat transfer in arbitrary geometries and materials based on the finite-difference time-domain method. Our simulations reveal a tradeoff between selectivity and near-field enhancement as the slab-slab separation decreases, with the patterned heat transfer eventually reducing to the unpatterned result multiplied by a fill factor (described by a standard proximity approximation). We also find that heat transfer can be further enhanced at selective frequencies when the slabs are brought into a glide-symmetric configuration, a consequence of the degeneracies associated with the nonsymmorphic symmetry group.

  15. Fat suppression strategies in MR imaging of breast cancer at 3.0 T. Comparison of the two-point dixon technique and the frequency selective inversion method

    International Nuclear Information System (INIS)

    Kaneko Mikami, Wakako; Kazama, Toshiki; Sato, Hirotaka

    2013-01-01

    The purpose of this study was to compare two fat suppression methods in contrast-enhanced MR imaging of breast cancer at 3.0 T: the two-point Dixon method and the frequency selective inversion method. Forty female patients with breast cancer underwent contrast-enhanced three-dimensional T1-weighted MR imaging at 3.0 T. Both the two-point Dixon method and the frequency selective inversion method were applied. Quantitative analyses of the residual fat signal-to-noise ratio and the contrast noise ratio (CNR) of lesion-to-breast parenchyma, lesion-to-fat, and parenchyma-to-fat were performed. Qualitative analyses of the uniformity of fat suppression, image contrast, and the visibility of breast lesions and axillary metastatic adenopathy were performed. The signal-to-noise ratio was significantly lower in the two-point Dixon method (P<0.001). All CNR values were significantly higher in the two-point Dixon method (P<0.001 and P=0.001, respectively). According to qualitative analysis, both the uniformity of fat suppression and image contrast with the two-point Dixon method were significantly higher (P<0.001 and P=0.002, respectively). Visibility of breast lesions and metastatic adenopathy was significantly better in the two-point Dixon method (P<0.001 and P=0.03, respectively). The two-point Dixon method suppressed the fat signal more potently and improved contrast and visibility of the breast lesions and axillary adenopathy. (author)

  16. Fat saturation in dynamic breast MRI at 3 Tesla: is the Dixon technique superior to spectral fat saturation? A visual grading characteristics study

    Energy Technology Data Exchange (ETDEWEB)

    Clauser, P. [University of Udine, Azienda Ospedaliero-Universitaria ' ' S.Maria della Misericordia' ' , Institute of Diagnostic Radiology, Udine (Italy); Medical University of Vienna, Department of Biomedical Imaging and Image-guided interventions, Division of Molecular and Gender Imaging, Vienna (Austria); Pinker, K.; Helbich, T.H.; Kapetas, P.; Bernathova, M.; Baltzer, P.A.T. [Medical University of Vienna, Department of Biomedical Imaging and Image-guided interventions, Division of Molecular and Gender Imaging, Vienna (Austria)

    2014-09-15

    To intra-individually compare the diagnostic image quality of Dixon and spectral fat suppression at 3 T. Fifty consecutive patients (mean age 55.1 years) undergoing 3 T breast MRI were recruited for this prospective study. The image protocol included pre-contrast and delayed post-contrast spectral and Dixon fat-suppressed T1w series. Two independent blinded readers compared spectral and Dixon fat-suppressed series by evaluating six ordinal (1 worst to 5 best) image quality criteria (image quality, delineation of anatomical structures, fat suppression in the breast and axilla, lesion delineation and internal enhancement). Breast density and size were assessed. Data analysis included Spearman's rank correlation coefficient and visual grading characteristics (VGC) analysis. Four examinations were excluded; 48 examinations in 46 patients were evaluated. In VGC analysis, the Dixon technique was superior regarding image quality criteria analysed (P < 0.01). Smaller breast size and lower breast density were significantly (P < 0.01) correlated with impaired spectral fat suppression quality. No such correlation was identified for the Dixon technique, which showed reconstruction-based water-fat mixups leading to insufficient image quality in 20.8 %. The Dixon technique outperformed spectral fat suppression in all evaluated criteria (P < 0.01). Non-diagnostic examinations can be avoided by fat and water image reconstruction. The superior image quality of the Dixon technique can improve breast MRI interpretation. (orig.)

  17. MR imaging of cranial nerve lesions using six different high-resolution T1- and T2(*)-weighted 3D and 2D sequences

    Energy Technology Data Exchange (ETDEWEB)

    Seitz, J.; Held, P.; Strotzer, M.; Voelk, M.; Nitz, W.R.; Dorenbeck, U.; Feuerbach, S. [Univ. Hospital of Regensburg (Germany). Dept. of Diagnostic Radiology; Stamato, S. [Univ. of California, San Diego, CA (United States). Dept. of Radiology

    2002-07-01

    Purpose: To find a suitable high-resolution MR protocol for the visualization of lesions of all 12 cranial nerves. Material and Methods: Thirty-eight pathologically changed cranial nerves (17 patients) were studied with MR imaging at 1.5T using 3D T2*-weighted CISS, T1-weighted 3D MP-RAGE (without and with i.v. contrast medium), T2-weighted 3D TSE, T2-weighted 2D TSE and T1-weighted fat saturation 2D TSE sequences. Visibility of the 38 lesions of the 12 cranial nerves in each sequence was evaluated by consensus of two radiologists using an evaluation scale from 1 (excellently visible) to 4 (not visible). Results: The 3D CISS sequence provided the best resolution of the cranial nerves and their lesions when surrounded by CSF. In nerves which were not surrounded by CSF, the 2D T1-weighted contrast-enhanced fat suppression technique was the best sequence. Conclusions: A combination of 3D CISS, the 2D T1-weighted fat suppressed sequence and a 3D contrast-enhanced MP-RAGE proved to be the most useful sequence to visualize all lesions of the cranial nerves. For the determination of enhancement, an additional 3D MP-RAGE sequence without contrast medium is required. This sequence is also very sensitive for the detection of hemorrhage.

  18. MR imaging of cranial nerve lesions using six different high-resolution T1- and T2(*)-weighted 3D and 2D sequences

    International Nuclear Information System (INIS)

    Seitz, J.; Held, P.; Strotzer, M.; Voelk, M.; Nitz, W.R.; Dorenbeck, U.; Feuerbach, S.; Stamato, S.

    2002-01-01

    Purpose: To find a suitable high-resolution MR protocol for the visualization of lesions of all 12 cranial nerves. Material and Methods: Thirty-eight pathologically changed cranial nerves (17 patients) were studied with MR imaging at 1.5T using 3D T2*-weighted CISS, T1-weighted 3D MP-RAGE (without and with i.v. contrast medium), T2-weighted 3D TSE, T2-weighted 2D TSE and T1-weighted fat saturation 2D TSE sequences. Visibility of the 38 lesions of the 12 cranial nerves in each sequence was evaluated by consensus of two radiologists using an evaluation scale from 1 (excellently visible) to 4 (not visible). Results: The 3D CISS sequence provided the best resolution of the cranial nerves and their lesions when surrounded by CSF. In nerves which were not surrounded by CSF, the 2D T1-weighted contrast-enhanced fat suppression technique was the best sequence. Conclusions: A combination of 3D CISS, the 2D T1-weighted fat suppressed sequence and a 3D contrast-enhanced MP-RAGE proved to be the most useful sequence to visualize all lesions of the cranial nerves. For the determination of enhancement, an additional 3D MP-RAGE sequence without contrast medium is required. This sequence is also very sensitive for the detection of hemorrhage

  19. Performance of Reverse-Link Synchronous DS-CDMA System on a Frequency-Selective Multipath Fading Channel with Imperfect Power Control

    Directory of Open Access Journals (Sweden)

    Duk Kyung Kim

    2002-08-01

    Full Text Available We analyze the performance for reverse-link synchronous DS-CDMA system in a frequency-selective Rayleigh fading channel with an imperfect power control scheme. The performance degradation due to power control error (PCE, which is approximated by a log-normally distributed random variable, is estimated as a function of the standard deviation of the PCE. In addition, we investigate the impacts of the multipath intensity profile (MIP shape and the number of resolvable paths on the performance. Finally, the coded bit error performance is evaluated in order to estimate the system capacity. Comparing with the conventional CDMA system, we show an achievable gain of from 59% to 23% for reverse-link synchronous transmission technique (RLSTT in the presence of imperfect power control over asynchronous transmission for BER=10−6. As well, the effect of tradeoff between orthogonality and diversity can be seen according to the number of multipaths, and the tendency is kept even in the presence of PCE. We conclude that the capacity can be further improved via the RLSTT, because the DS-CDMA system is very sensitive to power control imperfections.

  20. New Concept of PLC Modems: Multi-Carrier System for Frequency Selective Slow-Fading Channels Based on Layered SCCC Turbocodes

    Directory of Open Access Journals (Sweden)

    J. Zavrtalek

    2015-09-01

    Full Text Available The article introduces a novel concept of a PLC modem as a complement to the existing G3 and PRIME standards for communications using medium- or high-voltage overhead or cable lines. The proposed concept is based on the fact that the levels of impulse noise and frequency selectivity are lower on high-voltage lines than on low-voltage ones. Also, the demands for “cost-effective” circuitry design are not so crucial as in the case of modems for low-voltage level. In contract to these positive conditions, however, there is the need to overcome much longer distances and to take into account low SNR on the receiving side. With respect to the listed reasons, our concept makes use of MCM, instead of OFDM. The assumption of low SNR is compensated through the use of an efficient channel coding based on a serially concatenated turbo code. In addition, MCM offers lower latency and PAPR compared to OFDM. Therefore, when using MCM, it is possible to excite the line with higher power. The proposed concept has been verified during experimental transmission of testing data over a real, 5 km long, 22kV overhead line.

  1. Comparison of MRI pulse sequences in defining prostate volume after permanent implantation

    International Nuclear Information System (INIS)

    McLaughlin, P.W.; Narayana, V.; Drake, D.G.; Miller, B.M.; Marsh, L.; Chan, J.; Gonda, R.; Winfield, R.J.; Roberson, P.L.

    2002-01-01

    Purpose: To determine the relative value of three MRI pulse sequences in defining the prostate volume after permanent implantation. Methods and Materials: A total of 45 patients who received a permanent 125 I implant were studied. Two weeks after implantation, an axial CT scan (2 mm thickness) and T 1 -weighted, T 1 -weighted fat saturation, and T 2 -weighted axial MRI (3-mm) studies were obtained. The prostate volumes were compared with the initial ultrasound planning volumes, and subsequently the CT, T 1 -weighted, and T 1 -weighted fat saturation MRI volumes were compared with the T 2 -weighted volumes. Discrepancies in volume were evaluated by visual inspection of the registered axial images and the registration of axial volumes on the sagittal T 2 -weighted volumes. In a limited set of patients, pre- and postimplant CT and T 2 -weighted MRI studies were available for comparison to determine whether prostate volume changes after implant were dependent on the imaging modality. Results: T 1 -weighted and T 1 -weighted fat saturation MRI and CT prostate volumes were consistently larger than the T 2 -weighted MRI prostate volumes, with a volume on average 1.33 (SD 0.24) times the T 2 -weighted volume. This discrepancy was due to the superiority of T 2 -weighted MRI for prostate definition at the following critical interfaces: membranous urethra, apex, and anterior base-bladder and posterior base-seminal vesicle interfaces. The differences in prostate definition in the anterior base region suggest that the commonly reported underdose may be due to overestimation of the prostate in this region by CT. The consistent difference in volumes suggests that the degree of swelling observed after implantation is in part a function of the imaging modality. In patients with pre- and postimplant CT and T 2 -weighted MRI images, swelling on the T 2 -weighted images was 1.1 times baseline and on CT was 1.3 times baseline, confirming the imaging modality dependence of prostate

  2. Fast MR arthrography using VIBE sequences to evaluate the rotator cuff

    Energy Technology Data Exchange (ETDEWEB)

    Vandevenne, Jan E. [Ziekenhuizen Oost-Limburg, Department of Radiology, Genk (Belgium); Universitair Ziekenhuis Antwerpen, University of Antwerp, Department of Radiology, Edegem (Belgium); Vanhoenacker, Filip; Parizel, Paul M. [Universitair Ziekenhuis Antwerpen, University of Antwerp, Department of Radiology, Edegem (Belgium); Mahachie John, Jestinah M. [University of Hasselt, Centre for Statistics, Diepenbeek (Belgium); Gelin, Geert [Ziekenhuizen Oost-Limburg, Department of Radiology, Genk (Belgium)

    2009-07-15

    The purpose of this paper was to evaluate if short volumetric interpolated breath-hold examination (VIBE) sequences can be used as a substitute for T1-weighted with fat saturation (T1-FS) sequences when performing magnetic resonance (MR) arthrography to diagnose rotator cuff tears. Eighty-two patients underwent direct MR arthrography of the shoulder joint using VIBE (acquisition time of 13 s) and T1-FS (acquisition time of 5 min) sequences in the axial and paracoronal plane on a 1.0-T MR unit. Two radiologists scored rotator cuff tendons on VIBE and T1-FS images separately as normal, small/large partial thickness and full thickness tears with or without geyser sign. T1-FS sequences were considered the gold standard. Surgical correlation was available in a small sample. Sensitivity, specificity, and positive and negative predictive values of VIBE were greater than 92% for large articular-sided partial thickness and full thickness tears. For detecting fraying and articular-sided small partial thickness tears, these parameters were 55%, 94%, 94%, and 57%, respectively. The simple kappa value was 0.76, and the weighted kappa value was 0.86 for agreement between T1-FS and VIBE scores. All large partial and full thickness tears at surgery were correctly diagnosed using VIBE or T1-FS MR images. Fast MR arthrography of the shoulder joint using VIBE sequences showed good concordance with the classically used T1-FS sequences for the appearance of the rotator cuff, in particular for large articular-sided partial thickness tears and for full thickness tears. Due to its very short acquisition time, VIBE may be especially useful when performing MR arthrography in claustrophobic patients or patients with a painful shoulder. (orig.)

  3. Automated two-point dixon screening for the evaluation of hepatic steatosis and siderosis: comparison with R2-relaxometry and chemical shift-based sequences.

    Science.gov (United States)

    Henninger, B; Zoller, H; Rauch, S; Schocke, M; Kannengiesser, S; Zhong, X; Reiter, G; Jaschke, W; Kremser, C

    2015-05-01

    To evaluate the automated two-point Dixon screening sequence for the detection and estimated quantification of hepatic iron and fat compared with standard sequences as a reference. One hundred and two patients with suspected diffuse liver disease were included in this prospective study. The following MRI protocol was used: 3D-T1-weighted opposed- and in-phase gradient echo with two-point Dixon reconstruction and dual-ratio signal discrimination algorithm ("screening" sequence); fat-saturated, multi-gradient-echo sequence with 12 echoes; gradient-echo T1 FLASH opposed- and in-phase. Bland-Altman plots were generated and correlation coefficients were calculated to compare the sequences. The screening sequence diagnosed fat in 33, iron in 35 and a combination of both in 4 patients. Correlation between R2* values of the screening sequence and the standard relaxometry was excellent (r = 0.988). A slightly lower correlation (r = 0.978) was found between the fat fraction of the screening sequence and the standard sequence. Bland-Altman revealed systematically lower R2* values obtained from the screening sequence and higher fat fraction values obtained with the standard sequence with a rather high variability in agreement. The screening sequence is a promising method with fast diagnosis of the predominant liver disease. It is capable of estimating the amount of hepatic fat and iron comparable to standard methods. • MRI plays a major role in the clarification of diffuse liver disease. • The screening sequence was introduced for the assessment of diffuse liver disease. • It is a fast and automated algorithm for the evaluation of hepatic iron and fat. • It is capable of estimating the amount of hepatic fat and iron.

  4. Total fats, saturated Fatty acids, processed foods and acute coronary syndrome in transitional Albania.

    Science.gov (United States)

    Mone, Iris; Bulo, Anyla

    2012-01-01

    We aimed was to assess the association of acute coronary syndrome (ACS) with selected food groups pertinent to non-Mediterranean prototype in Albania, a transitional post-communist country in Southeast Europe. We conducted a case-control study in Tirana in 2003-2006 including 467 non-fatal consecutive ACS patients (370 men aged 59.1±8.7 years, 97 women aged 63.3±7.1 years; 88% response) and a population-based control group (469 men aged 53.1±10.4 years, 268 women aged 54.0±10.9 years; 69% response). A semi-quantitative food frequency questionnaire including 105 food items was administered to all participants based on which the daily calorie intake for selected food groups (meat products, overall oils and fats, sweets, and junk food) was calculated. General linear model was used to assess the association of food groups with ACS. Mean age-adjusted values of meat products, overall oils and fats, sweets and junk food were all considerably higher in cases than controls in both sexes. Cases had significantly higher mean "non-Mediterranean" diet scores (consisting of junk food, sweets, oils and fats except olive oil) than controls (10.3% vs. 5.9% in men and 15.2% vs. 8.3% in women, Pconsumption of processed foods was associated with considerable excess coronary risk which points to serious health implications for the Albanian adult population.

  5. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  6. 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 transcr......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...

  7. The value of MR imaging of PDFASAT sequence in the diagnosis of extremities occult fractures

    International Nuclear Information System (INIS)

    Lu Lingquan; Xu Mingshen; Wu Qianzhi; Mao Chunnan; Wang Shuzi; Zhou Xingfan; Wang Liping

    2004-01-01

    Objective: To investigate the value of MR imaging of proton density weighted-fat saturated (PDFASAT) sequence in detecting the occult fracture of extremities. Methods: Thirty-one patients with acute trauma were studied using radiography and MR imaging within 45 days. MR sequences included FSE T 1 WI, T 2 WI, and PDFASAT. 21 occult fractures occurred in the knee joint, 6 in the hip joint, 1 in the elbow joint, 2 in the shoulder, and 1 in the ankle. Results: All 31 cases had normal radiographic results. 10 cases with proximal fibula, 4 with proximal tibia and 7 with femur condyle occult fractures were found in 21 knee joint acute trauma cases. 2 cases with intertrochanteric, 2 with femoral neck and 2 with cotyle occult fractures were found in 6 hip joint trauma cases. 2 proximal humerus occult fractures were found in 2 shoulder cases. 1 distal humerus and 1 distal fibula occult fracture was found in elbow and ankle cases. MR imaging demonstrated irregular linear low signal in the subcortical region on both T 1 WI and T 2 WI, and high signal changes around low signal were seen on T 2 WI in some cases. The high signal in PDFASAT sequence was more remarkable and wider than that on both T 1 WI and T 2 WI. Conclusion: MR imaging could determine the diagnosis of acute and chronic occult fractures. MRI should be the next choice when plain films fail to reveal suspected fractures in setting of suggestive symptoms and positive physical examination. PDFASAT would be the best effective sequence among the T 1 WI, T 2 WI, and PDFASAT. (author)

  8. A systematic evaluation of three different cardiac T2-mapping sequences at 1.5 and 3T in healthy volunteers.

    Science.gov (United States)

    Baeßler, Bettina; Schaarschmidt, Frank; Stehning, Christian; Schnackenburg, Bernhard; Maintz, David; Bunck, Alexander C

    2015-11-01

    Previous studies showed that myocardial T2 relaxation times measured by cardiac T2-mapping vary significantly depending on sequence and field strength. Therefore, a systematic comparison of different T2-mapping sequences and the establishment of dedicated T2 reference values is mandatory for diagnostic decision-making. Phantom experiments using gel probes with a range of different T1 and T2 times were performed on a clinical 1.5T and 3T scanner. In addition, 30 healthy volunteers were examined at 1.5 and 3T in immediate succession. In each examination, three different T2-mapping sequences were performed at three short-axis slices: Multi Echo Spin Echo (MESE), T2-prepared balanced SSFP (T2prep), and Gradient Spin Echo with and without fat saturation (GraSEFS/GraSE). Segmented T2-Maps were generated according to the AHA 16-segment model and statistical analysis was performed. Significant intra-individual differences between mean T2 times were observed for all sequences. In general, T2prep resulted in lowest and GraSE in highest T2 times. A significant variation with field strength was observed for mean T2 in phantom as well as in vivo, with higher T2 values at 1.5T compared to 3T, regardless of the sequence used. Segmental T2 values for each sequence at 1.5 and 3T are presented. Despite a careful selection of sequence parameters and volunteers, significant variations of the measured T2 values were observed between field strengths, MR sequences and myocardial segments. Therefore, we present segmental T2 values for each sequence at 1.5 and 3T with the inherent potential to serve as reference values for future studies. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  9. Age determination of vessel wall hematoma in spontaneous cervical artery dissection: A multi-sequence 3T Cardiovascular Magnetic resonance study

    Directory of Open Access Journals (Sweden)

    Habs Maximilian

    2011-11-01

    Full Text Available Abstract Background Previously proposed classifications for carotid plaque and cerebral parenchymal hemorrhages are used to estimate the age of hematoma according to its signal intensities on T1w and T2w MR images. Using these classifications, we systematically investigated the value of cardiovascular magnetic resonance (CMR in determining the age of vessel wall hematoma (VWH in patients with spontaneous cervical artery dissection (sCAD. Methods 35 consecutive patients (mean age 43.6 ± 9.8 years with sCAD received a cervical multi-sequence 3T CMR with fat-saturated black-blood T1w-, T2w- and TOF images. Age of sCAD was defined as time between onset of symptoms (stroke, TIA or Horner's syndrome and the CMR scan. VWH were categorized into hyperacute, acute, early subacute, late subacute and chronic based on their signal intensities on T1w- and T2w images. Results The mean age of sCAD was 2.0, 5.8, 15.7 and 58.7 days in patients with acute, early subacute, late subacute and chronic VWH as classified by CMR (p Conclusions Signal intensities of VWH in sCAD vary over time and multi-sequence CMR can help to determine the age of an arterial dissection. Furthermore, findings of this study suggest that the time course of carotid hematomas differs from that of cerebral hematomas.

  10. MR arthrography of the shoulder: Optimizing pulse sequence protocols for the evaluation of cartilage and labrum

    Energy Technology Data Exchange (ETDEWEB)

    Guermazi, Ali, E-mail: Ali.Guermazi@aspetar.com [ASPETAR – Qatar Orthopaedic and Sports Medicine Hospital, Sport City Street, Near Khalifa Stadium, P.O. Box 29222 (Qatar); Department of Radiology, Boston University School of Medicine, 820 Harrison Avenue, FGH Building, 3rd Floor, Boston, MA 02118 (United States); Jomaah, Nabil [ASPETAR – Qatar Orthopaedic and Sports Medicine Hospital, Sport City Street, Near Khalifa Stadium, P.O. Box 29222 (Qatar); Hayashi, Daichi [ASPETAR – Qatar Orthopaedic and Sports Medicine Hospital, Sport City Street, Near Khalifa Stadium, P.O. Box 29222 (Qatar); Department of Radiology, Boston University School of Medicine, 820 Harrison Avenue, FGH Building, 3rd Floor, Boston, MA 02118 (United States); Department of Radiology, Bridgeport Hospital, Yale University School of Medicine, 267 Grant Street, Bridgeport, CT 06610 (United States); Jarraya, Mohamed [ASPETAR – Qatar Orthopaedic and Sports Medicine Hospital, Sport City Street, Near Khalifa Stadium, P.O. Box 29222 (Qatar); Department of Radiology, Boston University School of Medicine, 820 Harrison Avenue, FGH Building, 3rd Floor, Boston, MA 02118 (United States); Silva, Jose Roberto [Department of Radiology, Boston University School of Medicine, 820 Harrison Avenue, FGH Building, 3rd Floor, Boston, MA 02118 (United States); Niu, Jingbo [Clinical Epidemiology Research and Training Unit, Boston University School of Medicine, 650 Albany Street, Suite 200, Boston, MA 02118 (United States); Almusa, Emad; Landreau, Philippe [ASPETAR – Qatar Orthopaedic and Sports Medicine Hospital, Sport City Street, Near Khalifa Stadium, P.O. Box 29222 (Qatar); and others

    2014-08-15

    Objectives: To compare axial T1weighted fat-saturated (T1w fs) and T1w non-fs sequences, and coronal T1w-fs and T2w-fs sequences, for evaluation of cartilage and labrum using CT arthrography (CTA) as the reference. Methods: Patients had MR arthrography (MRA) and CTA of the shoulder on the same day. Cartilage was assessed for superficial and full thickness focal and diffuse damage. Labral lesions were graded for Bankart variants and SLAP lesions. CTA images were read for the same features. The diagnostic performance of MRA including area under the curve (AUC) was evaluated against CTA. Results: When comparing axial sequences, the diagnostic performance for cartilage lesion detection on T1w non-fs was 61.9% (sensitivity) 93.6% (specificity) and 89.5% (accuracy) with AUC 0.782, while that for T1w fs was 61.9%, 94.0%, 89.8% and 0.783. For labral assessment, it was 89.1%, 93.0%, 91.4% and 0.919 for T1w non-fs, and 89.9%, 94.0%, 92.6% and 0.922 for T1w fs. Comparing coronal sequences, diagnostic performance for cartilage was 42.5%, 97.5%, 89.8% and 0.702 for T1w fs, and 38.4%, 98.7%, 90.2%, and 0.686 for T2w fs. For the labrum it was 85.1%, 87.5%, 86.2%, and 0.868 for T1w fs, and 75.7%, 97.5%, 80.8% and 0.816 for T2w fs. Conclusions: Axial T1w fs and T1w non-fs sequences are comparable in their ability to diagnose cartilage and labral lesions. Coronal T1w fs sequence offers slightly higher sensitivity but slightly lower specificity than T2w fs sequence for diagnosis of cartilage and labral lesions.

  11. MR arthrography of the shoulder: Optimizing pulse sequence protocols for the evaluation of cartilage and labrum

    International Nuclear Information System (INIS)

    Guermazi, Ali; Jomaah, Nabil; Hayashi, Daichi; Jarraya, Mohamed; Silva, Jose Roberto; Niu, Jingbo; Almusa, Emad; Landreau, Philippe

    2014-01-01

    Objectives: To compare axial T1weighted fat-saturated (T1w fs) and T1w non-fs sequences, and coronal T1w-fs and T2w-fs sequences, for evaluation of cartilage and labrum using CT arthrography (CTA) as the reference. Methods: Patients had MR arthrography (MRA) and CTA of the shoulder on the same day. Cartilage was assessed for superficial and full thickness focal and diffuse damage. Labral lesions were graded for Bankart variants and SLAP lesions. CTA images were read for the same features. The diagnostic performance of MRA including area under the curve (AUC) was evaluated against CTA. Results: When comparing axial sequences, the diagnostic performance for cartilage lesion detection on T1w non-fs was 61.9% (sensitivity) 93.6% (specificity) and 89.5% (accuracy) with AUC 0.782, while that for T1w fs was 61.9%, 94.0%, 89.8% and 0.783. For labral assessment, it was 89.1%, 93.0%, 91.4% and 0.919 for T1w non-fs, and 89.9%, 94.0%, 92.6% and 0.922 for T1w fs. Comparing coronal sequences, diagnostic performance for cartilage was 42.5%, 97.5%, 89.8% and 0.702 for T1w fs, and 38.4%, 98.7%, 90.2%, and 0.686 for T2w fs. For the labrum it was 85.1%, 87.5%, 86.2%, and 0.868 for T1w fs, and 75.7%, 97.5%, 80.8% and 0.816 for T2w fs. Conclusions: Axial T1w fs and T1w non-fs sequences are comparable in their ability to diagnose cartilage and labral lesions. Coronal T1w fs sequence offers slightly higher sensitivity but slightly lower specificity than T2w fs sequence for diagnosis of cartilage and labral lesions

  12. MR imaging of hyaline cartilage at 0.5 T: a quantitative and qualitative in vitro evaluation of three types of sequences

    International Nuclear Information System (INIS)

    Linden, E. van der; Kroon, H.M.; Doornbos, J.; Bloem, J.L.; Hermans, J.

    1998-01-01

    Objective. To identify an optimal pulse sequence for in vitro imaging of hyaline cartilage at 0.5 T. Materials and methods. Twelve holes of varying diameter and depth were drilled in cartilage of two pig knees. These were submerged in saline and scanned with a 0.5-T MR system. Sixteen T1-weighted gradient echo (GE), two T2-weighted GE, and 16 fast spin echo sequences were used, by varying repetition time (TR), echo time (TE), flip angle (FA), echo train length, profile order, and by use of fat saturation. Contrast-to-noise ratios (CNR) of cartilage versus saline solution and cartilage versus subchondral bone were measured. Cartilaginous lesions were evaluated separately by three independent observers. Interobserver variability and correlation between the quantitative and qualitative analyses were calculated. Results. The mean CNRs of two specimens of cartilage versus saline solution ranged from 6.3 (±2.1) to 27.7 (±2.5), and those of cartilage versus subchondral bone from 0.3 (±0.2) to 22.5 (±1.4). The highest CNR was obtained with a T1-weighted spoiled 3D-GE technique (TR 65 ms, TE 11.5 ms, FA 45 ). The number of lesions observed per sequence varied from 35 to 69. Observer agreement was fair to good. The T1-weighted spoiled GE sequences with a TR of 65 ms, TE of 11.5 ms and FA of 30 and 45 were significantly superior to the other 34 sequences in the qualitative analysis. Conclusion. T1-weighted spoiled 3D-GE sequences with a TR of 65 ms, a TE of 11.5 ms, and a FA of 30-45 were found to be optimal for in vitro imaging of cartilage at 0.5 T. (orig.)

  13. MR imaging of hyaline cartilage at 0.5 T: a quantitative and qualitative in vitro evaluation of three types of sequences

    Energy Technology Data Exchange (ETDEWEB)

    Linden, E. van der; Kroon, H.M.; Doornbos, J.; Bloem, J.L. [Department of Radiology C2-S, Albinusdreef 2, Leiden University Medical Center, Postbus 9600, NL-2300 RC Leiden (Netherlands); Hermans, J. [Department of Medical Statistics, Leiden University Medical Center, Leiden (Netherlands)

    1998-06-01

    Objective. To identify an optimal pulse sequence for in vitro imaging of hyaline cartilage at 0.5 T. Materials and methods. Twelve holes of varying diameter and depth were drilled in cartilage of two pig knees. These were submerged in saline and scanned with a 0.5-T MR system. Sixteen T1-weighted gradient echo (GE), two T2-weighted GE, and 16 fast spin echo sequences were used, by varying repetition time (TR), echo time (TE), flip angle (FA), echo train length, profile order, and by use of fat saturation. Contrast-to-noise ratios (CNR) of cartilage versus saline solution and cartilage versus subchondral bone were measured. Cartilaginous lesions were evaluated separately by three independent observers. Interobserver variability and correlation between the quantitative and qualitative analyses were calculated. Results. The mean CNRs of two specimens of cartilage versus saline solution ranged from 6.3 ({+-}2.1) to 27.7 ({+-}2.5), and those of cartilage versus subchondral bone from 0.3 ({+-}0.2) to 22.5 ({+-}1.4). The highest CNR was obtained with a T1-weighted spoiled 3D-GE technique (TR 65 ms, TE 11.5 ms, FA 45 ). The number of lesions observed per sequence varied from 35 to 69. Observer agreement was fair to good. The T1-weighted spoiled GE sequences with a TR of 65 ms, TE of 11.5 ms and FA of 30 and 45 were significantly superior to the other 34 sequences in the qualitative analysis. Conclusion. T1-weighted spoiled 3D-GE sequences with a TR of 65 ms, a TE of 11.5 ms, and a FA of 30-45 were found to be optimal for in vitro imaging of cartilage at 0.5 T. (orig.) With 8 figs., 1 tab., 31 refs.

  14. Protocol optimization of sacroiliac joint MR Imaging at 3 Tesla: Impact of coil design and motion resistant sequences on image quality.

    Science.gov (United States)

    Gondim Teixeira, P A; Bravetti, M; Hossu, G; Lecocq, S; Petit, D; Loeuille, D; Blum, A

    2017-12-01

    To evaluate the impact of coil design and motion-resistant sequences on the quality of sacroiliac magnetic resonance imaging (MRI) examination in patients with spondyloarthropathy. One hundred and twenty-one patients with suspected sacroiliitis and referred for MRI of the sacroiliac joints were retrospectively evaluated with MRI at 3-Tesla. There were 78 women and 43 men with a mean age of 36.7±11.5 (SD) years (range: 15.8-78.4 years). Conventional and motion-resistant fat-saturated fast-spin echo T2-weighted sequences were performed with two different coils. Image quality was subjectively evaluated by two independent readers (R1 and R2) using a four-point scale. Confidence in the identification of bone marrow edema pattern (BMEP) was also evaluated subjectively using a three-point scale. Phased array body coil yielded improved image quality compared to surface coil (14.1 to 30.4% for R1 and 14.6 to 25.7% for R2; Pcoil with motion-resistant T2-weighted sequence (kappa 0.990). The smallest number of indeterminate BMEP zones was seen on MRI set acquired with the phased-array body coil and motion-resistant T2-weighted sequence. Phased array body coil and motion-resistant T2-weighted sequences perform better than surface coil and conventional T2-weighted sequences for the evaluation of sacroiliac joints, increasing confidence in the identification of BMEP. Copyright © 2017 Editions françaises de radiologie. Published by Elsevier Masson SAS. All rights reserved.

  15. Multi-Band Frequency Selective Surfaces: Analysis

    Science.gov (United States)

    2008-08-01

    performed by a graduate student from the University of Turin (Italy) in the frame of a six-month internship at TNO, following these steps: la Study the IEMEN...antennas using EBG substrates", Ph.D. dissertation, Departamento de Comunicaciones , Universidad Politecnica de Valencia, Valencia, Spain, 2006. [21

  16. Analytic clock frequency selection for global DVFS

    OpenAIRE

    Gerards, Marco Egbertus Theodorus; Hurink, Johann L.; Holzenspies, P.K.F.; Kuper, Jan; Smit, Gerardus Johannes Maria

    2014-01-01

    Computers can reduce their power consumption by decreasing their speed using Dynamic Voltage and Frequency Scaling (DVFS). A form of DVFS for multicore processors is global DVFS, where the voltage and clock frequency is shared among all processor cores. Because global DVFS is efficient and cheap to implement, it is used in modern multicore processors like the IBM Power 7, ARM Cortex A9 and NVIDIA Tegra 2. This theory oriented paper discusses energy optimal DVFS algorithms for such processors....

  17. Analytic clock frequency selection for global DVFS

    NARCIS (Netherlands)

    Gerards, Marco Egbertus Theodorus; Hurink, Johann L.; Holzenspies, P.K.F.; Kuper, Jan; Smit, Gerardus Johannes Maria

    2014-01-01

    Computers can reduce their power consumption by decreasing their speed using Dynamic Voltage and Frequency Scaling (DVFS). A form of DVFS for multicore processors is global DVFS, where the voltage and clock frequency is shared among all processor cores. Because global DVFS is efficient and cheap to

  18. Age determination of vessel wall hematoma in spontaneous cervical artery dissection: A multi-sequence 3T Cardiovascular Magnetic resonance study

    Science.gov (United States)

    2011-01-01

    Background Previously proposed classifications for carotid plaque and cerebral parenchymal hemorrhages are used to estimate the age of hematoma according to its signal intensities on T1w and T2w MR images. Using these classifications, we systematically investigated the value of cardiovascular magnetic resonance (CMR) in determining the age of vessel wall hematoma (VWH) in patients with spontaneous cervical artery dissection (sCAD). Methods 35 consecutive patients (mean age 43.6 ± 9.8 years) with sCAD received a cervical multi-sequence 3T CMR with fat-saturated black-blood T1w-, T2w- and TOF images. Age of sCAD was defined as time between onset of symptoms (stroke, TIA or Horner's syndrome) and the CMR scan. VWH were categorized into hyperacute, acute, early subacute, late subacute and chronic based on their signal intensities on T1w- and T2w images. Results The mean age of sCAD was 2.0, 5.8, 15.7 and 58.7 days in patients with acute, early subacute, late subacute and chronic VWH as classified by CMR (p hematomas with Cohen's kappa of 0.74 (p hematomas differs from that of cerebral hematomas. PMID:22122756

  19. Assessment of cartilage-dedicated sequences at ultra-high-field MRI: comparison of imaging performance and diagnostic confidence between 3.0 and 7.0 T with respect to osteoarthritis-induced changes at the knee joint

    Energy Technology Data Exchange (ETDEWEB)

    Stahl, Robert [University of California, Musculoskeletal and Quantitative Imaging Group, Department of Radiology, San Francisco, CA (United States); University Hospitals - Campus Grosshadern, Ludwig Maximilians University of Munich, Department of Clinical Radiology, Munich (Germany); Krug, Roland; Zuo, Jin; Majumdar, Sharmila; Link, Thomas M. [University of California, Musculoskeletal and Quantitative Imaging Group, Department of Radiology, San Francisco, CA (United States); Kelley, Douglas A.C. [General Electrics Healthcare Technologies, San Francisco, CA (United States); Ma, C.B. [University of California, Department of Orthopedic Surgery, San Francisco, CA (United States)

    2009-08-15

    The objectives of the study were to optimize three cartilage-dedicated sequences for in vivo knee imaging at 7.0 T ultra-high-field (UHF) magnetic resonance imaging (MRI) and to compare imaging performance and diagnostic confidence concerning osteoarthritis (OA)-induced changes at 7.0 and 3.0 T MRI. Optimized MRI sequences for cartilage imaging at 3.0 T were tailored for 7.0 T: an intermediate-weighted fast spin-echo (IM-w FSE), a fast imaging employing steady-state acquisition (FIESTA) and a T1-weighted 3D high-spatial-resolution volumetric fat-suppressed spoiled gradient-echo (SPGR) sequence. Three healthy subjects and seven patients with mild OA were examined. Signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), diagnostic confidence in assessing cartilage abnormalities, and image quality were determined. Abnormalities were assessed with the whole organ magnetic resonance imaging score (WORMS). Focal cartilage lesions and bone marrow edema pattern (BMEP) were also quantified. At 7.0 T, SNR was increased (p<0.05) for all sequences. For the IM-w FSE sequence, limitations with the specific absorption rate (SAR) required modifications of the scan parameters yielding an incomplete coverage of the knee joint, extensive artifacts, and a less effective fat saturation. CNR and image quality were increased (p<0.05) for SPGR and FIESTA and decreased for IM-w FSE. Diagnostic confidence for cartilage lesions was highest (p<0.05) for FIESTA at 7.0 T. Evaluation of BMEP was decreased (p < 0.05) at 7.0 T due to limited performance of IM-w FSE. Gradient echo-based pulse sequences like SPGR and FIESTA are well suited for imaging at UHF which may improve early detection of cartilage lesions. However, UHF IM-w FSE sequences are less feasible for clinical use. (orig.)

  20. Assessment of cartilage-dedicated sequences at ultra-high-field MRI: comparison of imaging performance and diagnostic confidence between 3.0 and 7.0 T with respect to osteoarthritis-induced changes at the knee joint

    International Nuclear Information System (INIS)

    Stahl, Robert; Krug, Roland; Zuo, Jin; Majumdar, Sharmila; Link, Thomas M.; Kelley, Douglas A.C.; Ma, C.B.

    2009-01-01

    The objectives of the study were to optimize three cartilage-dedicated sequences for in vivo knee imaging at 7.0 T ultra-high-field (UHF) magnetic resonance imaging (MRI) and to compare imaging performance and diagnostic confidence concerning osteoarthritis (OA)-induced changes at 7.0 and 3.0 T MRI. Optimized MRI sequences for cartilage imaging at 3.0 T were tailored for 7.0 T: an intermediate-weighted fast spin-echo (IM-w FSE), a fast imaging employing steady-state acquisition (FIESTA) and a T1-weighted 3D high-spatial-resolution volumetric fat-suppressed spoiled gradient-echo (SPGR) sequence. Three healthy subjects and seven patients with mild OA were examined. Signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), diagnostic confidence in assessing cartilage abnormalities, and image quality were determined. Abnormalities were assessed with the whole organ magnetic resonance imaging score (WORMS). Focal cartilage lesions and bone marrow edema pattern (BMEP) were also quantified. At 7.0 T, SNR was increased (p<0.05) for all sequences. For the IM-w FSE sequence, limitations with the specific absorption rate (SAR) required modifications of the scan parameters yielding an incomplete coverage of the knee joint, extensive artifacts, and a less effective fat saturation. CNR and image quality were increased (p<0.05) for SPGR and FIESTA and decreased for IM-w FSE. Diagnostic confidence for cartilage lesions was highest (p<0.05) for FIESTA at 7.0 T. Evaluation of BMEP was decreased (p < 0.05) at 7.0 T due to limited performance of IM-w FSE. Gradient echo-based pulse sequences like SPGR and FIESTA are well suited for imaging at UHF which may improve early detection of cartilage lesions. However, UHF IM-w FSE sequences are less feasible for clinical use. (orig.)

  1. 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.

  2. Compartmental modeling with nitrogen-15 to determine effects of degree of fat saturation on intraruminal N recycling.

    Science.gov (United States)

    Oldick, B S; Firkins, J L; Kohn, R A

    2000-09-01

    Two- and three-compartment models were developed to describe N kinetics within the rumen using three Holstein heifers and one nonlactating Holstein cow fitted with ruminal and duodenal cannulas. A 4 x 4 Latin square design included a control diet containing no supplemental fat and diets containing 4.85% of diet dry matter as partially hydrogenated tallow (iodine value = 13), tallow (iodine value = 51), or animal-vegetable fat (iodine value = 110). Effects of fat on intraruminal N recycling and relationships between intraruminal N recycling and ruminal protozoa concentration or the efficiency of microbial protein synthesis were determined. A pulse dose of 15(NH4)2SO4 was introduced into the ruminal NH3 N pool, and samples were taken over time from the ruminal NH3 N and nonammonia N pools. For the three-compartment model, precipitates of nonammonia N after trichloroacetic acid and ethanol extraction were defined as slowly turning over nonammonia N; rapidly turning over nonammonia N was determined by difference. Curves of 15N enrichment were fit to models with two (NH3 N and nonammonia N) or three (NH3 N, rapidly turning over nonammonia N, and slowly turning over nonammonia N) compartments using the software SAAM II. Because the three-compartment model did not remove a small systematic bias or improve the fit of the data, the two-compartment model was used to provide measurements of intraruminal N recycling. Intraruminal NH3 N recycling (45% for control) decreased linearly as fat unsaturation increased (50.2, 43.0, and 41.7% for partially hydrogenated tallow, tallow, and animal-vegetable fat, respectively). Intraruminal nitrogen recycling was not correlated with efficiency of microbial protein synthesis or ruminal protozoa counts.

  3. 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.

  4. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. 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...

  6. Comparison of modern 3D and 2D MR imaging sequences of the wrist at 3 Tesla

    International Nuclear Information System (INIS)

    Rehnitz, C.; Klaan, B.; Amarteifio, E.; Kauczor, H.U.; Weber, M.A.; Stillfried, F. von; Burkholder, I.

    2016-01-01

    To compare the image quality of modern 3 D and 2 D sequences for dedicated wrist imaging at 3 Tesla (T) MRI. At 3 T MRI, 18 patients (mean age: 36.2 years) with wrist pain and 16 healthy volunteers (mean age: 26.4 years) were examined using 2 D proton density-weighted fat-saturated (PDfs), isotropic 3 D TrueFISP, 3 D MEDIC, and 3 D PDfs SPACE sequences. Image quality was rated on a five-point scale (0 - 4) including overall image quality (OIQ), visibility of important structures (cartilage, ligaments, TFCC) and degree of artifacts. Signal-to-noise ratios (SNR) and contrast-to-noise ratios (CNR) of cartilage/bone/muscle/fluid as well as the mean overall SNR/CNR were calculated using region-of-interest analysis. ANOVA, paired t-, and Wilcoxon-signed-rank tests were applied. The image quality of all tested sequences was superior to 3 D PDfs SPACE (p < 0.01). 3 D TrueFISP had the highest combined cartilage score (mean: 3.4) and performed better in cartilage comparisons against 3 D PDfs SPACE in both groups and 2 D PDfs in volunteers (p < 0.05). 3 D MEDIC performed better in 7 of 8 comparisons (p < 0.05) regarding ligaments and TFCC. 2 D PDfs provided constantly high scores. The mean overall SNR/CNR for 2 D PDfs, 3 D PDfs SPACE, 3 D TrueFISP, and 3 D MEDIC were 68/65, 32/27, 45/47, and 57/45, respectively. 2 D PDfs performed best in most SNR/CNR comparisons (p < 0.05) and 3 D MEDIC performed best within the 3 D sequences (p < 0.05). Except 3 D PDfs SPACE, all tested 3 D and 2 D sequences provided high image quality. 3 D TrueFISP was best for cartilage imaging, 3 D MEDIC for ligaments and TFCC and 2 D PDfs for general wrist imaging.

  7. Detection of liver lesions with gadolinium-enhanced VIBE sequence in comparison with SPIO-enhanced MRI; Detektion von Leberlaesionen mit der Gadolinium-verstaerkten VIBE-Sequenz im Vergleich zur SPIO-verstaerkten MRT

    Energy Technology Data Exchange (ETDEWEB)

    Heim, P.; Steiner, P.; Dieckmann, C.; Adam, G. [Universitaetsklinikum Hamburg-Eppendorf (Germany). Klinik und Poliklinik fuer Diagnostische und Interventionelle Radiologie; Schoder, V. [Universitaetsklinikum Hamburg-Eppendorf (Germany). Inst. fuer Medizinische Biometrie und Epidemiologie; Kuhlencordt, R. [Universitaetsklinikum Hamburg-Eppendorf (Germany). Klinik und Poliklinik fuer Allgemein-, Viszeral-, und Thoraxchirurgie

    2003-10-01

    Purpose: Detection of malignant liver lesions with gadolinium-enhanced volumetric interpolated breath-hold examination (VIBE) in comparison with SPIO-enhanced MRT (four different SPIO-enhanced T2w sequences) and histological and imaging follow-up in non-cirrhotic livers at 1.5 T. Patients and methods: Twenty-two patients with suspected focal liver lesions prospectively underwent a gadolinium-enhanced 3D VIBE. Four T2w sequences (HASTE sequence, fast spin-echo-sequence with and without fat-saturation, FLASH 2D gradient echo-sequence) after administration of superparamagnetic iron oxide (SPIO) served as gold standard combined with histological work-up in 17 patients and histological and imaging follow-up in five patients. The image quality was evaluated and the detectability of intrahepatic lesions was rated by the alternative free-response receiver operating characteristic (AFROC) analysis. In addition, the contrast-to-noise ration was compared. Results: Altogether 49 malignant and 35 benign liver lesions were found. Concerning the image quality, VIBE turned out to be of slightly poorer image quality than the SPIO-enhanced examination with HASTE sequence (4.95 vs. 5.0). The fast spin-echo-sequence without fat-saturation demonstrated the highest contrast-to-noise ratio. All sequences showed a comparable certainty in detecting lesion (area under the curve 0.68-0.74) and identifying malignant liver lesions. Conclusions: Despite the small number of patients, VIBE seems to be a comparable, inexpensive and fast method in diagnosing malignant liver lesions. (orig.) [German] Ziel: Detektion maligner Leberlaesionen mit der Gadolinium-verstaerkten 3D-Gradientenecho-Sequenz in Atemanhaltetechnik (VIBE-Sequenz) im Vergleich mit der SPIO-verstaerkten MRT (vier verschiedene SPIO-verstaerkte T2-gew. Sequenzen) sowie histologischen und bildgebenden (Verlaufs-) Untersuchungen in nicht-zirrhotischen Lebern bei 1,5 T. Patienten und Methoden: 22 Patienten mit Verdacht auf maligne

  8. Chronic anterior cruciate ligament tears and associated meniscal and traumatic cartilage lesions: evaluation with morphological sequences at 3.0 T

    Energy Technology Data Exchange (ETDEWEB)

    Vlychou, Marianna; Fezoulidis, Ioannis V. [University Hospital of Larissa, Department of Radiology, Medical School of Thessaly, Larissa (Greece); Hantes, Michalis; Michalitsis, Sotirios; Malizos, Konstantinos [University Hospital of Larissa, Department of Orthopaedic Surgery, Medical School of Thessaly, Larissa (Greece); Tsezou, Aspasia [University Hospital of Larissa, Department of Molecular Genetics and Cytogenetics, Medical School of Thessaly, Larissa (Greece)

    2011-06-15

    To investigate the diagnostic efficacy of morphological sequences at 3.0 T MR imaging in detecting anterior cruciate ligament (ACL), meniscal pathology and traumatic cartilage legions in young patients with chronic deficient anterior cruciate ligament knees. This prospective study included 43 patients (39 male) between the age of 15 and 37 years (mean age 22.6 years) with a history of knee injury sustained at least 3 months prior to the decision to repair a torn ACL. All patients underwent a 3.0 T MR scan with the same standard protocol, including intermediate-weighted and three-dimensional spoiled gradient-recalled T1-weighted sequences with fat saturation and subsequently surgical reconstruction of the ACL, along with meniscal and cartilage repair, when necessary. All ACL tears were correctly interpreted by 3.0 T MR images. The sensitivity of the MR scans regarding tears of the medial meniscus was 93.7%, the specificity 92.6%, the positive predictive value 88.2% and the negative predictive value 95.8%. The sensitivity of the MR scans regarding tears of lateral meniscus was 85.7%, the specificity was 93.1%, the positive predictive value 85.7% and the negative predictive value 93.1%. With regard to the grading of the cartilage lesions, Cohen's kappa coefficient indicated moderate agreement for grade I and II cartilage lesions (0.5), substantial agreement for grade III and IV cartilage lesions (0.70 and 0.66) and substantial agreement for normal regions (0.75). Regarding location of the cartilage lesions, Cohen's kappa coefficient varied between almost perfect agreement in the lateral femoral condyle and no agreement in the trochlea. In the setting of chronic ACL deficiency, MR imaging at 3.0 T achieves satisfactory diagnostic performance regarding meniscal and ligamentous pathology. In the detection of cartilage lesions MRI is less successful. (orig.)

  9. 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.

  10. 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.

  11. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  12. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  13. 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...

  14. 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.

  15. 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....

  16. A novel method for fat suppression in RARE sequences

    International Nuclear Information System (INIS)

    Higuchi, Nobuya

    1999-01-01

    Rapid acquisition relaxation-enhanced (RARE) sequences utilize one or several Carr-Purcell-Meiboom-Gill (CPMG) echo trains to sample a number of k-space lines each repetition time TR. The technique can rapidly generate multislice T2-weighted images which, as a rule, are strikingly similar in contrast to conventional T2-weighted spin-echo (SE) images. An exception to this rule is the appearance of very bright signal from fat in T2-weighted RARE images as compared to conventional T2-weighted SE images. To reduce this fat signal, we introduce a time delay, τc, between the 90 degrees x and first 180 degrees y pulse of each echo train such that a phase angle of pi/2 develops between fat and the reference (water) line at echo maxima. The technique leads to single-acquisition fat suppression without the use of frequency-selective saturation pulses and concomitant loss of slices per TR. A Bloch equation analysis is used to identify two major mechanisms contributing to suppression of off-resonance spins such that w τc =pi/2. Namely, the CPMG sequence becomes a CP sequence with no self-correction properties for imperfect 180 degrees pulses leading to enhanced signal decay, and the raw k-space data matrix become segmented into blocks alternately multiplied by +/- i, leading to signal dispersion following Fourier transformation. (K.H.)

  17. 3D-imaging of the knee with an optimized 3D-FSE-sequence and a 15-channel knee-coil

    Energy Technology Data Exchange (ETDEWEB)

    Notohamiprodjo, Mike, E-mail: mike.notohamiprodjo@med.uni-muenchen.de [Department of Clinical Radiology, University Hospitals Munich, Marchioninistrasse 15, 81377 Munich (Germany); Department of Radiology, Langone Medical Center, Bernard and Irene Schwartz Center for Biomedical Imaging New York University, 660 First Avenue, 4th Floor, New York, NY 10016 (United States); Horng, Annie; Kuschel, Bernhard [Department of Clinical Radiology, University Hospitals Munich, Marchioninistrasse 15, 81377 Munich (Germany); Paul, Dominik [Siemens Healthcare, Erlangen, Henkestr. 127, 91054 Erlangen (Germany); Li, Guobin [Siemens Mindit Magnetic Resonance Ltd., Shenzhen, Guang Dong (China); Raya, Jose G. [Department of Radiology, Langone Medical Center, Bernard and Irene Schwartz Center for Biomedical Imaging New York University, 660 First Avenue, 4th Floor, New York, NY 10016 (United States); Reiser, Maximilian F. [Department of Clinical Radiology, University Hospitals Munich, Marchioninistrasse 15, 81377 Munich (Germany); Glaser, Christian [Department of Clinical Radiology, University Hospitals Munich, Marchioninistrasse 15, 81377 Munich (Germany); Department of Radiology, Langone Medical Center, Bernard and Irene Schwartz Center for Biomedical Imaging New York University, 660 First Avenue, 4th Floor, New York, NY 10016 (United States)

    2012-11-15

    Objectives: To evaluate the clinical usefulness of an optimized 3D-Fast-Spin-Echo-sequence (3D-SPACE) in combination with a 15-channel knee-coil for 3D-imaging of the knee at 3 T. Methods: 15 volunteers and 50 consecutive patients were examined at 3 T with fat-saturated moderately T2-weighted 3D-SPACE (Voxel-size (VS): 0.6 mm Multiplication-Sign 0.5 mm Multiplication-Sign 0.5 mm/acquisition-time (AT) 10:44 min) using a 15-channel knee-coil. Flip angle optimization and radial k-space reordering were applied. Signal- and contrast-to-noise-ratios (SNR, CNR) were compared to non-optimized 3D-SPACE (8-channel knee-coil) and conventional 2D-FSE (VS: 0.4 mm Multiplication-Sign 0.4 mm Multiplication-Sign 3 mm/total AT: 12 min). Two radiologists independently rated depiction of internal knee structures and assessed detection and depiction of cartilage and meniscus abnormalities compared to conventional 2D-FSE-sequences. Sensitivity and specificity were calculated for a subgroup with arthroscopy as reference standard. Statistical analysis was performed with paired t-tests, confidence intervals and weighted-{kappa}-coefficients. Results: SNR and CNR particularly of fluid/cartilage of optimized 3D-SPACE were significantly higher (p < 0.05) than of the non-optimized 3D-sequence and conventional 2D-sequence. Blurring and image inhomogeneity were reduced in the optimized sequence. The thin slice-thickness was beneficial for depiction of problematical anatomical structures such as meniscal roots. 3D-SPACE showed significantly higher diagnostic confidence (p < 0.05) for diagnosis of cartilage lesions of the femoral trochlea. Overall sensitivity and specificity of 3D-SPACE and 2D-FSE for cartilage lesions was 82.3%/80.2% and 79.4%/84.2% and 100%/86.4% and 92.3%/81.8% for meniscus lesions. Conclusions: Optimized 3D-SPACE provides significantly higher signal and contrast compared to conventional 2D-FSE, particularly for fluid and cartilage, leading to improved diagnostic confidence

  18. 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…

  19. 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.

  20. 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.

  1. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  2. 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

  3. 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.

  4. 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...

  5. 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...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... 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...

  6. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  7. 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.

  8. 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}.

  9. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  10. Optimal Superimposed Training Sequences for Channel Estimation in MIMO-OFDM Systems

    Directory of Open Access Journals (Sweden)

    Ratnam V. Raja Kumar

    2010-01-01

    Full Text Available In this work an iterative time domain Least Squares (LS based channel estimation method using superimposed training (ST for a Multiple Input Multiple Output Orthogonal Frequency Division Multiplexing (MIMO-OFDM system over time varying frequency selective fading channels is proposed. The performance of the channel estimator is analyzed in terms of the Mean Square Estimation Error (MSEE and its impact on the uncoded Bit Error Rate (BER of the MIMO-OFDM system is studied. A new selection criterion for the training sequences that jointly optimizes the MSEE and the BER of the OFDM system is proposed. Chirp based sequences are proposed and shown to satisfy the same. These are compared with the other sequences proposed in the literature and are found to yield a superior performance. The sequences, one for each transmitting antenna, offers fairness through providing equal interference in all the data carriers unlike earlier proposals. The effectiveness of the mathematical analysis presented is demonstrated through a comparison with the simulation studies. Experimental studies are carried out to study and validate the improved performance of the proposed scheme. The scheme is applied to the IEEE 802.16e OFDM standard and a case is made with the required design of the sequence.

  11. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    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.

  12. 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.

  13. Main sequence mass loss

    International Nuclear Information System (INIS)

    Brunish, W.M.; Guzik, J.A.; Willson, L.A.; Bowen, G.

    1987-01-01

    It has been hypothesized that variable stars may experience mass loss, driven, at least in part, by oscillations. The class of stars we are discussing here are the δ Scuti variables. These are variable stars with masses between about 1.2 and 2.25 M/sub θ/, lying on or very near the main sequence. According to this theory, high rotation rates enhance the rate of mass loss, so main sequence stars born in this mass range would have a range of mass loss rates, depending on their initial rotation velocity and the amplitude of the oscillations. The stars would evolve rapidly down the main sequence until (at about 1.25 M/sub θ/) a surface convection zone began to form. The presence of this convective region would slow the rotation, perhaps allowing magnetic braking to occur, and thus sharply reduce the mass loss rate. 7 refs

  14. Electricity sequence control

    International Nuclear Information System (INIS)

    Shin, Heung Ryeol

    2010-03-01

    The contents of the book are introduction of control system, like classification and control signal, introduction of electricity power switch, such as push-button and detection switch sensor for induction type and capacitance type machinery for control, solenoid valve, expression of sequence and type of electricity circuit about using diagram, time chart, marking and term, logic circuit like Yes, No, and, or and equivalence logic, basic electricity circuit, electricity sequence control, added condition, special program control about choice and jump of program, motor control, extra circuit on repeat circuit, pause circuit in a conveyer, safety regulations and rule about classification of electricity disaster and protective device for insulation.

  15. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    , 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...... information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity...

  16. 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...

  17. 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

  18. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  19. simple sequence repeat (SSR)

    African Journals Online (AJOL)

    In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 linkage groups of adzuki bean were evaluated for transferability to mungbean and related Vigna spp. 41 markers amplified characteristic bands in at least one Vigna species. The transferability percentage across the genotypes ranged ...

  20. Targeted sequencing of plant genomes

    Science.gov (United States)

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  1. Almost convergence of triple sequences

    OpenAIRE

    Ayhan Esi; M.Necdet Catalbas

    2013-01-01

    In this paper we introduce and study the concepts of almost convergence and almost Cauchy for triple sequences. Weshow that the set of almost convergent triple sequences of 0's and 1's is of the first category and also almost everytriple sequence of 0's and 1's is not almost convergent.Keywords: almost convergence, P-convergent, triple sequence.

  2. A few Smarandache Integer Sequences

    OpenAIRE

    Ibstedt, Henry

    2010-01-01

    This paper deals with the analysis of a few Smarandache Integer Sequences which first appeared in Properties or the Numbers, F. Smarandache, University or Craiova Archives, 1975. The first four sequences are recurrence generated sequences while the last three are concatenation sequences.

  3. 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...... 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....

  4. Fat-suppressed MRI of musculoskeletal infection: fast T2-weighted techniques versus gadolinium-enhanced T1-weighted images

    International Nuclear Information System (INIS)

    Miller, T.T.; Randolph, D.A. Jr.; Staron, R.B.; Feldman, F.; Cushin, S.

    1997-01-01

    Purpose. To investigate gadolinium's role in imaging musculoskeletal infection by comparing the conspicuity and extent of inflammatory changes demonstrated on gadolinium-enhanced fat-suppressed T1-weighted images versus fat-suppressed fast T2-weighted sequences. Design. Eighteen patients with infection were imaged in a 1.5-T unit, using frequency-selective and/or inversion recovery fat-suppressed fast T2-weighted images (T2WI) and gadolinium-enhanced frequency-selective fat-suppressed T1-weighted images (T1WI). Thirty-four imaging planes with both a fat-suppressed gadolinium-enhanced T1-weighted sequence and a fat-suppressed T2-weighted sequence were obtained. Comparison of the extent and conspicuity of signal intensity changes was made for both bone and soft tissue in each plane. Results. In bone, inflammatory change was equal in extent and conspicuity on fat-suppressed T2WI and fat-suppressed T1WI with gadolinium in 19 planes, more extensive or conspicuous on T2WI in three planes, and less so on T2WI in two planes. Marrow was normal on all three sequences in 10 cases. In soft tissue, inflammatory change was seen equally well in 20 instances, more extensively or conspicuously on the T2WI in 11 instances, and less so on T2WI in 2 instances. One case had no soft tissue involvement on any of the sequences. Five abscesses and three joint effusions were present, all more conspicuously delineated from surrounding inflammatory change on the fat-saturated T1WI with gadolinium. The average imaging time for the fat-saturated T1WI with gadolinium was 6.75 min, while that of the T2-weighted sequences was 5.75 min. Conclusion. Routine use of gadolinium is not warranted. Instead, gadolinium should be reserved for clinically suspected infection in or around a joint, and in cases refractory to medical or surgical treatment due to possible abscess formation. (orig.)

  5. Multilocus Sequence Typing

    OpenAIRE

    Belén, Ana; Pavón, Ibarz; Maiden, Martin C.J.

    2009-01-01

    Multilocus sequence typing (MLST) was first proposed in 1998 as a typing approach that enables the unambiguous characterization of bacterial isolates in a standardized, reproducible, and portable manner using the human pathogen Neisseria meningitidis as the exemplar organism. Since then, the approach has been applied to a large and growing number of organisms by public health laboratories and research institutions. MLST data, shared by investigators over the world via the Internet, have been ...

  6. Achalasia Carcinoma Sequence

    OpenAIRE

    Makmun, Dadang

    2001-01-01

    We report a case of carcinoma of the esophagus in a 58 years old woman with achalasia, who has been diagnosed since 30 years ago, which initiated by surgical treatment (myotomy) and the symptoms recurred since 3 years ago. According to the progress of the disease, Malignancy was strongly suspected due to prolonged stasis and mucosal irritation caused by achalasia (achalasia carcinoma sequence). Because of these contributing factors for the development of serious complications such as Malignan...

  7. 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.

  8. Sequencing BPS spectra

    International Nuclear Information System (INIS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-01-01

    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.

  9. 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 ...

  10. Behavioral estimates of human frequency selectivity at low frequencies

    DEFF Research Database (Denmark)

    Orellana, Carlos Andrés Jurado

    A fundamental property of our hearing organ is its ability to break down sound into different spectral components, allowing us to make use of the richness in natural sound phenomena. Auditory filters, which conceptualize this property of the ear, however, have not been appropriately described at ...

  11. Broadband Reflectionless Metasheets: Frequency-Selective Transmission and Perfect Absorption

    Directory of Open Access Journals (Sweden)

    V. S. Asadchy

    2015-07-01

    Full Text Available Energy of propagating electromagnetic waves can be fully absorbed in a thin lossy layer, but only in a narrow frequency band, as follows from the causality principle. On the other hand, it appears that there are no fundamental limitations on broadband matching of thin resonant absorbing layers. However, known thin absorbers produce significant reflections outside of the resonant absorption band. In this paper, we explore possibilities to realize a thin absorbing layer that produces no reflected waves in a very wide frequency range, while the transmission coefficient has a narrow peak of full absorption. Here we show, both theoretically and experimentally, that a thin resonant absorber, invisible in reflection in a very wide frequency range, can be realized if one and the same resonant mode of the absorbing array unit cells is utilized to create both electric and magnetic responses. We test this concept using chiral particles in each unit cell, arranged in a periodic planar racemic array, utilizing chirality coupling in each unit cell but compensating the field coupling at the macroscopic level. We prove that the concept and the proposed realization approach also can be used to create nonreflecting layers for full control of transmitted fields. Our results can have a broad range of potential applications over the entire electromagnetic spectrum including, for example, perfect ultracompact wave filters and selective multifrequency sensors.

  12. Patterns of food and nutrient intakes of Dutch adults according to intakes of total fat, saturated fatty acids, dietary fibre, and of fruit and vegetables

    NARCIS (Netherlands)

    Löwik, M.R.H.; Hulshof, K.F.A.M.; Brussaard, J.H.

    1999-01-01

    Dietary intake characteristics were studied among 3833 adults of the second Dutch National Food Consumption Survey held in 1992. The subjects were classified into three groups based on their intake of total fat (% energy), saturated fatty acids (% energy), dietary fibre (g/MJ), and fruit and

  13. Foundations of Sequence-to-Sequence Modeling for Time Series

    OpenAIRE

    Kuznetsov, Vitaly; Mariet, Zelda

    2018-01-01

    The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

  14. 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 ...

  15. 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

  16. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    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

  17. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  18. 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.

  19. The advantages of SMRT sequencing

    OpenAIRE

    Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

    2013-01-01

    Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

  20. 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

  1. Region segmentation along image sequence

    International Nuclear Information System (INIS)

    Monchal, L.; Aubry, P.

    1995-01-01

    A method to extract regions in sequence of images is proposed. Regions are not matched from one image to the following one. The result of a region segmentation is used as an initialization to segment the following and image to track the region along the sequence. The image sequence is exploited as a spatio-temporal event. (authors). 12 refs., 8 figs

  2. Log-balanced combinatorial sequences

    Directory of Open Access Journals (Sweden)

    Tomislav Došlic

    2005-01-01

    Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.

  3. 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

  4. 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.

  5. Universal sequence map (USM of arbitrary discrete sequences

    Directory of Open Access Journals (Sweden)

    Almeida Jonas S

    2002-02-01

    Full Text Available Abstract Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM, is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR. The latter enables the representation of 4 unit type sequences (like DNA as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules.

  6. 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

  7. Genomic sequencing in clinical trials

    OpenAIRE

    Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

    2011-01-01

    Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

  8. 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.

  9. 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.

  10. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    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.

  11. 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.

  12. 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...

  13. 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

  14. SVX Sequencer Board

    International Nuclear Information System (INIS)

    Utes, M.

    1997-01-01

    The SVX Sequencer boards are 9U by 280mm circuit boards that reside in slots 2 through 21 of each of eight Eurocard crates in the D0 Detector Platform. The basic purpose is to control the SVX chips for data acquisition and when a trigger occurs, to gather the SVX data and relay the data to the VRB boards in the Movable Counting House. Functions and features are as follows: (1) Initialization of eight SVX chip strings using the MIL-STD-1553 data bus; (2) Real time manipulation of the SVX control lines to effect data acquisition, digitization, and readout based on the NRZ/Clock signals from the Controller; (3) Conversion of 8-bit electrical SVX readout data to an optical signal operating at 1.062 Gbit/sec, sent to the VRB. Eight HDIs will be serviced per board; (4) Built-in logic analyzer which can record the most important control and data lines during a data acquisition cycle and put this recorded information onto the 1553 bus; (5) Identification header and end of data trailer tacked onto data stream; (6) 1553 register which can read the current values of the control and data lines; (7) 1553 register which can test the optical link; (8) 1553 registers for crossing pulse width, calibration pulse voltage, and calibration pipeline select; (9) 1553 register for reading the optical drivers status link; (10) 1553 register for power control of SVX chips and ignoring bad SVX strings; (11) Front panel displays and LEDs show the board status at a glance; (12) In-system programmable EPLDs are programmed via 1553 or Altera's 'Bitblaster'; (13) Automatic readout abort after 45us; (14) Supplies BUSY signal back to Trigger Framework; (15) Supports a heartbeat system to prevent excessive SVX current draw; and (16) Supports a SVX power trip feature if heartbeat failure occurs.

  15. Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

    International Nuclear Information System (INIS)

    Rauzy, Antoine B.

    2011-01-01

    A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

  16. 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.

  17. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

    The original methods of RNA sequence analysis were based on enzymatic production and chromatographic separation of overlapping oligonucleotide fragments from within an RNA molecule followed by identification of the mononucleotides comprising the oligomer. Over the past decade the field of nucleic acid sequencing has changed dramatically, however, and RNA molecules now can be sequenced in a variety of more streamlined fashions. Most of the more recent advances in RNA sequencing have involved one-dimensional electrophoretic separation of 32 P-end-labeled oligoribonucleotides on polyacrylamide gels. In this chapter the author discusses two of these methods for determining the nucleotide sequences of RNA molecules rapidly: the chemical method and the enzymatic method. Both methods are direct and degradative, i.e., they rely on fragmatic and chemical approaches should be utilized. The single-strand-specific ribonucleases (A, T 1 , T 2 , and S 1 ) provide an efficient means to locate double-helical regions rapidly, and the chemical reactions provide a means to determine the RNA sequence within these regions. In addition, the chemical reactions allow one to assign interactions to specific atoms and to distinguish secondary interactions from tertiary ones. If the RNA molecule is small enough to be sequenced directly by the enzymatic or chemical method, the probing reactions can be done easily at the same time as sequencing reactions

  18. 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.

  19. Farey sequences and resistor networks

    Indian Academy of Sciences (India)

    Green's function, while the perturbation of a network is investigated in [3]. ... In Theorem 1 below, we employ the Farey sequence to establish a strict .... We next show that the Farey sequence method is applicable for circuits with n or fewer.

  20. 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

  1. 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

  2. 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.

  3. Commercial Art: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a commercial art 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…

  4. 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

  5. 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

  6. Accident sequence quantification with KIRAP

    Energy Technology Data Exchange (ETDEWEB)

    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.

  7. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S K

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  8. [Complete genome sequencing and sequence analysis of BCG Tice].

    Science.gov (United States)

    Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

    2012-10-04

    The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

  9. GROUPING WEB ACCESS SEQUENCES uSING SEQUENCE ALIGNMENT METHOD

    OpenAIRE

    BHUPENDRA S CHORDIA; KRISHNAKANT P ADHIYA

    2011-01-01

    In web usage mining grouping of web access sequences can be used to determine the behavior or intent of a set of users. Grouping websessions is how to measure the similarity between web sessions. There are many shortcomings in traditional measurement methods. The taskof grouping web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-groupsimilarity is done using sequence alignment method. This paper introduces a new method to group we...

  10. LPTAU, Quasi Random Sequence Generator

    International Nuclear Information System (INIS)

    Sobol, Ilya M.

    1993-01-01

    1 - Description of program or function: LPTAU generates quasi random sequences. These are uniformly distributed sets of L=M N points in the N-dimensional unit cube: I N =[0,1]x...x[0,1]. These sequences are used as nodes for multidimensional integration; as searching points in global optimization; as trial points in multi-criteria decision making; as quasi-random points for quasi Monte Carlo algorithms. 2 - Method of solution: Uses LP-TAU sequence generation (see references). 3 - Restrictions on the complexity of the problem: The number of points that can be generated is L 30 . The dimension of the space cannot exceed 51

  11. Weak disorder in Fibonacci sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Naim, E [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Krapivsky, P L [Department of Physics and Center for Molecular Cybernetics, Boston University, Boston, MA 02215 (United States)

    2006-05-19

    We study how weak disorder affects the growth of the Fibonacci series. We introduce a family of stochastic sequences that grow by the normal Fibonacci recursion with probability 1 - {epsilon}, but follow a different recursion rule with a small probability {epsilon}. We focus on the weak disorder limit and obtain the Lyapunov exponent that characterizes the typical growth of the sequence elements, using perturbation theory. The limiting distribution for the ratio of consecutive sequence elements is obtained as well. A number of variations to the basic Fibonacci recursion including shift, doubling and copying are considered. (letter to the editor)

  12. 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.

  13. 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

  14. Optimization of sequence alignment for simple sequence repeat regions

    Directory of Open Access Journals (Sweden)

    Ogbonnaya Francis C

    2011-07-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

  15. ADDRESS SEQUENCES FOR MULTI RUN RAM TESTING

    Directory of Open Access Journals (Sweden)

    V. N. Yarmolik

    2014-01-01

    Full Text Available A universal approach for generation of address sequences with specified properties is proposed and analyzed. A modified version of the Antonov and Saleev algorithm for Sobol sequences genera-tion is chosen as a mathematical description of the proposed method. Within the framework of the proposed universal approach, the Sobol sequences form a subset of the address sequences. Other sub-sets are also formed, which are Gray sequences, anti-Gray sequences, counter sequences and sequenc-es with specified properties.

  16. Fast and secure retrieval of DNA sequences

    NARCIS (Netherlands)

    2014-01-01

    Sequence models are retrieved from a sequences index. The sequence models model DNA or RNA sequences stored in a database, and each comprises a finite memory tree source model and parameters for the finite memory tree source model. One or more DNA or RNA sequences stored in the database are

  17. Decidability of uniform recurrence of morphic sequences

    OpenAIRE

    Durand , Fabien

    2012-01-01

    We prove that the uniform recurrence of morphic sequences is decidable. For this we show that the number of derived sequences of uniformly recurrent morphic sequences is bounded. As a corollary we obtain that uniformly recurrent morphic sequences are primitive substitutive sequences.

  18. 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.

  19. Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing.

    Science.gov (United States)

    Tan, M K

    1991-08-01

    A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup of the ancient supercontinent, Pangaea. These regions of the rRNA sequences have thus been conserved for at least 160 million years and are here compared with other eukaryotic, especially plant rRNAs.

  20. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    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.

  1. 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.

  2. 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.

  3. 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.

  4. Explaining the harmonic sequence paradox.

    Science.gov (United States)

    Schmidt, Ulrich; Zimper, Alexander

    2012-05-01

    According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced. ©2011 The British Psychological Society.

  5. 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

  6. Matrix transformations and sequence spaces

    International Nuclear Information System (INIS)

    Nanda, S.

    1983-06-01

    In most cases the most general linear operator from one sequence space into another is actually given by an infinite matrix and therefore the theory of matrix transformations has always been of great interest in the study of sequence spaces. The study of general theory of matrix transformations was motivated by the special results in summability theory. This paper is a review article which gives almost all known results on matrix transformations. This also suggests a number of open problems for further study and will be very useful for research workers. (author)

  7. Green's theorem and Gorenstein sequences

    OpenAIRE

    Ahn, Jeaman; Migliore, Juan C.; Shin, Yong-Su

    2016-01-01

    We study consequences, for a standard graded algebra, of extremal behavior in Green's Hyperplane Restriction Theorem. First, we extend his Theorem 4 from the case of a plane curve to the case of a hypersurface in a linear space. Second, assuming a certain Lefschetz condition, we give a connection to extremal behavior in Macaulay's theorem. We apply these results to show that $(1,19,17,19,1)$ is not a Gorenstein sequence, and as a result we classify the sequences of the form $(1,a,a-2,a,1)$ th...

  8. 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.

  9. 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

  10. 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)

  11. Degree sequence in message transfer

    Science.gov (United States)

    Yamuna, M.

    2017-11-01

    Message encryption is always an issue in current communication scenario. Methods are being devised using various domains. Graphs satisfy numerous unique properties which can be used for message transfer. In this paper, I propose a message encryption method based on degree sequence of graphs.

  12. Fractals in DNA sequence analysis

    Institute of Scientific and Technical Information of China (English)

    Yu Zu-Guo(喻祖国); Vo Anh; Gong Zhi-Min(龚志民); Long Shun-Chao(龙顺潮)

    2002-01-01

    Fractal methods have been successfully used to study many problems in physics, mathematics, engineering, finance,and even in biology. There has been an increasing interest in unravelling the mysteries of DNA; for example, how can we distinguish coding and noncoding sequences, and the problems of classification and evolution relationship of organisms are key problems in bioinformatics. Although much research has been carried out by taking into consideration the long-range correlations in DNA sequences, and the global fractal dimension has been used in these works by other people, the models and methods are somewhat rough and the results are not satisfactory. In recent years, our group has introduced a time series model (statistical point of view) and a visual representation (geometrical point of view)to DNA sequence analysis. We have also used fractal dimension, correlation dimension, the Hurst exponent and the dimension spectrum (multifractal analysis) to discuss problems in this field. In this paper, we introduce these fractal models and methods and the results of DNA sequence analysis.

  13. 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

  14. Is sequence awareness mandatory for perceptual sequence learning: An assessment using a pure perceptual sequence learning design.

    Science.gov (United States)

    Deroost, Natacha; Coomans, Daphné

    2018-02-01

    We examined the role of sequence awareness in a pure perceptual sequence learning design. Participants had to react to the target's colour that changed according to a perceptual sequence. By varying the mapping of the target's colour onto the response keys, motor responses changed randomly. The effect of sequence awareness on perceptual sequence learning was determined by manipulating the learning instructions (explicit versus implicit) and assessing the amount of sequence awareness after the experiment. In the explicit instruction condition (n = 15), participants were instructed to intentionally search for the colour sequence, whereas in the implicit instruction condition (n = 15), they were left uninformed about the sequenced nature of the task. Sequence awareness after the sequence learning task was tested by means of a questionnaire and the process-dissociation-procedure. The results showed that the instruction manipulation had no effect on the amount of perceptual sequence learning. Based on their report to have actively applied their sequence knowledge during the experiment, participants were subsequently regrouped in a sequence strategy group (n = 14, of which 4 participants from the implicit instruction condition and 10 participants from the explicit instruction condition) and a no-sequence strategy group (n = 16, of which 11 participants from the implicit instruction condition and 5 participants from the explicit instruction condition). Only participants of the sequence strategy group showed reliable perceptual sequence learning and sequence awareness. These results indicate that perceptual sequence learning depends upon the continuous employment of strategic cognitive control processes on sequence knowledge. Sequence awareness is suggested to be a necessary but not sufficient condition for perceptual learning to take place. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Teaching Task Sequencing via Verbal Mediation.

    Science.gov (United States)

    Rusch, Frank R.; And Others

    1987-01-01

    Verbal sequence training was used to teach a moderately mentally retarded woman to sequence job-related tasks. Learning to say the tasks in the proper sequence resulted in the employee performing her tasks in that sequence, and the employee was capable of mediating her own work behavior when scheduled changes occurred. (Author/JDD)

  16. 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 ...

  17. 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.

  18. Multi-qubit compensation sequences

    International Nuclear Information System (INIS)

    Tomita, Y; Merrill, J T; Brown, K R

    2010-01-01

    The Hamiltonian control of n qubits requires precision control of both the strength and timing of interactions. Compensation pulses relax the precision requirements by reducing unknown but systematic errors. Using composite pulse techniques designed for single qubits, we show that systematic errors for n-qubit systems can be corrected to arbitrary accuracy given either two non-commuting control Hamiltonians with identical systematic errors or one error-free control Hamiltonian. We also examine composite pulses in the context of quantum computers controlled by two-qubit interactions. For quantum computers based on the XY interaction, single-qubit composite pulse sequences naturally correct systematic errors. For quantum computers based on the Heisenberg or exchange interaction, the composite pulse sequences reduce the logical single-qubit gate errors but increase the errors for logical two-qubit gates.

  19. 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.

  20. Sequence complexity and work extraction

    International Nuclear Information System (INIS)

    Merhav, Neri

    2015-01-01

    We consider a simplified version of a solvable model by Mandal and Jarzynski, which constructively demonstrates the interplay between work extraction and the increase of the Shannon entropy of an information reservoir which is in contact with a physical system. We extend Mandal and Jarzynski’s main findings in several directions: first, we allow sequences of correlated bits rather than just independent bits. Secondly, at least for the case of binary information, we show that, in fact, the Shannon entropy is only one measure of complexity of the information that must increase in order for work to be extracted. The extracted work can also be upper bounded in terms of the increase in other quantities that measure complexity, like the predictability of future bits from past ones. Third, we provide an extension to the case of non-binary information (i.e. a larger alphabet), and finally, we extend the scope to the case where the incoming bits (before the interaction) form an individual sequence, rather than a random one. In this case, the entropy before the interaction can be replaced by the Lempel–Ziv (LZ) complexity of the incoming sequence, a fact that gives rise to an entropic meaning of the LZ complexity, not only in information theory, but also in physics. (paper)

  1. 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.

  2. Method and apparatus for biological sequence comparison

    Science.gov (United States)

    Marr, T.G.; Chang, W.I.

    1997-12-23

    A method and apparatus are disclosed for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. 5 figs.

  3. 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

  4. 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.

  5. Multineuronal Spike Sequences Repeat with Millisecond Precision

    Directory of Open Access Journals (Sweden)

    Koki eMatsumoto

    2013-06-01

    Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

  6. Static multiplicities in heterogeneous azeotropic distillation sequences

    DEFF Research Database (Denmark)

    Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay

    1998-01-01

    In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... different static behavior. The method of Petlyuk and Avet'yan (1971), Bekiaris et al. (1993), which assumes infinite reflux and infinite number of stages, is extended to and applied on heterogeneous azeotropic distillation sequences. The predictions are substantiated through simulations. The static sequence...

  7. Blind sequence-length estimation of low-SNR cyclostationary sequences

    CSIR Research Space (South Africa)

    Vlok, JD

    2014-06-01

    Full Text Available Several existing direct-sequence spread spectrum (DSSS) detection and estimation algorithms assume prior knowledge of the symbol period or sequence length, although very few sequence-length estimation techniques are available in the literature...

  8. Infinite matrices and sequence spaces

    CERN Document Server

    Cooke, Richard G

    2014-01-01

    This clear and correct summation of basic results from a specialized field focuses on the behavior of infinite matrices in general, rather than on properties of special matrices. Three introductory chapters guide students to the manipulation of infinite matrices, covering definitions and preliminary ideas, reciprocals of infinite matrices, and linear equations involving infinite matrices.From the fourth chapter onward, the author treats the application of infinite matrices to the summability of divergent sequences and series from various points of view. Topics include consistency, mutual consi

  9. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed; Mansour, Essam; Kalnis, Panos

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern

  10. Computational analysis of sequence selection mechanisms.

    Science.gov (United States)

    Meyerguz, Leonid; Grasso, Catherine; Kleinberg, Jon; Elber, Ron

    2004-04-01

    Mechanisms leading to gene variations are responsible for the diversity of species and are important components of the theory of evolution. One constraint on gene evolution is that of protein foldability; the three-dimensional shapes of proteins must be thermodynamically stable. We explore the impact of this constraint and calculate properties of foldable sequences using 3660 structures from the Protein Data Bank. We seek a selection function that receives sequences as input, and outputs survival probability based on sequence fitness to structure. We compute the number of sequences that match a particular protein structure with energy lower than the native sequence, the density of the number of sequences, the entropy, and the "selection" temperature. The mechanism of structure selection for sequences longer than 200 amino acids is approximately universal. For shorter sequences, it is not. We speculate on concrete evolutionary mechanisms that show this behavior.

  11. The recurrence sequences via Sylvester matrices

    Science.gov (United States)

    Karaduman, Erdal; Deveci, Ömür

    2017-07-01

    In this work, we define the Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by using the Slyvester matrices which are obtained from the characteristic polynomials of the Pell and Jacobsthal sequences and then, we study the sequences defined modulo m. Also, we obtain the cyclic groups and the semigroups from the generating matrices of these sequences when read modulo m and then, we derive the relationships among the orders of the cyclic groups and the periods of the sequences. Furthermore, we redefine Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by means of the elements of the groups and then, we examine them in the finite groups.

  12. ON SOME RECURRENCE TYPE SMARANDACHE SEQUENCES

    OpenAIRE

    MAJUMDAR, A.A.K.; GUNARTO, H.

    2000-01-01

    In this paper, we study some properties of ten recurrence type Smarandache sequences, namely, the Smarandache odd, even, prime product, square product, higher-power product, permutation, consecutive, reverse, symmetric, and pierced chain sequences.

  13. "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.

  14. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    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...... diseases in Europe. As part of the EURL proficiency test for fish diseases it is required to sequence any RANA virus isolates found in any of the samples. It is also highly recommended to sequence the ISA virus to determine whether it be HPRΔ or HPR0. Furthermore, it is recommended that any VHSV and IHNV...... isolates be genotyped. As part of the evaluation of the proficiency results it was decided this year to look into the quality and similarity of the sequence results for selected viruses. Ampoule III in the proficiency test 2013 contained an EHNV isolate. The EURL received 43 sequences from 41 laboratories...

  15. Perfect sequences over the real quaternions

    OpenAIRE

    Kuznetsov, Oleg

    2017-01-01

    In this Thesis, perfect sequences over the real quaternions are first considered. Definitions for the right and left periodic autocorrelation functions are given, and right and left perfect sequences introduced. It is shown that the right (left) perfection of any sequence implies the left (right) perfection, so concepts of right and left perfect sequences over the real quaternions are equivalent. Unitary transformations of the quaternion space ℍ are then considered. Using the equivalence of t...

  16. Information decomposition method to analyze symbolical sequences

    International Nuclear Information System (INIS)

    Korotkov, E.V.; Korotkova, M.A.; Kudryashov, N.A.

    2003-01-01

    The information decomposition (ID) method to analyze symbolical sequences is presented. This method allows us to reveal a latent periodicity of any symbolical sequence. The ID method is shown to have advantages in comparison with application of the Fourier transformation, the wavelet transform and the dynamic programming method to look for latent periodicity. Examples of the latent periods for poetic texts, DNA sequences and amino acids are presented. Possible origin of a latent periodicity for different symbolical sequences is discussed

  17. Optimizing functional MR urography: prime time for a 30-minutes-or-less fMRU

    Energy Technology Data Exchange (ETDEWEB)

    Delgado, Jorge; Bedoya, Maria A.; Adeb, Melkamu; Carson, Robert H.; Khrichenko, Dmitry [The Children' s Hospital of Philadelphia, Department of Radiology, Philadelphia, PA (United States); Johnson, Ann M.; Darge, Kassa [The Children' s Hospital of Philadelphia, Department of Radiology, Philadelphia, PA (United States); University of Pennsylvania, Department of Radiology, The Perelman School of Medicine, Philadelphia, PA (United States); Canning, Douglas A. [University of Pennsylvania, Division of Urology, Department of Surgery, The Children' s Hospital of Philadelphia, The Perelman School of Medicine, Philadelphia, PA (United States)

    2015-08-15

    Current protocols for functional MR urography (fMRU) require long scan times, limiting its widespread use. Our goal was to use pre-defined criteria to reduce the number of sequences and thus the examination time without compromising the morphological and functional results. The standard fMRU protocol in our department consists of eight sequences, including a 17-min dynamic post-contrast scan. Ninety-nine children and young adults (43 male, 56 female, mean age 7 years) were evaluated with this protocol. Each sequence was retrospectively analyzed for its utility and factors that affect its duration. Mean scan time to perform the eight sequences, without including the variable time between sequences, was 40.5 min. Five sequences were categorized as essential: (1) sagittal T2 for planning the oblique coronal plane, (2) axial T2 with fat saturation for the assessment of corticomedullary differentiation and parenchymal thickness, (3) coronal 3-D T2 with fat saturation for multiplanar and 3-D reconstructions, (4) pre-contrast coronal T1 with fat saturation to ensure an appropriate scan prior to injecting the contrast material and (5) the coronal post-contrast dynamic series. Functional information was obtained after 8 min of dynamic imaging in the majority of children. The coronal fat-saturated T2, coronal T1, and post-contrast sagittal fat-saturated T1 sequences did not provide additional information. Because of the effects of pelvicalyceal dilation and ureteropelvic angle on the renal transit time, prone position is recommended, at least in children with high-grade pelvicalyceal dilation. Comprehensive fMRU requires approximately 19 min for sequence acquisition. Allowing for time between sequences and motion correction, the total study time can be reduced to about 30 min. Four pre-contrast sequences and a shortened post-contrast dynamic scan, optimally with the child in prone position, are sufficient. (orig.)

  18. Parallel sequencing lives, or what makes large sequencing projects successful.

    Science.gov (United States)

    Quilez, Javier; Vidal, Enrique; Dily, François Le; Serra, François; Cuartero, Yasmina; Stadhouders, Ralph; Graf, Thomas; Marti-Renom, Marc A; Beato, Miguel; Filion, Guillaume

    2017-11-01

    T47D_rep2 and b1913e6c1_51720e9cf were 2 Hi-C samples. They were born and processed at the same time, yet their fates were very different. The life of b1913e6c1_51720e9cf was simple and fruitful, while that of T47D_rep2 was full of accidents and sorrow. At the heart of these differences lies the fact that b1913e6c1_51720e9cf was born under a lab culture of Documentation, Automation, Traceability, and Autonomy and compliance with the FAIR Principles. Their lives are a lesson for those who wish to embark on the journey of managing high-throughput sequencing data. © The Author 2017. Published by Oxford University Press.

  19. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole

    1999-01-01

    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...

  20. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.

    2008-01-01

    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment me...

  1. DNA sequence modeling based on context trees

    NARCIS (Netherlands)

    Kusters, C.J.; Ignatenko, T.; Roland, J.; Horlin, F.

    2015-01-01

    Genomic sequences contain instructions for protein and cell production. Therefore understanding and identification of biologically and functionally meaningful patterns in DNA sequences is of paramount importance. Modeling of DNA sequences in its turn can help to better understand and identify such

  2. Compact flow diagrams for state sequences

    NARCIS (Netherlands)

    Buchin, K.A.; Buchin, M.E.; Gudmundsson, J.; Horton, M.J.; Sijben, S.

    2016-01-01

    We introduce the concept of compactly representing a large number of state sequences, e.g., sequences of activities, as a flow diagram. We argue that the flow diagram representation gives an intuitive summary that allows the user to detect patterns among large sets of state sequences. Simplified,

  3. Blazar Sequence in Fermi Era Liang Chen

    Indian Academy of Sciences (India)

    Abstract. 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 and ...

  4. Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

    Science.gov (United States)

    Tedersoo, Leho; Abarenkov, Kessy; Nilsson, R Henrik; Schüssler, Arthur; Grelet, Gwen-Aëlle; Kohout, Petr; Oja, Jane; Bonito, Gregory M; Veldre, Vilmar; Jairus, Teele; Ryberg, Martin; Larsson, Karl-Henrik; Kõljalg, Urmas

    2011-01-01

    Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

  5. Permutation Entropy for Random Binary Sequences

    Directory of Open Access Journals (Sweden)

    Lingfeng Liu

    2015-12-01

    Full Text Available In this paper, we generalize the permutation entropy (PE measure to binary sequences, which is based on Shannon’s entropy, and theoretically analyze this measure for random binary sequences. We deduce the theoretical value of PE for random binary sequences, which can be used to measure the randomness of binary sequences. We also reveal the relationship between this PE measure with other randomness measures, such as Shannon’s entropy and Lempel–Ziv complexity. The results show that PE is consistent with these two measures. Furthermore, we use PE as one of the randomness measures to evaluate the randomness of chaotic binary sequences.

  6. 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.

  7. Data selector group sequencer interface

    International Nuclear Information System (INIS)

    Zizka, G.; Turko, B.

    1984-01-01

    A CAMAC-based module for high rate data selection and transfer to Tracor Northern TN-1700 multichannel analysis system is described. The module can select any group of 4096 consecutive addresses of events, in the range of 24 bits. This module solves the problem of connecting a number of time digitizing systems to the memory of a multichannel analyzer. Continuous processing rate up to 200,000 events per second along with the live display make the testing of the above systems very efficient and relatively inexpensive. The module also can be programmed for storing the preset group of addresses into more than one section of the memory. The events are analyzed in each section of the memory during the preset time. Multiple spectra can thus be taken automatically in a sequence

  8. A main sequence for quasars

    Science.gov (United States)

    Marziani, Paola; Dultzin, Deborah; Sulentic, Jack W.; Del Olmo, Ascensión; Negrete, C. A.; Martínez-Aldama, Mary L.; D'Onofrio, Mauro; Bon, Edi; Bon, Natasa; Stirpe, Giovanna M.

    2018-03-01

    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.

  9. 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

  10. 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.

  11. RANDNA: a random DNA sequence generator.

    Science.gov (United States)

    Piva, Francesco; Principato, Giovanni

    2006-01-01

    Monte Carlo simulations are useful to verify the significance of data. Genomic regularities, such as the nucleotide correlations or the not uniform distribution of the motifs throughout genomic or mature mRNA sequences, exist and their significance can be checked by means of the Monte Carlo test. The test needs good quality random sequences in order to work, moreover they should have the same nucleotide distribution as the sequences in which the regularities have been found. Random DNA sequences are also useful to estimate the background score of an alignment, that is a threshold below which the resulting score is merely due to chance. We have developed RANDNA, a free software which allows to produce random DNA or RNA sequences setting both their length and the percentage of nucleotide composition. Sequences having the same nucleotide distribution of exonic, intronic or intergenic sequences can be generated. Its graphic interface makes it possible to easily set the parameters that characterize the sequences being produced and saved in a text format file. The pseudo-random number generator function of Borland Delphi 6 is used, since it guarantees a good randomness, a long cycle length and a high speed. We have checked the quality of sequences generated by the software, by means of well-known tests, both by themselves and versus genuine random sequences. We show the good quality of the generated sequences. The software, complete with examples and documentation, is freely available to users from: http://www.introni.it/en/software.

  12. Locomotor sequence learning in visually guided walking

    DEFF Research Database (Denmark)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-01-01

    walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 years, N = 20) could learn a specific sequence...... of step lengths over 300 training steps. Younger children (age 6-10 years, N = 8) have lower baseline performance, but their magnitude and rate of sequence learning was the same compared to older children (11-16 years, N = 10) and healthy adults. In addition, learning capacity may be more limited...... to modify step length from one trial to the next. Our sequence learning paradigm is derived from the serial reaction-time (SRT) task that has been used in upper limb studies. Both random and ordered sequences of step lengths were used to measure sequence-specific and sequence non-specific learning during...

  13. The RNA world, automatic sequences and oncogenetics

    Energy Technology Data Exchange (ETDEWEB)

    Tahir Shah, K

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. (1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. (2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or ``accept`` other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs.

  14. The RNA world, automatic sequences and oncogenetics

    International Nuclear Information System (INIS)

    Tahir Shah, K.

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. 1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. 2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or 'accept' other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs

  15. Targeted assembly of short sequence reads.

    Directory of Open Access Journals (Sweden)

    René L Warren

    Full Text Available As next-generation sequence (NGS production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled stringently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming genomic mutations, polymorphisms, fusions and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly.

  16. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    DeRonne, Kevin W; Karypis, George

    2013-01-01

    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  17. Hierarchically nested river landform sequences

    Science.gov (United States)

    Pasternack, G. B.; Weber, M. D.; Brown, R. A.; Baig, D.

    2017-12-01

    River corridors exhibit landforms nested within landforms repeatedly down spatial scales. In this study we developed, tested, and implemented a new way to create river classifications by mapping domains of fluvial processes with respect to the hierarchical organization of topographic complexity that drives fluvial dynamism. We tested this approach on flow convergence routing, a morphodynamic mechanism with different states depending on the structure of nondimensional topographic variability. Five nondimensional landform types with unique functionality (nozzle, wide bar, normal channel, constricted pool, and oversized) represent this process at any flow. When this typology is nested at base flow, bankfull, and floodprone scales it creates a system with up to 125 functional types. This shows how a single mechanism produces complex dynamism via nesting. Given the classification, we answered nine specific scientific questions to investigate the abundance, sequencing, and hierarchical nesting of these new landform types using a 35-km gravel/cobble river segment of the Yuba River in California. The nested structure of flow convergence routing landforms found in this study revealed that bankfull landforms are nested within specific floodprone valley landform types, and these types control bankfull morphodynamics during moderate to large floods. As a result, this study calls into question the prevailing theory that the bankfull channel of a gravel/cobble river is controlled by in-channel, bankfull, and/or small flood flows. Such flows are too small to initiate widespread sediment transport in a gravel/cobble river with topographic complexity.

  18. Sequencing intractable DNA to close microbial genomes.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

    Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  19. Sequencing Intractable DNA to Close Microbial Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL; Podar, Mircea [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

    2012-01-01

    Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  20. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    Science.gov (United States)

    de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

  1. cis sequence effects on gene expression

    Directory of Open Access Journals (Sweden)

    Jacobs Kevin

    2007-08-01

    Full Text Available Abstract Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.

  2. Multiple tag labeling method for DNA sequencing

    Science.gov (United States)

    Mathies, R.A.; Huang, X.C.; Quesada, M.A.

    1995-07-25

    A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

  3. Exome sequencing and genetic testing for MODY.

    Directory of Open Access Journals (Sweden)

    Stefan Johansson

    Full Text Available Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard Sanger sequencing-based diagnostics is inconclusive.The aim of the study was to examine the performance of exome sequencing for a molecular diagnosis of MODY in patients who have undergone conventional diagnostic sequencing of candidate genes with negative results.We performed exome enrichment followed by high-throughput sequencing in nine patients with suspected MODY. They were Sanger sequencing-negative for mutations in the HNF1A, HNF4A, GCK, HNF1B and INS genes. We excluded common, non-coding and synonymous gene variants, and performed in-depth analysis on filtered sequence variants in a pre-defined set of 111 genes implicated in glucose metabolism.On average, we obtained 45 X median coverage of the entire targeted exome and found 199 rare coding variants per individual. We identified 0-4 rare non-synonymous and nonsense variants per individual in our a priori list of 111 candidate genes. Three of the variants were considered pathogenic (in ABCC8, HNF4A and PPARG, respectively, thus exome sequencing led to a genetic diagnosis in at least three of the nine patients. Approximately 91% of known heterozygous SNPs in the target exomes were detected, but we also found low coverage in some key diabetes genes using our current exome sequencing approach. Novel variants in the genes ARAP1, GLIS3, MADD, NOTCH2 and WFS1 need further investigation to reveal their possible role in diabetes.Our results demonstrate that exome sequencing can improve molecular diagnostics of MODY when used as a complement to Sanger sequencing. However, improvements will be needed, especially concerning coverage, before the full potential of exome sequencing can be realized.

  4. Identifying driver mutations in sequenced cancer genomes

    DEFF Research Database (Denmark)

    Raphael, Benjamin J; Dobson, Jason R; Oesper, Layla

    2014-01-01

    High-throughput DNA sequencing is revolutionizing the study of cancer and enabling the measurement of the somatic mutations that drive cancer development. However, the resulting sequencing datasets are large and complex, obscuring the clinically important mutations in a background of errors, nois...... patterns of mutual exclusivity. These techniques, coupled with advances in high-throughput DNA sequencing, are enabling precision medicine approaches to the diagnosis and treatment of cancer....

  5. EGNAS: an exhaustive DNA sequence design algorithm

    Directory of Open Access Journals (Sweden)

    Kick Alfred

    2012-06-01

    Full Text Available Abstract Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

  6. Genome Sequencing and Analysis Conference IV

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-31

    J. Craig Venter and C. Thomas Caskey co-chaired Genome Sequencing and Analysis Conference IV held at Hilton Head, South Carolina from September 26--30, 1992. Venter opened the conference by noting that approximately 400 researchers from 16 nations were present four times as many participants as at Genome Sequencing Conference I in 1989. Venter also introduced the Data Fair, a new component of the conference allowing exchange and on-site computer analysis of unpublished sequence data.

  7. FRESCO: Referential compression of highly similar sequences.

    Science.gov (United States)

    Wandelt, Sebastian; Leser, Ulf

    2013-01-01

    In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware.

  8. Robustness analysis of chiller sequencing control

    International Nuclear Information System (INIS)

    Liao, Yundan; Sun, Yongjun; Huang, Gongsheng

    2015-01-01

    Highlights: • Uncertainties with chiller sequencing control were systematically quantified. • Robustness of chiller sequencing control was systematically analyzed. • Different sequencing control strategies were sensitive to different uncertainties. • A numerical method was developed for easy selection of chiller sequencing control. - Abstract: Multiple-chiller plant is commonly employed in the heating, ventilating and air-conditioning system to increase operational feasibility and energy-efficiency under part load condition. In a multiple-chiller plant, chiller sequencing control plays a key role in achieving overall energy efficiency while not sacrifices the cooling sufficiency for indoor thermal comfort. Various sequencing control strategies have been developed and implemented in practice. Based on the observation that (i) uncertainty, which cannot be avoided in chiller sequencing control, has a significant impact on the control performance and may cause the control fail to achieve the expected control and/or energy performance; and (ii) in current literature few studies have systematically addressed this issue, this paper therefore presents a study on robustness analysis of chiller sequencing control in order to understand the robustness of various chiller sequencing control strategies under different types of uncertainty. Based on the robustness analysis, a simple and applicable method is developed to select the most robust control strategy for a given chiller plant in the presence of uncertainties, which will be verified using case studies

  9. Multiplexed microsatellite recovery using massively parallel sequencing

    Science.gov (United States)

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  10. Digital Recovery Sequencer - Advanced Concept Ejection Seats

    National Research Council Canada - National Science Library

    Ross, David A; Cotter, Lee; Culhane, David; Press, Matthew J

    2005-01-01

    .... Continued usage of the Analog Sequencer is undesirable due to limitations with respect to its installed life, electronic component obsolescence, flexibility to accommodate seat safety improvements...

  11. Quantitative phenotyping via deep barcode sequencing.

    Science.gov (United States)

    Smith, Andrew M; Heisler, Lawrence E; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J; Chee, Mark; Roth, Frederick P; Giaever, Guri; Nislow, Corey

    2009-10-01

    Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.

  12. Hardware Accelerated Sequence Alignment with Traceback

    Directory of Open Access Journals (Sweden)

    Scott Lloyd

    2009-01-01

    in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

  13. Multipliers on Generalized Mixed Norm Sequence Spaces

    Directory of Open Access Journals (Sweden)

    Oscar Blasco

    2014-01-01

    Full Text Available Given 1≤p,q≤∞ and sequences of integers (nkk and (nk′k such that nk≤nk′≤nk+1, the generalized mixed norm space ℓℐ(p,q is defined as those sequences (ajj such that ((∑j∈Ik‍|aj|p1/pk∈ℓq where Ik={j∈ℕ0 s.t. nk≤jsequence λ=(λjj to belong to the space of multipliers (ℓℐ(r,s,ℓ(u,v, for different sequences ℐ and of intervals in ℕ0, are determined.

  14. Recursive sequences in first-year calculus

    Science.gov (United States)

    Krainer, Thomas

    2016-02-01

    This article provides ready-to-use supplementary material on recursive sequences for a second-semester calculus class. It equips first-year calculus students with a basic methodical procedure based on which they can conduct a rigorous convergence or divergence analysis of many simple recursive sequences on their own without the need to invoke inductive arguments as is typically required in calculus textbooks. The sequences that are accessible to this kind of analysis are predominantly (eventually) monotonic, but also certain recursive sequences that alternate around their limit point as they converge can be considered.

  15. A measurement of disorder in binary sequences

    Science.gov (United States)

    Gong, Longyan; Wang, Haihong; Cheng, Weiwen; Zhao, Shengmei

    2015-03-01

    We propose a complex quantity, AL, to characterize the degree of disorder of L-length binary symbolic sequences. As examples, we respectively apply it to typical random and deterministic sequences. One kind of random sequences is generated from a periodic binary sequence and the other is generated from the logistic map. The deterministic sequences are the Fibonacci and Thue-Morse sequences. In these analyzed sequences, we find that the modulus of AL, denoted by |AL | , is a (statistically) equivalent quantity to the Boltzmann entropy, the metric entropy, the conditional block entropy and/or other quantities, so it is a useful quantitative measure of disorder. It can be as a fruitful index to discern which sequence is more disordered. Moreover, there is one and only one value of |AL | for the overall disorder characteristics. It needs extremely low computational costs. It can be easily experimentally realized. From all these mentioned, we believe that the proposed measure of disorder is a valuable complement to existing ones in symbolic sequences.

  16. Polynomial sequences generated by infinite Hessenberg matrices

    Directory of Open Access Journals (Sweden)

    Verde-Star Luis

    2017-01-01

    Full Text Available We show that an infinite lower Hessenberg matrix generates polynomial sequences that correspond to the rows of infinite lower triangular invertible matrices. Orthogonal polynomial sequences are obtained when the Hessenberg matrix is tridiagonal. We study properties of the polynomial sequences and their corresponding matrices which are related to recurrence relations, companion matrices, matrix similarity, construction algorithms, and generating functions. When the Hessenberg matrix is also Toeplitz the polynomial sequences turn out to be of interpolatory type and we obtain additional results. For example, we show that every nonderogative finite square matrix is similar to a unique Toeplitz-Hessenberg matrix.

  17. Genomic sequencing of Pleistocene cave bears

    Energy Technology Data Exchange (ETDEWEB)

    Noonan, James P.; Hofreiter, Michael; Smith, Doug; Priest, JamesR.; Rohland, Nadin; Rabeder, Gernot; Krause, Johannes; Detter, J. Chris; Paabo, Svante; Rubin, Edward M.

    2005-04-01

    Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

  18. Design of Long Period Pseudo-Random Sequences from the Addition of -Sequences over

    Directory of Open Access Journals (Sweden)

    Ren Jian

    2004-01-01

    Full Text Available Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of -sequences with pairwise-prime linear spans (AMPLS. Using -sequences as building blocks, the proposed method proved to be an efficient and flexible approach to construct long period pseudo-random sequences with desirable properties from short period sequences. Applying the proposed method to , a signal set is constructed.

  19. Compressing DNA sequence databases with coil

    Directory of Open Access Journals (Sweden)

    Hendy Michael D

    2008-05-01

    Full Text Available Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

  20. Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

    Directory of Open Access Journals (Sweden)

    Marta Brozynska

    Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

  1. Step out - Step in Sequencing Games

    NARCIS (Netherlands)

    Musegaas, M.; Borm, P.E.M.; Quant, M.

    2014-01-01

    In this paper a new class of relaxed sequencing games is introduced: the class of Step out - Step in sequencing games. In this relaxation any player within a coalition is allowed to step out from his position in the processing order and to step in at any position later in the processing order.

  2. Step out-step in sequencing games

    NARCIS (Netherlands)

    Musegaas, Marieke; Borm, Peter; Quant, Marieke

    2015-01-01

    In this paper a new class of relaxed sequencing games is introduced: the class of Step out–Step in sequencing games. In this relaxation any player within a coalition is allowed to step out from his position in the processing order and to step in at any position later in the processing order. First,

  3. Enhanced throughput for infrared automated DNA sequencing

    Science.gov (United States)

    Middendorf, Lyle R.; Gartside, Bill O.; Humphrey, Pat G.; Roemer, Stephen C.; Sorensen, David R.; Steffens, David L.; Sutter, Scott L.

    1995-04-01

    Several enhancements have been developed and applied to infrared automated DNA sequencing resulting in significantly higher throughput. A 41 cm sequencing gel (31 cm well- to-read distance) combines high resolution of DNA sequencing fragments with optimized run times yielding two runs per day of 500 bases per sample. A 66 cm sequencing gel (56 cm well-to-read distance) produces sequence read lengths of up to 1000 bases for ds and ss templates using either T7 polymerase or cycle-sequencing protocols. Using a multichannel syringe to load 64 lanes allows 16 samples (compatible with 96-well format) to be visualized for each run. The 41 cm gel configuration allows 16,000 bases per day (16 samples X 500 bases/sample X 2 ten hour runs/day) to be sequenced with the advantages of infrared technology. Enhancements to internal labeling techniques using an infrared-labeled dATP molecule (Boehringer Mannheim GmbH, Penzberg, Germany; Sequenase (U.S. Biochemical) have also been made. The inclusion of glycerol in the sequencing reactions yields greatly improved results for some primer and template combinations. The inclusion of (alpha) -Thio-dNTP's in the labeling reaction increases signal intensity two- to three-fold.

  4. Thread extraction for polyadic instruction sequences

    NARCIS (Netherlands)

    Bergstra, J.; Middelburg, C.

    2011-01-01

    In this paper, we study the phenomenon that instruction sequences are split into fragments which somehow produce a joint behaviour. In order to bring this phenomenon better into the picture, we formalize a simple mechanism by which several instruction sequence fragments can produce a joint

  5. Genome sequence of Lactobacillus rhamnosus ATCC 8530.

    Science.gov (United States)

    Pittet, Vanessa; Ewen, Emily; Bushell, Barry R; Ziola, Barry

    2012-02-01

    Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences.

  6. Genome Sequence of Lactobacillus rhamnosus ATCC 8530

    OpenAIRE

    Pittet, Vanessa; Ewen, Emily; Bushell, Barry R.; Ziola, Barry

    2012-01-01

    Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences.

  7. Question-answer sequences in survey interviews

    NARCIS (Netherlands)

    Dijkstra, W.; Ongena, Y.P.

    2006-01-01

    Interaction analysis was used to analyze a total of 14,265 question-answer sequences of (Q-A Sequences) 80 questions that originated from two face-to-face and three telephone surveys. The analysis was directed towards the causes and effects of particular interactional problems. Our results showed

  8. Trace maps for arbitrary substitution sequences

    International Nuclear Information System (INIS)

    Avishai, Y.

    1993-01-01

    The discovery of quasi-crystals and their 1-dimensional modeling have led to a deep mathematical study of Schroedinger operators with an arbitrary deterministic potential sequence. In this work we address this problem and find trace maps for an arbitrary substitution sequence. our trace maps have lower dimensionality than those of Kolar and Nori, which make them quite attractive for actual applications. (authors)

  9. Stochastic modelling of daily rainfall sequences

    NARCIS (Netherlands)

    Buishand, T.A.

    1977-01-01

    Rainfall series of different climatic regions were analysed with the aim of generating daily rainfall sequences. A survey of the data is given in I, 1. When analysing daily rainfall sequences one must be aware of the following points:
    a. Seasonality. Because of seasonal variation

  10. Learning of Sensory Sequences in Cerebellar Patients

    Science.gov (United States)

    Frings, Markus; Boenisch, Raoul; Gerwig, Marcus; Diener, Hans-Christoph; Timmann, Dagmar

    2004-01-01

    A possible role of the cerebellum in detecting and recognizing event sequences has been proposed. The present study sought to determine whether patients with cerebellar lesions are impaired in the acquisition and discrimination of sequences of sensory stimuli of different modalities. A group of 26 cerebellar patients and 26 controls matched for…

  11. On peculiar Šindel sequences

    Czech Academy of Sciences Publication Activity Database

    Křížek, Michal; Somer, L.

    2010-01-01

    Roč. 17, č. 2 (2010), s. 129-140 ISSN 0972-5555 R&D Projects: GA AV ČR(CZ) IAA100190803 Institutional research plan: CEZ:AV0Z10190503 Keywords : quadratic residue * Chinese remainder theorem * primitive Šindel sequences * Prague clock sequence Subject RIV: BA - General Mathematics http://www.pphmj.com/abstract/5095.htm

  12. Protecting genomic sequence anonymity with generalization lattices.

    Science.gov (United States)

    Malin, B A

    2005-01-01

    Current genomic privacy technologies assume the identity of genomic sequence data is protected if personal information, such as demographics, are obscured, removed, or encrypted. While demographic features can directly compromise an individual's identity, recent research demonstrates such protections are insufficient because sequence data itself is susceptible to re-identification. To counteract this problem, we introduce an algorithm for anonymizing a collection of person-specific DNA sequences. The technique is termed DNA lattice anonymization (DNALA), and is based upon the formal privacy protection schema of k -anonymity. Under this model, it is impossible to observe or learn features that distinguish one genetic sequence from k-1 other entries in a collection. To maximize information retained in protected sequences, we incorporate a concept generalization lattice to learn the distance between two residues in a single nucleotide region. The lattice provides the most similar generalized concept for two residues (e.g. adenine and guanine are both purines). The method is tested and evaluated with several publicly available human population datasets ranging in size from 30 to 400 sequences. Our findings imply the anonymization schema is feasible for the protection of sequences privacy. The DNALA method is the first computational disclosure control technique for general DNA sequences. Given the computational nature of the method, guarantees of anonymity can be formally proven. There is room for improvement and validation, though this research provides the groundwork from which future researchers can construct genomics anonymization schemas tailored to specific datasharing scenarios.

  13. Occupational Sequences: Auto Engines 1. AT 121.

    Science.gov (United States)

    Korb, A. W.; And Others

    In an attempt to individualize an automotive course, the Vocational-Technical Division of Northern Montana College has developed Occupational Sequences for an engine rebuilding course. Occupational Sequences, a learning or teaching aid, is an analysis of numbered operations involved in engine rebuilding. Job sheets, included in the book, provide a…

  14. Sequencing Events: Exploring Art and Art Jobs.

    Science.gov (United States)

    Stephens, Pamela Geiger; Shaddix, Robin K.

    2000-01-01

    Presents an activity for upper-elementary students that correlates the actions of archaeologists, patrons, and artists with the sequencing of events in a logical order. Features ancient Egyptian art images. Discusses the preparation of materials, motivation, a pre-writing activity, and writing a story in sequence. (CMK)

  15. Wijsman Orlicz Asymptotically Ideal -Statistical Equivalent Sequences

    Directory of Open Access Journals (Sweden)

    Bipan Hazarika

    2013-01-01

    in Wijsman sense and present some definitions which are the natural combination of the definition of asymptotic equivalence, statistical equivalent, -statistical equivalent sequences in Wijsman sense. Finally, we introduce the notion of Cesaro Orlicz asymptotically -equivalent sequences in Wijsman sense and establish their relationship with other classes.

  16. Nitrogen chronology of massive main sequence stars

    NARCIS (Netherlands)

    Köhler, K.; Borzyszkowski, M.; Brott, I.; Langer, N.; de Koter, A.

    2012-01-01

    Context. Rotational mixing in massive main sequence stars is predicted to monotonically increase their surface nitrogen abundance with time. Aims. We use this effect to design a method for constraining the age and the inclination angle of massive main sequence stars, given their observed luminosity,

  17. Massively parallel sequencing of forensic STRs

    DEFF Research Database (Denmark)

    Parson, Walther; Ballard, David; Budowle, Bruce

    2016-01-01

    The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that...

  18. Novel algorithms for protein sequence analysis

    NARCIS (Netherlands)

    Ye, Kai

    2008-01-01

    Each protein is characterized by its unique sequential order of amino acids, the so-called protein sequence. Biology”s paradigm is that this order of amino acids determines the protein”s architecture and function. In this thesis, we introduce novel algorithms to analyze protein sequences. Chapter 1

  19. Cyprinus carpio Genome sequencing and assembly

    NARCIS (Netherlands)

    Kolder, I.C.R.M.; Plas-Duivesteijn, van der Suzanne J.; Tan, G.; Wiegertjes, G.; Forlenza, M.; Guler, A.T.; Travin, D.Y.; Nakao, M.; Moritomo, T.; Irnazarow, I.; Jansen, H.J.

    2013-01-01

    Sequencing of the common carp (Cyprinus carpio carpio Linnaeus, 1758) genome, with the objective of establishing carp as a model organism to supplement the closely related zebrafish (Danio rerio). The sequenced individual is a homozygous female (by gynogenesis) of R3 x R8 carp, the heterozygous

  20. Sequence Comparison: Close and Open problems

    NARCIS (Netherlands)

    Lenzini, Gabriele; Cerrai, P.; Freguglia, P.

    Comparing sequences is a very important activity both in computer science and in a many other areas as well. For example thank to text editors, everyone knows the particular instance of a sequence comparison problem knonw as ``string mathcing problem''. It consists in searching a given work

  1. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

    Archibald, Alan L.; Bolund, Lars; Churcher, Carol

    2010-01-01

    preferentially selected for sequencing. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement the data have been released into public sequence repositories (Genbank/EMBL, NCBI/Ensembl trace repositories) in a timely manner and in advance of publication. CONCLUSIONS...

  2. Swab-to-Sequence: Real-time Data Analysis Platform for the Biomolecule Sequencer

    Data.gov (United States)

    National Aeronautics and Space Administration — DNA was successfully sequenced on the ISS in 2016, but the DNA sequenced was prepared on the ground. With FY’16 IRAD funds, the same team developed a...

  3. From Sequence to Morphology - Long-Range Correlations in Complete Sequenced Genomes

    NARCIS (Netherlands)

    T.A. Knoch (Tobias)

    2004-01-01

    textabstractThe largely unresolved sequential organization, i.e. the relations within DNA sequences, and its connection to the three-dimensional organization of genomes was investigated by correlation analyses of completely sequenced chromosomes from Viroids, Archaea, Bacteria, Arabidopsis

  4. Nucleotide sequence preservation of human mitochondrial DNA

    International Nuclear Information System (INIS)

    Monnat, R.J. Jr.; Loeb, L.A.

    1985-01-01

    Recombinant DNA techniques have been used to quantitate the amount of nucleotide sequence divergence in the mitochondrial DNA population of individual normal humans. Mitochondrial DNA was isolated from the peripheral blood lymphocytes of five normal humans and cloned in M13 mp11; 49 kilobases of nucleotide sequence information was obtained from 248 independently isolated clones from the five normal donors. Both between- and within-individual differences were identified. Between-individual differences were identified in approximately = to 1/200 nucleotides. In contrast, only one within-individual difference was identified in 49 kilobases of nucleotide sequence information. This high degree of mitochondrial nucleotide sequence homogeneity in human somatic cells is in marked contrast to the rapid evolutionary divergence of human mitochondrial DNA and suggests the existence of mechanisms for the concerted preservation of mammalian mitochondrial DNA sequences in single organisms

  5. Snake Genome Sequencing: Results and Future Prospects.

    Science.gov (United States)

    Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

    2016-12-01

    Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  6. Sequencing Cyclic Peptides by Multistage Mass Spectrometry

    Science.gov (United States)

    Mohimani, Hosein; Yang, Yu-Liang; Liu, Wei-Ting; Hsieh, Pei-Wen; Dorrestein, Pieter C.; Pevzner, Pavel A.

    2012-01-01

    Some of the most effective antibiotics (e.g., Vancomycin and Daptomycin) are cyclic peptides produced by non-ribosomal biosynthetic pathways. While hundreds of biomedically important cyclic peptides have been sequenced, the computational techniques for sequencing cyclic peptides are still in their infancy. Previous methods for sequencing peptide antibiotics and other cyclic peptides are based on Nuclear Magnetic Resonance spectroscopy, and require large amount (miligrams) of purified materials that, for most compounds, are not possible to obtain. Recently, development of mass spectrometry based methods has provided some hope for accurate sequencing of cyclic peptides using picograms of materials. In this paper we develop a method for sequencing of cyclic peptides by multistage mass spectrometry, and show its advantages over single stage mass spectrometry. The method is tested on known and new cyclic peptides from Bacillus brevis, Dianthus superbus and Streptomyces griseus, as well as a new family of cyclic peptides produced by marine bacteria. PMID:21751357

  7. Snake Genome Sequencing: Results and Future Prospects

    Directory of Open Access Journals (Sweden)

    Harald M. I. Kerkkamp

    2016-12-01

    Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  8. Sequencing and comparing whole mitochondrial genomes ofanimals

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  9. Divide and conquer: enriching environmental sequencing data.

    Directory of Open Access Journals (Sweden)

    Anne Bergeron

    2007-09-01

    Full Text Available In environmental sequencing projects, a mix of DNA from a whole microbial community is fragmented and sequenced, with one of the possible goals being to reconstruct partial or complete genomes of members of the community. In communities with high diversity of species, a significant proportion of the sequences do not overlap any other fragment in the sample. This problem will arise not only in situations with a relatively even distribution of many species, but also when the community in a particular environment is routinely dominated by the same few species. In the former case, no genomes may be assembled at all, while in the latter case a few dominant species in an environment will always be sequenced at high coverage to the detriment of coverage of the greater number of sparse species.Here we show that, with the same global sequencing effort, separating the species into two or more sub-communities prior to sequencing can yield a much higher proportion of sequences that can be assembled. We first use the Lander-Waterman model to show that, if the expected percentage of singleton sequences is higher than 25%, then, under the uniform distribution hypothesis, splitting the community is always a wise choice. We then construct simulated microbial communities to show that the results hold for highly non-uniform distributions. We also show that, for the distributions considered in the experiments, it is possible to estimate quite accurately the relative diversity of the two sub-communities.Given the fact that several methods exist to split microbial communities based on physical properties such as size, density, surface biochemistry, or optical properties, we strongly suggest that groups involved in environmental sequencing, and expecting high diversity, consider splitting their communities in order to maximize the information content of their sequencing effort.

  10. Sequence Matters but How Exactly? A Method for Evaluating Activity Sequences from Data

    Science.gov (United States)

    Doroudi, Shayan; Holstein, Kenneth; Aleven, Vincent; Brunskill, Emma

    2016-01-01

    How should a wide variety of educational activities be sequenced to maximize student learning? Although some experimental studies have addressed this question, educational data mining methods may be able to evaluate a wider range of possibilities and better handle many simultaneous sequencing constraints. We introduce Sequencing Constraint…

  11. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    DEFF Research Database (Denmark)

    de Souza, S J; Camargo, A A; Briones, M R

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central ...

  12. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

    Science.gov (United States)

    Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

    2017-07-01

    PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

  13. A comparative evaluation of sequence classification programs

    Directory of Open Access Journals (Sweden)

    Bazinet Adam L

    2012-05-01

    Full Text Available Abstract Background A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics. Several different methods have been proposed for doing this effectively and efficiently, and many have been implemented in software. In addition to varying their basic algorithmic approach to classification, some methods screen sequence reads for ’barcoding genes’ like 16S rRNA, or various types of protein-coding genes. Due to the sheer number and complexity of methods, it can be difficult for a researcher to choose one that is well-suited for a particular analysis. Results We divided the very large number of programs that have been released in recent years for solving the sequence classification problem into three main categories based on the general algorithm they use to compare a query sequence against a database of sequences. We also evaluated the performance of the leading programs in each category on data sets whose taxonomic and functional composition is known. Conclusions We found significant variability in classification accuracy, precision, and resource consumption of sequence classification programs when used to analyze various metagenomics data sets. However, we observe some general trends and patterns that will be useful to researchers who use sequence classification programs.

  14. 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.

  15. 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.

  16. CATEGORIZATION OF EVENT SEQUENCES FOR LICENSE APPLICATION

    International Nuclear Information System (INIS)

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

    2005-01-01

    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

  17. 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.

  18. Comparison of two Next Generation sequencing platforms for full genome sequencing of Classical Swine Fever Virus

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Höper, Dirk

    2013-01-01

    to the consensus sequence. Additionally, we got an average sequence depth for the genome of 4000 for the Iontorrent PGM and 400 for the FLX platform making the mapping suitable for single nucleotide variant (SNV) detection. The analysis revealed a single non-silent SNV A10665G leading to the amino acid change D......Next Generation Sequencing (NGS) is becoming more adopted into viral research and will be the preferred technology in the years to come. We have recently sequenced several strains of Classical Swine Fever Virus (CSFV) by NGS on both Genome Sequencer FLX (GS FLX) and Iontorrent PGM platforms...

  19. Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

    Directory of Open Access Journals (Sweden)

    Jian eWu

    2012-11-01

    Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

  20. Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer.

    Science.gov (United States)

    Wang, Ji; Ke, Yue Hua; Zhang, Yong; Huang, Ke Qiang; Wang, Lei; Shen, Xin Xin; Dong, Xiao Ping; Xu, Wen Bo; Ma, Xue Jun

    2017-10-01

    Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  1. 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)

  2. Whole-genome sequencing of veterinary pathogens

    DEFF Research Database (Denmark)

    Ronco, Troels

    -electrophoresis and single-locus sequencing has been widely used to characterize such types of veterinary pathogens. However, DNA sequencing techniques have become fast and cost effective in recent years and whole-genome sequencing data provide a much higher discriminative power and reproducibility than any...... genetic background. This indicates that dairy cows can be natural carriers of S. aureus subtypes that in certain cases lead to CM. A group of isolates that mostly belonged to ST151 carried three pathogenicity islands that were primarily found in this group. The prevalence of resistance genes was generally...

  3. Spreadsheet macros for coloring sequence alignments.

    Science.gov (United States)

    Haygood, M G

    1993-12-01

    This article describes a set of Microsoft Excel macros designed to color amino acid and nucleotide sequence alignments for review and preparation of visual aids. The colored alignments can then be modified to emphasize features of interest. Procedures for importing and coloring sequences are described. The macro file adds a new menu to the menu bar containing sequence-related commands to enable users unfamiliar with Excel to use the macros more readily. The macros were designed for use with Macintosh computers but will also run with the DOS version of Excel.

  4. Tensor products of higher almost split sequences

    OpenAIRE

    Pasquali, Andrea

    2015-01-01

    We investigate how the higher almost split sequences over a tensor product of algebras are related to those over each factor. Herschend and Iyama gave a precise criterion for when the tensor product of an $n$-representation finite algebra and an $m$-representation finite algebra is $(n+m)$-representation finite. In this case we give a complete description of the higher almost split sequences over the tensor product by expressing every higher almost split sequence as the mapping cone of a suit...

  5. Arbitrarily accurate twin composite π -pulse sequences

    Science.gov (United States)

    Torosov, Boyan T.; Vitanov, Nikolay V.

    2018-04-01

    We present three classes of symmetric broadband composite pulse sequences. The composite phases are given by analytic formulas (rational fractions of π ) valid for any number of constituent pulses. The transition probability is expressed by simple analytic formulas and the order of pulse area error compensation grows linearly with the number of pulses. Therefore, any desired compensation order can be produced by an appropriate composite sequence; in this sense, they are arbitrarily accurate. These composite pulses perform equally well as or better than previously published ones. Moreover, the current sequences are more flexible as they allow total pulse areas of arbitrary integer multiples of π .

  6. Modeling of Prepregs during Automated Draping Sequences

    DEFF Research Database (Denmark)

    Krogh, Christian; Glud, Jens Ammitzbøll; Jakobsen, Johnny

    2017-01-01

    algorithm used to generate target points on the mold which are used as input to a draping sequence planner. The draping sequence planner prescribes the displacement history for each gripper in the drape tool and these displacements are then applied to each gripper in a transient model of the draping...... sequence. The model is based on a transient finite element analysis with the material’s constitutive behavior currently being approximated as linear elastic orthotropic. In-plane tensile and bias-extension tests as well as bending tests are conducted and used as input for the model. The virtual draping...

  7. Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Joern Toedling

    Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

  8. Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform

    Directory of Open Access Journals (Sweden)

    Shan Wei

    2018-05-01

    Full Text Available Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples’ genomic DNA in under three hours, including library preparation and sequencing. This novel method shows great promise as a clinical diagnostic test for applications requiring rapid short-read DNA sequencing.

  9. Probabilistic Motor Sequence Yields Greater Offline and Less Online Learning than Fixed Sequence.

    Science.gov (United States)

    Du, Yue; Prashad, Shikha; Schoenbrun, Ilana; Clark, Jane E

    2016-01-01

    It is well acknowledged that motor sequences can be learned quickly through online learning. Subsequently, the initial acquisition of a motor sequence is boosted or consolidated by offline learning. However, little is known whether offline learning can drive the fast learning of motor sequences (i.e., initial sequence learning in the first training session). To examine offline learning in the fast learning stage, we asked four groups of young adults to perform the serial reaction time (SRT) task with either a fixed or probabilistic sequence and with or without preliminary knowledge (PK) of the presence of a sequence. The sequence and PK were manipulated to emphasize either procedural (probabilistic sequence; no preliminary knowledge (NPK)) or declarative (fixed sequence; with PK) memory that were found to either facilitate or inhibit offline learning. In the SRT task, there were six learning blocks with a 2 min break between each consecutive block. Throughout the session, stimuli followed the same fixed or probabilistic pattern except in Block 5, in which stimuli appeared in a random order. We found that PK facilitated the learning of a fixed sequence, but not a probabilistic sequence. In addition to overall learning measured by the mean reaction time (RT), we examined the progressive changes in RT within and between blocks (i.e., online and offline learning, respectively). It was found that the two groups who performed the fixed sequence, regardless of PK, showed greater online learning than the other two groups who performed the probabilistic sequence. The groups who performed the probabilistic sequence, regardless of PK, did not display online learning, as indicated by a decline in performance within the learning blocks. However, they did demonstrate remarkably greater offline improvement in RT, which suggests that they are learning the probabilistic sequence offline. These results suggest that in the SRT task, the fast acquisition of a motor sequence is driven

  10. Optimization of a sequence of reactors

    DEFF Research Database (Denmark)

    Vidal, Rene Victor Valqui

    1991-01-01

    Concerns the optimal production of sulphuric acid in a sequence of reactors. Using a suitable approximation to the objective function, this problem can easily be solved using the maximum principle. A numerical example documents the applicability of the suggested approach...

  11. Fluency First: Reversing the Traditional ESL Sequence.

    Science.gov (United States)

    MacGowan-Gilhooly, Adele

    1991-01-01

    Describes an ESL department's whole language approach to writing and reading, replacing its traditional grammar-based ESL instructional sequence. Reports the positive quantitative and qualitative results of the first three years of using the new approach. (KEH)

  12. Expressed sequence tags (ESTs) and single nucleotide ...

    African Journals Online (AJOL)

    SERVER

    2008-02-19

    Feb 19, 2008 ... the discovery of the DNA, a new area of modern plant biotechnology begun. In plant ... Marker Assisted Breeding and Sequence Tagged Sites. (STS) are all in use in modern ...... and behaviour in the honey bee. Genome Res.

  13. DNA Replication Profiling Using Deep Sequencing.

    Science.gov (United States)

    Saayman, Xanita; Ramos-Pérez, Cristina; Brown, Grant W

    2018-01-01

    Profiling of DNA replication during progression through S phase allows a quantitative snap-shot of replication origin usage and DNA replication fork progression. We present a method for using deep sequencing data to profile DNA replication in S. cerevisiae.

  14. Supervised Sequence Labelling with Recurrent Neural Networks

    CERN Document Server

    Graves, Alex

    2012-01-01

    Supervised sequence labelling is a vital area of machine learning, encompassing tasks such as speech, handwriting and gesture recognition, protein secondary structure prediction and part-of-speech tagging. Recurrent neural networks are powerful sequence learning tools—robust to input noise and distortion, able to exploit long-range contextual information—that would seem ideally suited to such problems. However their role in large-scale sequence labelling systems has so far been auxiliary.    The goal of this book is a complete framework for classifying and transcribing sequential data with recurrent neural networks only. Three main innovations are introduced in order to realise this goal. Firstly, the connectionist temporal classification output layer allows the framework to be trained with unsegmented target sequences, such as phoneme-level speech transcriptions; this is in contrast to previous connectionist approaches, which were dependent on error-prone prior segmentation. Secondly, multidimensional...

  15. The International Nucleotide Sequence Database Collaboration.

    Science.gov (United States)

    Cochrane, Guy; Karsch-Mizrachi, Ilene; Nakamura, Yasukazu

    2011-01-01

    Under the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org), globally comprehensive public domain nucleotide sequence is captured, preserved and presented. The partners of this long-standing collaboration work closely together to provide data formats and conventions that enable consistent data submission to their databases and support regular data exchange around the globe. Clearly defined policy and governance in relation to free access to data and relationships with journal publishers have positioned INSDC databases as a key provider of the scientific record and a core foundation for the global bioinformatics data infrastructure. While growth in sequence data volumes comes no longer as a surprise to INSDC partners, the uptake of next-generation sequencing technology by mainstream science that we have witnessed in recent years brings a step-change to growth, necessarily making a clear mark on INSDC strategy. In this article, we introduce the INSDC, outline data growth patterns and comment on the challenges of increased growth.

  16. Interference management using direct sequence spread spectrum ...

    African Journals Online (AJOL)

    Interference management using direct sequence spread spectrum (DSSS) technique ... Journal of Fundamental and Applied Sciences ... Keywords: DSSS, LTE network; Wi-Fi network; SINR; interference management and interference power.

  17. Characterizing leader sequences of CRISPR loci

    DEFF Research Database (Denmark)

    Alkhnbashi, Omer; Shah, Shiraz Ali; Garrett, Roger Antony

    2016-01-01

    The CRISPR-Cas system is an adaptive immune system in many archaea and bacteria, which provides resistance against invading genetic elements. The first phase of CRISPR-Cas immunity is called adaptation, in which small DNA fragments are excised from genetic elements and are inserted into a CRISPR...... array generally adjacent to its so called leader sequence at one end of the array. It has been shown that transcription initiation and adaptation signals of the CRISPR array are located within the leader. However, apart from promoters, there is very little knowledge of sequence or structural motifs...... sequences by focusing on the consensus repeat of the adjacent CRISPR array and weak upstream conservation signals. We applied our tool to the analysis of a comprehensive genomic database and identified several characteristic properties of leader sequences specific to archaea and bacteria, ranging from...

  18. 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.

  19. Galaxy LIMS for next-generation sequencing

    NARCIS (Netherlands)

    Scholtalbers, J.; Rossler, J.; Sorn, P.; Graaf, J. de; Boisguerin, V.; Castle, J.; Sahin, U.

    2013-01-01

    SUMMARY: We have developed a laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform. The system provides lab technicians standard and customizable sample information forms, barcoded submission forms, tracking of input

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

    African Journals Online (AJOL)

    Akanksha Pandey

    2012-10-06

    Oct 6, 2012 ... Abstract Genome sequencing can play a vital role in health and several other domains such as in .... ter have imposed some serious questions over the security is- ... strontium and barium from aqueous environment and store.

  1. Generalized locally Toeplitz sequences theory and applications

    CERN Document Server

    Garoni, Carlo

    2017-01-01

    Based on their research experience, the authors propose a reference textbook in two volumes on the theory of generalized locally Toeplitz sequences and their applications. This first volume focuses on the univariate version of the theory and the related applications in the unidimensional setting, while the second volume, which addresses the multivariate case, is mainly devoted to concrete PDE applications. This book systematically develops the theory of generalized locally Toeplitz (GLT) sequences and presents some of its main applications, with a particular focus on the numerical discretization of differential equations (DEs). It is the first book to address the relatively new field of GLT sequences, which occur in numerous scientific applications and are especially dominant in the context of DE discretizations. Written for applied mathematicians, engineers, physicists, and scientists who (perhaps unknowingly) encounter GLT sequences in their research, it is also of interest to those working in the fields of...

  2. High resolution sequence stratigraphy in China

    International Nuclear Information System (INIS)

    Zhang Shangfeng; Zhang Changmin; Yin Yanshi; Yin Taiju

    2008-01-01

    Since high resolution sequence stratigraphy was introduced into China by DENG Hong-wen in 1995, it has been experienced two development stages in China which are the beginning stage of theory research and development of theory research and application, and the stage of theoretical maturity and widely application that is going into. It is proved by practices that high resolution sequence stratigraphy plays more and more important roles in the exploration and development of oil and gas in Chinese continental oil-bearing basin and the research field spreads to the exploration of coal mine, uranium mine and other strata deposits. However, the theory of high resolution sequence stratigraphy still has some shortages, it should be improved in many aspects. The authors point out that high resolution sequence stratigraphy should be characterized quantitatively and modelized by computer techniques. (authors)

  3. Genetic sequences derived from suppression subtractive ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-06-17

    Jun 17, 2008 ... their possible roles in Xanthomonas albilineans ... Technology, P. O. Box 1334, Durban 4000, Republic of South Africa. Accepted 4 ... Clones selected were sequenced (using a Perkin Elmer ABI PRISM Dye terminator cycle.

  4. Special Issue: Next Generation DNA Sequencing

    Directory of Open Access Journals (Sweden)

    Paul Richardson

    2010-10-01

    Full Text Available Next Generation Sequencing (NGS refers to technologies that do not rely on traditional dideoxy-nucleotide (Sanger sequencing where labeled DNA fragments are physically resolved by electrophoresis. These new technologies rely on different strategies, but essentially all of them make use of real-time data collection of a base level incorporation event across a massive number of reactions (on the order of millions versus 96 for capillary electrophoresis for instance. The major commercial NGS platforms available to researchers are the 454 Genome Sequencer (Roche, Illumina (formerly Solexa Genome analyzer, the SOLiD system (Applied Biosystems/Life Technologies and the Heliscope (Helicos Corporation. The techniques and different strategies utilized by these platforms are reviewed in a number of the papers in this special issue. These technologies are enabling new applications that take advantage of the massive data produced by this next generation of sequencing instruments. [...

  5. Nursing Student Perceptions Regarding Simulation Experience Sequencing.

    Science.gov (United States)

    Woda, Aimee A; Gruenke, Theresa; Alt-Gehrman, Penny; Hansen, Jamie

    2016-09-01

    The use of simulated learning experiences (SLEs) have increased within nursing curricula with positive learning outcomes for nursing students. The purpose of this study is to explore nursing students' perceptions of their clinical decision making (CDM) related to the block sequencing of different patient care experiences, SLEs versus hospital-based learning experiences (HLEs). A qualitative descriptive design used open-ended survey questions to generate information about the block sequencing of SLEs and its impact on nursing students' perceived CDM. Three themes emerged from the data: Preexperience Anxiety, Real-Time Decision Making, and Increased Patient Care Experiences. Nursing students identified that having SLEs prior to HLEs provided several benefits. Even when students preferred SLEs prior to HLEs, the sequence did not impact their CDM. This suggests that alternating block sequencing can be used without impacting the students' perceptions of their ability to make decisions. [J Nurs Educ. 2016;55(9):528-532.]. Copyright 2016, SLACK Incorporated.

  6. Sequence finishing and mapping of Drosophila melanogasterheterochromatin

    Energy Technology Data Exchange (ETDEWEB)

    Hoskins, Roger A.; Carlson, Joseph W.; Kennedy, Cameron; Acevedo,David; Evans-Holm, Martha; Frise, Erwin; Wan, Kenneth H.; Park, Soo; Mendez-Lago, Maria; Rossi, Fabrizio; Villasante, Alfredo; Dimitri,Patrizio; Karpen, Gary H.; Celniker, Susan E.

    2007-06-15

    Genome sequences for most metazoans are incomplete due tothe presence of repeated DNA in the pericentromeric heterochromatin. Theheterochromatic regions of D. melanogaster contain 20 Mb of sequenceamenable to mapping, sequence assembly and finishing. Here we describethe generation of 15 Mb of finished or improved heterochromatic sequenceusing available clone resources and assembly and mapping methods. We alsoconstructed a BAC-based physical map that spans approximately 13 Mb ofthe pericentromeric heterochromatin, and a cytogenetic map that positionsapproximately 11 Mb of BAC contigs and sequence scaffolds in specificchromosomal locations. The integrated sequence assembly and maps greatlyimprove our understanding of the structure and composition of this poorlyunderstood fraction of a metazoan genome and provide a framework forfunctional analyses.

  7. 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

  8. Ancestral sequence alignment under optimal conditions

    Directory of Open Access Journals (Sweden)

    Brown Daniel G

    2005-11-01

    Full Text Available Abstract Background Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs heuristic, where the score of a multiple alignment is the sum of its induced pairwise alignment scores. However, the biological meaning of the sum-of-pairs of pairs heuristic is not obvious. Additionally, many algorithms based on the sum-of-pairs heuristic are complicated and slow, compared to pairwise alignment algorithms. An alternative approach to aligning alignments is to first infer ancestral sequences for each alignment, and then align the two ancestral sequences. In addition to being fast, this method has a clear biological basis that takes into account the evolution implied by an underlying phylogenetic tree. In this study we explore the accuracy of aligning alignments by ancestral sequence alignment. We examine the use of both maximum likelihood and parsimony to infer ancestral sequences. Additionally, we investigate the effect on accuracy of allowing ambiguity in our ancestral sequences. Results We use synthetic sequence data that we generate by simulating evolution on a phylogenetic tree. We use two different types of phylogenetic trees: trees with a period of rapid growth followed by a period of slow growth, and trees with a period of slow growth followed by a period of rapid growth. We examine the alignment accuracy of four ancestral sequence reconstruction and alignment methods: parsimony, maximum likelihood, ambiguous parsimony, and ambiguous maximum likelihood. Additionally, we compare against the alignment accuracy of two sum-of-pairs algorithms: ClustalW and the heuristic of Ma, Zhang, and Wang. Conclusion We find that allowing ambiguity in ancestral sequences does not lead to better multiple alignments. Regardless of whether we use parsimony or maximum likelihood, the

  9. Fibonacci difference sequence spaces for modulus functions

    Directory of Open Access Journals (Sweden)

    Kuldip Raj

    2015-05-01

    Full Text Available In the present paper we introduce Fibonacci difference sequence spaces l(F, Ƒ, p, u and  l_∞(F, Ƒ, p, u by using a sequence of modulus functions and a new band matrix F. We also make an effort to study some inclusion relations, topological and geometric properties of these spaces. Furthermore, the alpha, beta, gamma duals and matrix transformation of the space l(F, Ƒ, p, u are determined.

  10. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

  11. Enhanced Dynamic Algorithm of Genome Sequence Alignments

    OpenAIRE

    Arabi E. keshk

    2014-01-01

    The merging of biology and computer science has created a new field called computational biology that explore the capacities of computers to gain knowledge from biological data, bioinformatics. Computational biology is rooted in life sciences as well as computers, information sciences, and technologies. The main problem in computational biology is sequence alignment that is a way of arranging the sequences of DNA, RNA or protein to identify the region of similarity and relationship between se...

  12. Trace maps of general substitutional sequences

    International Nuclear Information System (INIS)

    Kolar, M.; Nori, F.

    1990-01-01

    It is shown that for arbitrary n, there exists a trace map for any n-letter substitutional sequence. Trace maps are explicitly obtained for the well-known circle and Rudin-Shapiro sequences which can be defined by means of substitution rules on three and four letters, respectively. The properties of the two trace maps and their consequences for various spectral properties are briefly discussed

  13. Human Chromosome 7: DNA Sequence and Biology

    OpenAIRE

    Scherer, Stephen W.; Cheung, Joseph; MacDonald, Jeffrey R.; Osborne, Lucy R.; Nakabayashi, Kazuhiko; Herbrick, Jo-Anne; Carson, Andrew R.; Parker-Katiraee, Layla; Skaug, Jennifer; Khaja, Razi; Zhang, Junjun; Hudek, Alexander K.; Li, Martin; Haddad, May; Duggan, Gavin E.

    2003-01-01

    DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. This approach enabled the discovery of candidate gene...

  14. DESCRIPTION OF THE RHIC SEQUENCER SYSTEM

    International Nuclear Information System (INIS)

    DOTTAVIO, T.; FRAK, B.; MORRIS, J.; SATOGATA, T.; VAN ZEIJTS, J.

    2001-01-01

    The movement of the Relativistic Heavy Ion Collider (RHIC) through its various states (eg. injection, acceleration, storage, collisions) is controlled by an application called the Sequencer. This program orchestrates most magnet and instrumentation systems and is responsible for the coordinated acquisition and saving of data from various systems. The Sequencer system, its software infrastructure, support programs, and the language used to drive it are discussed in this paper. Initial operational experience is also described

  15. Complete Genome Sequence of Ikoma Lyssavirus

    OpenAIRE

    Marston, Denise A.; Ellis, Richard J.; Horton, Daniel L.; Kuzmin, Ivan V.; Wise, Emma L.; McElhinney, Lorraine M.; Banyard, Ashley C.; Ngeleja, Chanasa; Keyyu, Julius; Cleaveland, Sarah; Lembo, Tiziana; Rupprecht, Charles E.; Fooks, Anthony R.

    2012-01-01

    Lyssaviruses (family Rhabdoviridae) constitute one of the most important groups of viral zoonoses globally. All lyssaviruses cause the disease rabies, an acute progressive encephalitis for which, once symptoms occur, there is no effective cure. Currently available vaccines are highly protective against the predominantly circulating lyssavirus species. Using next-generation sequencing technologies, we have obtained the whole-genome sequence for a novel lyssavirus, Ikoma lyssavirus (IKOV), isol...

  16. Chromatid interchanges at intrachromosomal telomeric DNA sequences

    International Nuclear Information System (INIS)

    Fernandez, J.L.; Vazquez-Gundin, F.; Bilbao, A.; Gosalvez, J.; Goyanes, V.

    1997-01-01

    Chinese hamster Don cells were exposed to X-rays, mitomycin C and teniposide (VM-26) to induce chromatid exchanges (quadriradials and triradials). After fluorescence in situ hybridization (FISH) of telomere sequences it was found that interstitial telomere-like DNA sequence arrays presented around five times more breakage-rearrangements than the genome overall. This high recombinogenic capacity was independent of the clastogen, suggesting that this susceptibility is not related to the initial mechanisms of DNA damage. (author)

  17. On statistical acceleration convergence of double sequences

    Directory of Open Access Journals (Sweden)

    Bipan Hazarika

    2017-04-01

    Full Text Available In this article the notion of statistical acceleration convergence of double sequences in Pringsheim's sense has been introduced. We prove the decompostion theorems for  statistical acceleration convergence of double sequences and some theorems related to that concept have been established using the four dimensional matrix transformations. We provided some examples, where the results of acceleration convergence fails to hold for the statistical cases.

  18. Filovirus Glycoprotein Sequence, Structure and Virulence

    OpenAIRE

    Phillips, J. C.

    2014-01-01

    Leading Ebola subtypes exhibit a wide mortality range, here explained at the molecular level by using fractal hydropathic scaling of amino acid sequences based on protein self-organized criticality. Specific hydrophobic features in the hydrophilic mucin-like domain suffice to account for the wide mortality range. Significance statement: Ebola virus is spreading rapidly in Africa. The connection between protein amino acid sequence and mortality is identified here.

  19. Aspects of coverage in medical DNA sequencing

    Directory of Open Access Journals (Sweden)

    Wilson Richard K

    2008-05-01

    Full Text Available Abstract Background DNA sequencing is now emerging as an important component in biomedical studies of diseases like cancer. Short-read, highly parallel sequencing instruments are expected to be used heavily for such projects, but many design specifications have yet to be conclusively established. Perhaps the most fundamental of these is the redundancy required to detect sequence variations, which bears directly upon genomic coverage and the consequent resolving power for discerning somatic mutations. Results We address the medical sequencing coverage problem via an extension of the standard mathematical theory of haploid coverage. The expected diploid multi-fold coverage, as well as its generalization for aneuploidy are derived and these expressions can be readily evaluated for any project. The resulting theory is used as a scaling law to calibrate performance to that of standard BAC sequencing at 8× to 10× redundancy, i.e. for expected coverages that exceed 99% of the unique sequence. A differential strategy is formalized for tumor/normal studies wherein tumor samples are sequenced more deeply than normal ones. In particular, both tumor alleles should be detected at least twice, while both normal alleles are detected at least once. Our theory predicts these requirements can be met for tumor and normal redundancies of approximately 26× and 21×, respectively. We explain why these values do not differ by a factor of 2, as might intuitively be expected. Future technology developments should prompt even deeper sequencing of tumors, but the 21× value for normal samples is essentially a constant. Conclusion Given the assumptions of standard coverage theory, our model gives pragmatic estimates for required redundancy. The differential strategy should be an efficient means of identifying potential somatic mutations for further study.

  20. Determinant Representations of Sequences: A Survey

    Directory of Open Access Journals (Sweden)

    Moghaddamfar A. R.

    2014-01-01

    Full Text Available This is a survey of recent results concerning (integer matrices whose leading principal minors are well-known sequences such as Fibonacci, Lucas, Jacobsthal and Pell (subsequences. There are different ways for constructing such matrices. Some of these matrices are constructed by homogeneous or nonhomogeneous recurrence relations, and others are constructed by convolution of two sequences. In this article, we will illustrate the idea of these methods by constructing some integer matrices of this type.

  1. Normal form theory and spectral sequences

    OpenAIRE

    Sanders, Jan A.

    2003-01-01

    The concept of unique normal form is formulated in terms of a spectral sequence. As an illustration of this technique some results of Baider and Churchill concerning the normal form of the anharmonic oscillator are reproduced. The aim of this paper is to show that spectral sequences give us a natural framework in which to formulate normal form theory. © 2003 Elsevier Science (USA). All rights reserved.

  2. Bunches of random cross-correlated sequences

    International Nuclear Information System (INIS)

    Maystrenko, A A; Melnik, S S; Pritula, G M; Usatenko, O V

    2013-01-01

    The statistical properties of random cross-correlated sequences constructed by the convolution method (likewise referred to as the Rice or the inverse Fourier transformation) are examined. We clarify the meaning of the filtering function—the kernel of the convolution operator—and show that it is the value of the cross-correlation function which describes correlations between the initial white noise and constructed correlated sequences. The matrix generalization of this method for constructing a bunch of N cross-correlated sequences is presented. Algorithms for their generation are reduced to solving the problem of decomposition of the Fourier transform of the correlation matrix into a product of two mutually conjugate matrices. Different decompositions are considered. The limits of weak and strong correlations for the one-point probability and pair correlation functions of sequences generated by the method under consideration are studied. Special cases of heavy-tailed distributions of the generated sequences are analyzed. We show that, if the filtering function is rather smooth, the distribution function of generated variables has the Gaussian or Lévy form depending on the analytical properties of the distribution (or characteristic) functions of the initial white noise. Anisotropic properties of statistically homogeneous random sequences related to the asymmetry of a filtering function are revealed and studied. These asymmetry properties are expressed in terms of the third- or fourth-order correlation functions. Several examples of the construction of correlated chains with a predefined correlation matrix are given. (paper)

  3. Leaf sequencing algorithms for segmented multileaf collimation

    International Nuclear Information System (INIS)

    Kamath, Srijit; Sahni, Sartaj; Li, Jonathan; Palta, Jatinder; Ranka, Sanjay

    2003-01-01

    The delivery of intensity-modulated radiation therapy (IMRT) with a multileaf collimator (MLC) requires the conversion of a radiation fluence map into a leaf sequence file that controls the movement of the MLC during radiation delivery. It is imperative that the fluence map delivered using the leaf sequence file is as close as possible to the fluence map generated by the dose optimization algorithm, while satisfying hardware constraints of the delivery system. Optimization of the leaf sequencing algorithm has been the subject of several recent investigations. In this work, we present a systematic study of the optimization of leaf sequencing algorithms for segmental multileaf collimator beam delivery and provide rigorous mathematical proofs of optimized leaf sequence settings in terms of monitor unit (MU) efficiency under most common leaf movement constraints that include minimum leaf separation constraint and leaf interdigitation constraint. Our analytical analysis shows that leaf sequencing based on unidirectional movement of the MLC leaves is as MU efficient as bidirectional movement of the MLC leaves

  4. Leaf sequencing algorithms for segmented multileaf collimation

    Energy Technology Data Exchange (ETDEWEB)

    Kamath, Srijit [Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL (United States); Sahni, Sartaj [Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL (United States); Li, Jonathan [Department of Radiation Oncology, University of Florida, Gainesville, FL (United States); Palta, Jatinder [Department of Radiation Oncology, University of Florida, Gainesville, FL (United States); Ranka, Sanjay [Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL (United States)

    2003-02-07

    The delivery of intensity-modulated radiation therapy (IMRT) with a multileaf collimator (MLC) requires the conversion of a radiation fluence map into a leaf sequence file that controls the movement of the MLC during radiation delivery. It is imperative that the fluence map delivered using the leaf sequence file is as close as possible to the fluence map generated by the dose optimization algorithm, while satisfying hardware constraints of the delivery system. Optimization of the leaf sequencing algorithm has been the subject of several recent investigations. In this work, we present a systematic study of the optimization of leaf sequencing algorithms for segmental multileaf collimator beam delivery and provide rigorous mathematical proofs of optimized leaf sequence settings in terms of monitor unit (MU) efficiency under most common leaf movement constraints that include minimum leaf separation constraint and leaf interdigitation constraint. Our analytical analysis shows that leaf sequencing based on unidirectional movement of the MLC leaves is as MU efficient as bidirectional movement of the MLC leaves.

  5. 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.

  6. A Unified Theoretical Framework for Cognitive Sequencing.

    Science.gov (United States)

    Savalia, Tejas; Shukla, Anuj; Bapi, Raju S

    2016-01-01

    The capacity to sequence information is central to human performance. Sequencing ability forms the foundation stone for higher order cognition related to language and goal-directed planning. Information related to the order of items, their timing, chunking and hierarchical organization are important aspects in sequencing. Past research on sequencing has emphasized two distinct and independent dichotomies: implicit vs. explicit and goal-directed vs. habits. We propose a theoretical framework unifying these two streams. Our proposal relies on brain's ability to implicitly extract statistical regularities from the stream of stimuli and with attentional engagement organizing sequences explicitly and hierarchically. Similarly, sequences that need to be assembled purposively to accomplish a goal require engagement of attentional processes. With repetition, these goal-directed plans become habits with concomitant disengagement of attention. Thus, attention and awareness play a crucial role in the implicit-to-explicit transition as well as in how goal-directed plans become automatic habits. Cortico-subcortical loops basal ganglia-frontal cortex and hippocampus-frontal cortex loops mediate the transition process. We show how the computational principles of model-free and model-based learning paradigms, along with a pivotal role for attention and awareness, offer a unifying framework for these two dichotomies. Based on this framework, we make testable predictions related to the potential influence of response-to-stimulus interval (RSI) on developing awareness in implicit learning tasks.

  7. A Unified Theoretical Framework for Cognitive Sequencing

    Directory of Open Access Journals (Sweden)

    Tejas Savalia

    2016-11-01

    Full Text Available The capacity to sequence information is central to human performance. Sequencing ability forms the foundation stone for higher order cognition related to language and goal-directed planning. Information related to the order of items, their timing, chunking and hierarchical organization are important aspects in sequencing. Past research on sequencing has emphasized two distinct and independent dichotomies: implicit versus explicit and goal-directed versus habits. We propose a theoretical framework unifying these two streams. Our proposal relies on brain's ability to implicitly extract statistical regularities from the stream of stimuli and with attentional engagement organizing sequences explicitly and hierarchically. Similarly, sequences that need to be assembled purposively to accomplish a goal require engagement of attentional processes. With repetition, these goal-directed plans become habits with concomitant disengagement of attention. Thus attention and awareness play a crucial role in the implicit-to-explicit transition as well as in how goal-directed plans become automatic habits. Cortico-subcortical loops ─ basal ganglia-frontal cortex and hippocampus-frontal cortex loops ─ mediate the transition process. We show how the computational principles of model-free and model-based learning paradigms, along with a pivotal role for attention and awareness, offer a unifying framework for these two dichotomies. Based on this framework, we make testable predictions related to the potential influence of response-to-stimulus interval (RSI on developing awareness in implicit learning tasks.

  8. Sequence determinants of human microsatellite variability

    Directory of Open Access Journals (Sweden)

    Jakobsson Mattias

    2009-12-01

    Full Text Available Abstract Background Microsatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database. Results Calibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length, under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity. Conclusions These results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability.

  9. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    Phylogenetic analysis suggests that our sequences are clustered with sequences reported from Japan. This is the first phylogenetic analysis of HCV core gene from Pakistani population. Our sequences and sequences from Japan are grouped into same cluster in the phylogenetic tree. Sequence comparison and ...

  10. Synaptotagmin gene content of the sequenced genomes

    Directory of Open Access Journals (Sweden)

    Craxton Molly

    2004-07-01

    Full Text Available Abstract Background Synaptotagmins exist as a large gene family in mammals. There is much interest in the function of certain family members which act crucially in the regulated synaptic vesicle exocytosis required for efficient neurotransmission. Knowledge of the functions of other family members is relatively poor and the presence of Synaptotagmin genes in plants indicates a role for the family as a whole which is wider than neurotransmission. Identification of the Synaptotagmin genes within completely sequenced genomes can provide the entire Synaptotagmin gene complement of each sequenced organism. Defining the detailed structures of all the Synaptotagmin genes and their encoded products can provide a useful resource for functional studies and a deeper understanding of the evolution of the gene family. The current rapid increase in the number of sequenced genomes from different branches of the tree of life, together with the public deposition of evolutionarily diverse transcript sequences make such studies worthwhile. Results I have compiled a detailed list of the Synaptotagmin genes of Caenorhabditis, Anopheles, Drosophila, Ciona, Danio, Fugu, Mus, Homo, Arabidopsis and Oryza by examining genomic and transcript sequences from public sequence databases together with some transcript sequences obtained by cDNA library screening and RT-PCR. I have compared all of the genes and investigated the relationship between plant Synaptotagmins and their non-Synaptotagmin counterparts. Conclusions I have identified and compared 98 Synaptotagmin genes from 10 sequenced genomes. Detailed comparison of transcript sequences reveals abundant and complex variation in Synaptotagmin gene expression and indicates the presence of Synaptotagmin genes in all animals and land plants. Amino acid sequence comparisons indicate patterns of conservation and diversity in function. Phylogenetic analysis shows the origin of Synaptotagmins in multicellular eukaryotes and their

  11. 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/.

  12. 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/.

  13. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.

    Science.gov (United States)

    Huber, Thomas; Faulkner, Geoffrey; Hugenholtz, Philip

    2004-09-22

    Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments. Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/~huber/bellerophon.pl

  14. Clinical evaluation of further-developed MRCP sequences in comparison with standard MRCP sequences

    International Nuclear Information System (INIS)

    Hundt, W.; Scheidler, J.; Reiser, M.; Petsch, R.

    2002-01-01

    The purpose of this study was the comparison of technically improved single-shot magnetic resonance cholangiopancreatography (MRCP) sequences with standard single-shot rapid acquisition with relaxation enhancement (RARE) and half-Fourier acquired single-shot turbo spin-echo (HASTE) sequences in evaluating the normal and abnormal biliary duct system. The bile duct system of 45 patients was prospectively investigated on a 1.5-T MRI system. The investigation was performed with RARE and HASTE MR cholangiography sequences with standard and high spatial resolutions, and with a delayed-echo half-Fourier RARE (HASTE) sequence. Findings of the improved MRCP sequences were compared with the standard MRCP sequences. The level of confidence in assessing the diagnosis was divided into five groups. The Wilcoxon signed-rank test at a level of p<0.05 was applied. In 15 patients no pathology was found. The MRCP showed stenoses of the bile duct system in 10 patients and choledocholithiasis and cholecystolithiasis in 16 patients. In 12 patients a dilatation of the bile duct system was found. Comparison of the low- and high spatial resolution sequences and the short and long TE times of the half-Fourier RARE (HASTE) sequence revealed no statistically significant differences regarding accuracy of the examination. The diagnostic confidence level in assessing normal or pathological findings for the high-resolution RARE and half-Fourier RARE (HASTE) was significantly better than for the standard sequences. For the delayed-echo half-Fourier RARE (HASTE) sequence no statistically significant difference was seen. The high-resolution RARE and half-Fourier RARE (HASTE) sequences had a higher confidence level, but there was no significant difference in diagnosis in terms of detection and assessment of pathological changes in the biliary duct system compared with standard sequences. (orig.)

  15. 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)

  16. Inverted temperature sequences: role of deformation partitioning

    Science.gov (United States)

    Grujic, D.; Ashley, K. T.; Coble, M. A.; Coutand, I.; Kellett, D.; Whynot, N.

    2015-12-01

    The inverted metamorphism associated with the Main Central thrust zone in the Himalaya has been historically attributed to a number of tectonic processes. Here we show that there is actually a composite peak and deformation temperature sequence that formed in succession via different tectonic processes. The deformation partitioning seems to the have played a key role, and the magnitude of each process has varied along strike of the orogen. To explain the formation of the inverted metamorphic sequence across the Lesser Himalayan Sequence (LHS) in eastern Bhutan, we used Raman spectroscopy of carbonaceous material (RSCM) to determine the peak metamorphic temperatures and Ti-in-quartz thermobarometry to determine the deformation temperatures combined with thermochronology including published apatite and zircon U-Th/He and fission-track data and new 40Ar/39Ar dating of muscovite. The dataset was inverted using 3D-thermal-kinematic modeling to constrain the ranges of geological parameters such as fault geometry and slip rates, location and rates of localized basal accretion, and thermal properties of the crust. RSCM results indicate that there are two peak temperature sequences separated by a major thrust within the LHS. The internal temperature sequence shows an inverted peak temperature gradient of 12 °C/km; in the external (southern) sequence, the peak temperatures are constant across the structural sequence. Thermo-kinematic modeling suggest that the thermochronologic and thermobarometric data are compatible with a two-stage scenario: an Early-Middle Miocene phase of fast overthrusting of a hot hanging wall over a downgoing footwall and inversion of the synkinematic isotherms, followed by the formation of the external duplex developed by dominant underthrusting and basal accretion. To reconcile our observations with the experimental data, we suggest that pervasive ductile deformation within the upper LHS and along the Main Central thrust zone at its top stopped at

  17. Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

    Science.gov (United States)

    Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

    2012-01-01

    The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697

  18. Enrichment of target sequences for next-generation sequencing applications in research and diagnostics.

    Science.gov (United States)

    Altmüller, Janine; Budde, Birgit S; Nürnberg, Peter

    2014-02-01

    Abstract Targeted re-sequencing such as gene panel sequencing (GPS) has become very popular in medical genetics, both for research projects and in diagnostic settings. The technical principles of the different enrichment methods have been reviewed several times before; however, new enrichment products are constantly entering the market, and researchers are often puzzled about the requirement to take decisions about long-term commitments, both for the enrichment product and the sequencing technology. This review summarizes important considerations for the experimental design and provides helpful recommendations in choosing the best sequencing strategy for various research projects and diagnostic applications.

  19. Detection of M-Sequences from Spike Sequence in Neuronal Networks

    Directory of Open Access Journals (Sweden)

    Yoshi Nishitani

    2012-01-01

    Full Text Available In circuit theory, it is well known that a linear feedback shift register (LFSR circuit generates pseudorandom bit sequences (PRBS, including an M-sequence with the maximum period of length. In this study, we tried to detect M-sequences known as a pseudorandom sequence generated by the LFSR circuit from time series patterns of stimulated action potentials. Stimulated action potentials were recorded from dissociated cultures of hippocampal neurons grown on a multielectrode array. We could find several M-sequences from a 3-stage LFSR circuit (M3. These results show the possibility of assembling LFSR circuits or its equivalent ones in a neuronal network. However, since the M3 pattern was composed of only four spike intervals, the possibility of an accidental detection was not zero. Then, we detected M-sequences from random spike sequences which were not generated from an LFSR circuit and compare the result with the number of M-sequences from the originally observed raster data. As a result, a significant difference was confirmed: a greater number of “0–1” reversed the 3-stage M-sequences occurred than would have accidentally be detected. This result suggests that some LFSR equivalent circuits are assembled in neuronal networks.

  20. A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data.

    Science.gov (United States)

    Fernández-Caballero Rico, Jose Ángel; Chueca Porcuna, Natalia; Álvarez Estévez, Marta; Mosquera Gutiérrez, María Del Mar; Marcos Maeso, María Ángeles; García, Federico

    2018-02-01

    To show how to generate a consensus sequence from the information of massive parallel sequences data obtained from routine HIV anti-retroviral resistance studies, and that may be suitable for molecular epidemiology studies. Paired Sanger (Trugene-Siemens) and next-generation sequencing (NGS) (454 GSJunior-Roche) HIV RT and protease sequences from 62 patients were studied. NGS consensus sequences were generated using Mesquite, using 10%, 15%, and 20% thresholds. Molecular evolutionary genetics analysis (MEGA) was used for phylogenetic studies. At a 10% threshold, NGS-Sanger sequences from 17/62 patients were phylogenetically related, with a median bootstrap-value of 88% (IQR83.5-95.5). Association increased to 36/62 sequences, median bootstrap 94% (IQR85.5-98)], using a 15% threshold. Maximum association was at the 20% threshold, with 61/62 sequences associated, and a median bootstrap value of 99% (IQR98-100). A safe method is presented to generate consensus sequences from HIV-NGS data at 20% threshold, which will prove useful for molecular epidemiological studies. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  1. Sequencing of BAC pools by different next generation sequencing platforms and strategies

    Directory of Open Access Journals (Sweden)

    Scholz Uwe

    2011-10-01

    Full Text Available Abstract Background Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.

  2. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-07-19

    Jul 19, 2010 ... and antisense primers, a single band of 573 base pairs .... Amino acid sequence alignment of Cluster I and Cluster II of phylogenetic tree. First ten sequences ... sequence weighting, postion-spiecific gap penalties and weight.

  3. Axioms for behavioural congruence of single-pass instruction sequences

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2017-01-01

    In program algebra, an algebraic theory of single-pass instruction sequences, three congruences on instruction sequences are paid attention to: instruction sequence congruence, structural congruence, and behavioural congruence. Sound and complete axiom systems for the first two congruences were

  4. Tournaments, oriented graphs and football sequences

    Directory of Open Access Journals (Sweden)

    Pirzada S.

    2017-08-01

    Full Text Available Consider the result of a soccer league competition where n teams play each other exactly once. A team gets three points for each win and one point for each draw. The total score obtained by each team vi is called the f-score of vi and is denoted by fi. The sequences of all f-scores [fi]i=1n$\\left[ {{\\rm{f}}_{\\rm{i}} } \\right]_{{\\rm{i}} = 1}^{\\rm{n}} $ arranged in non-decreasing order is called the f-score sequence of the competition. We raise the following problem: Which sequences of non-negative integers in non-decreasing order is a football sequence, that is the outcome of a soccer league competition. We model such a competition by an oriented graph with teams represented by vertices in which the teams play each other once, with an arc from team u to team v if and only if u defeats v. We obtain some necessary conditions for football sequences and some characterizations under restrictions.

  5. SNAD: sequence name annotation-based designer

    Directory of Open Access Journals (Sweden)

    Gorbalenya Alexander E

    2009-08-01

    Full Text Available Abstract Background A growing diversity of biological data is tagged with unique identifiers (UIDs associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Results Here we introduce SNAD (Sequence Name Annotation-based Designer that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. Conclusion A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

  6. Variable depth recursion algorithm for leaf sequencing

    International Nuclear Information System (INIS)

    Siochi, R. Alfredo C.

    2007-01-01

    The processes of extraction and sweep are basic segmentation steps that are used in leaf sequencing algorithms. A modified version of a commercial leaf sequencer changed the way that the extracts are selected and expanded the search space, but the modification maintained the basic search paradigm of evaluating multiple solutions, each one consisting of up to 12 extracts and a sweep sequence. While it generated the best solutions compared to other published algorithms, it used more computation time. A new, faster algorithm selects one extract at a time but calls itself as an evaluation function a user-specified number of times, after which it uses the bidirectional sweeping window algorithm as the final evaluation function. To achieve a performance comparable to that of the modified commercial leaf sequencer, 2-3 calls were needed, and in all test cases, there were only slight improvements beyond two calls. For the 13 clinical test maps, computation speeds improved by a factor between 12 and 43, depending on the constraints, namely the ability to interdigitate and the avoidance of the tongue-and-groove under dose. The new algorithm was compared to the original and modified versions of the commercial leaf sequencer. It was also compared to other published algorithms for 1400, random, 15x15, test maps with 3-16 intensity levels. In every single case the new algorithm provided the best solution

  7. Modeling of prepregs during automated draping sequences

    Science.gov (United States)

    Krogh, Christian; Glud, Jens A.; Jakobsen, Johnny

    2017-10-01

    The behavior of wowen prepreg fabric during automated draping sequences is investigated. A drape tool under development with an arrangement of grippers facilitates the placement of a woven prepreg fabric in a mold. It is essential that the draped configuration is free from wrinkles and other defects. The present study aims at setting up a virtual draping framework capable of modeling the draping process from the initial flat fabric to the final double curved shape and aims at assisting the development of an automated drape tool. The virtual draping framework consists of a kinematic mapping algorithm used to generate target points on the mold which are used as input to a draping sequence planner. The draping sequence planner prescribes the displacement history for each gripper in the drape tool and these displacements are then applied to each gripper in a transient model of the draping sequence. The model is based on a transient finite element analysis with the material's constitutive behavior currently being approximated as linear elastic orthotropic. In-plane tensile and bias-extension tests as well as bending tests are conducted and used as input for the model. The virtual draping framework shows a good potential for obtaining a better understanding of the drape process and guide the development of the drape tool. However, results obtained from using the framework on a simple test case indicate that the generation of draping sequences is non-trivial.

  8. Extended sequence diagram for human system interaction

    International Nuclear Information System (INIS)

    Hwang, Jong Rok; Choi, Sun Woo; Ko, Hee Ran; Kim, Jong Hyun

    2012-01-01

    Unified Modeling Language (UML) is a modeling language in the field of object oriented software engineering. The sequence diagram is a kind of interaction diagram that shows how processes operate with one another and in what order. It is a construct of a message sequence chart. It depicts the objects and classes involved in the scenario and the sequence of messages exchanged between the objects needed to carry out the functionality of the scenario. This paper proposes the Extended Sequence Diagram (ESD), which is capable of depicting human system interaction for nuclear power plants, as well as cognitive process of operators analysis. In the conventional sequence diagram, there is a limit to only identify the activities of human and systems interactions. The ESD is extended to describe operators' cognitive process in more detail. The ESD is expected to be used as a task analysis method for describing human system interaction. The ESD can also present key steps causing abnormal operations or failures and diverse human errors based on cognitive condition

  9. Sequence analysis by iterated maps, a review.

    Science.gov (United States)

    Almeida, Jonas S

    2014-05-01

    Among alignment-free methods, Iterated Maps (IMs) are on a particular extreme: they are also scale free (order free). The use of IMs for sequence analysis is also distinct from other alignment-free methodologies in being rooted in statistical mechanics instead of computational linguistics. Both of these roots go back over two decades to the use of fractal geometry in the characterization of phase-space representations. The time series analysis origin of the field is betrayed by the title of the manuscript that started this alignment-free subdomain in 1990, 'Chaos Game Representation'. The clash between the analysis of sequences as continuous series and the better established use of Markovian approaches to discrete series was almost immediate, with a defining critique published in same journal 2 years later. The rest of that decade would go by before the scale-free nature of the IM space was uncovered. The ensuing decade saw this scalability generalized for non-genomic alphabets as well as an interest in its use for graphic representation of biological sequences. Finally, in the past couple of years, in step with the emergence of BigData and MapReduce as a new computational paradigm, there is a surprising third act in the IM story. Multiple reports have described gains in computational efficiency of multiple orders of magnitude over more conventional sequence analysis methodologies. The stage appears to be now set for a recasting of IMs with a central role in processing nextgen sequencing results.

  10. Harnessing Whole Genome Sequencing in Medical Mycology.

    Science.gov (United States)

    Cuomo, Christina A

    2017-01-01

    Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically important fungal pathogens. Genomes for some important fungal pathogens were only recently assembled, revealing gene family expansions in many species and extreme gene loss in one obligate species. The scale and scope of species sequenced is rapidly expanding, leveraging technological advances to assemble and annotate genomes with higher precision. By using iteratively improved reference assemblies or those generated de novo for new species, recent studies have compared the sequence of isolates representing populations or clinical cohorts. Whole genome approaches provide the resolution necessary for comparison of closely related isolates, for example, in the analysis of outbreaks or sampled across time within a single host. Genomic analysis of fungal pathogens has enabled both basic research and diagnostic studies. The increased scale of sequencing can be applied across populations, and new metagenomic methods allow direct analysis of complex samples.

  11. OTU analysis using metagenomic shotgun sequencing data.

    Directory of Open Access Journals (Sweden)

    Xiaolin Hao

    Full Text Available Because of technological limitations, the primer and amplification biases in targeted sequencing of 16S rRNA genes have veiled the true microbial diversity underlying environmental samples. However, the protocol of metagenomic shotgun sequencing provides 16S rRNA gene fragment data with natural immunity against the biases raised during priming and thus the potential of uncovering the true structure of microbial community by giving more accurate predictions of operational taxonomic units (OTUs. Nonetheless, the lack of statistically rigorous comparison between 16S rRNA gene fragments and other data types makes it difficult to interpret previously reported results using 16S rRNA gene fragments. Therefore, in the present work, we established a standard analysis pipeline that would help confirm if the differences in the data are true or are just due to potential technical bias. This pipeline is built by using simulated data to find optimal mapping and OTU prediction methods. The comparison between simulated datasets revealed a relationship between 16S rRNA gene fragments and full-length 16S rRNA sequences that a 16S rRNA gene fragment having a length >150 bp provides the same accuracy as a full-length 16S rRNA sequence using our proposed pipeline, which could serve as a good starting point for experimental design and making the comparison between 16S rRNA gene fragment-based and targeted 16S rRNA sequencing-based surveys possible.

  12. Attentional load and implicit sequence learning.

    Science.gov (United States)

    Shanks, David R; Rowland, Lee A; Ranger, Mandeep S

    2005-06-01

    A widely employed conceptualization of implicit learning hypothesizes that it makes minimal demands on attentional resources. This conjecture was investigated by comparing learning under single-task and dual-task conditions in the sequential reaction time (SRT) task. Participants learned probabilistic sequences, with dual-task participants additionally having to perform a counting task using stimuli that were targets in the SRT display. Both groups were then tested for sequence knowledge under single-task (Experiments 1 and 2) or dual-task (Experiment 3) conditions. Participants also completed a free generation task (Experiments 2 and 3) under inclusion or exclusion conditions to determine if sequence knowledge was conscious or unconscious in terms of its access to intentional control. The experiments revealed that the secondary task impaired sequence learning and that sequence knowledge was consciously accessible. These findings disconfirm both the notion that implicit learning is able to proceed normally under conditions of divided attention, and that the acquired knowledge is inaccessible to consciousness. A unitary framework for conceptualizing implicit and explicit learning is proposed.

  13. BLEACHING EUCALYPTUS PULPS WITH SHORT SEQUENCES

    Directory of Open Access Journals (Sweden)

    Flaviana Reis Milagres

    2011-03-01

    Full Text Available Eucalyptus spp kraft pulp, due to its high content of hexenuronic acids, is quite easy to bleach. Therefore, investigations have been made attempting to decrease the number of stages in the bleaching process in order to minimize capital costs. This study focused on the evaluation of short ECF (Elemental Chlorine Free and TCF (Totally Chlorine Free sequences for bleaching oxygen delignified Eucalyptus spp kraft pulp to 90% ISO brightness: PMoDP (Molybdenum catalyzed acid peroxide, chlorine dioxide and hydrogen peroxide, PMoD/P (Molybdenum catalyzed acid peroxide, chlorine dioxide and hydrogen peroxide, without washing PMoD(PO (Molybdenum catalyzed acid peroxide, chlorine dioxide and pressurized peroxide, D(EPODP (chlorine dioxide, extraction oxidative with oxygen and peroxide, chlorine dioxide and hydrogen peroxide, PMoQ(PO (Molybdenum catalyzed acid peroxide, DTPA and pressurized peroxide, and XPMoQ(PO (Enzyme, molybdenum catalyzed acid peroxide, DTPA and pressurized peroxide. Uncommon pulp treatments, such as molybdenum catalyzed acid peroxide (PMo and xylanase (X bleaching stages, were used. Among the ECF alternatives, the two-stage PMoD/P sequence proved highly cost-effective without affecting pulp quality in relation to the traditional D(EPODP sequence and produced better quality effluent in relation to the reference. However, a four stage sequence, XPMoQ(PO, was required to achieve full brightness using the TCF technology. This sequence was highly cost-effective although it only produced pulp of acceptable quality.

  14. Human Genome Sequencing in Health and Disease

    Science.gov (United States)

    Gonzaga-Jauregui, Claudia; Lupski, James R.; Gibbs, Richard A.

    2013-01-01

    Following the “finished,” euchromatic, haploid human reference genome sequence, the rapid development of novel, faster, and cheaper sequencing technologies is making possible the era of personalized human genomics. Personal diploid human genome sequences have been generated, and each has contributed to our better understanding of variation in the human genome. We have consequently begun to appreciate the vastness of individual genetic variation from single nucleotide to structural variants. Translation of genome-scale variation into medically useful information is, however, in its infancy. This review summarizes the initial steps undertaken in clinical implementation of personal genome information, and describes the application of whole-genome and exome sequencing to identify the cause of genetic diseases and to suggest adjuvant therapies. Better analysis tools and a deeper understanding of the biology of our genome are necessary in order to decipher, interpret, and optimize clinical utility of what the variation in the human genome can teach us. Personal genome sequencing may eventually become an instrument of common medical practice, providing information that assists in the formulation of a differential diagnosis. We outline herein some of the remaining challenges. PMID:22248320

  15. 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.

  16. Winnowing sequences from a database search.

    Science.gov (United States)

    Berman, P; Zhang, Z; Wolf, Y I; Koonin, E V; Miller, W

    2000-01-01

    In database searches for sequence similarity, matches to a distinct sequence region (e.g., protein domain) are frequently obscured by numerous matches to another region of the same sequence. In order to cope with this problem, algorithms are developed to discard redundant matches. One model for this problem begins with a list of intervals, each with an associated score; each interval gives the range of positions in the query sequence that align to a database sequence, and the score is that of the alignment. If interval I is contained in interval J, and I's score is less than J's, then I is said to be dominated by J. The problem is then to identify each interval that is dominated by at least K other intervals, where K is a given level of "tolerable redundancy." An algorithm is developed to solve the problem in O(N log N) time and O(N*) space, where N is the number of intervals and N* is a precisely defined value that never exceeds N and is frequently much smaller. This criterion for discarding database hits has been implemented in the Blast program, as illustrated herein with examples. Several variations and extensions of this approach are also described.

  17. 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.

  18. End Sequencing and Finger Printing of Human & Mouse BAC Libraries

    Energy Technology Data Exchange (ETDEWEB)

    Fraser, C

    2005-09-27

    This project provided for continued end sequencing of existing and new BAC libraries constructed to support human sequencing as well as to initiate BAC end sequencing from the mouse BAC libraries constructed to support mouse sequencing. The clones, the sequences, and the fingerprints are now an available resource for the community at large. Research and development of new metaodologies for BAC end sequencing have reduced costs and increase throughput.

  19. 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

  20. 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.

  1. Automated constraint checking of spacecraft command sequences

    Science.gov (United States)

    Horvath, Joan C.; Alkalaj, Leon J.; Schneider, Karl M.; Spitale, Joseph M.; Le, Dang

    1995-01-01

    Robotic spacecraft are controlled by onboard sets of commands called "sequences." Determining that sequences will have the desired effect on the spacecraft can be expensive in terms of both labor and computer coding time, with different particular costs for different types of spacecraft. Specification languages and appropriate user interface to the languages can be used to make the most effective use of engineering validation time. This paper describes one specification and verification environment ("SAVE") designed for validating that command sequences have not violated any flight rules. This SAVE system was subsequently adapted for flight use on the TOPEX/Poseidon spacecraft. The relationship of this work to rule-based artificial intelligence and to other specification techniques is discussed, as well as the issues that arise in the transfer of technology from a research prototype to a full flight system.

  2. Transforming clinical microbiology with bacterial genome sequencing.

    Science.gov (United States)

    Didelot, Xavier; Bowden, Rory; Wilson, Daniel J; Peto, Tim E A; Crook, Derrick W

    2012-09-01

    Whole-genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we review the current status of clinical microbiology and how it has already begun to be transformed by using next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties, such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. We predict that the application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.

  3. The double main sequence of Omega Centauri

    Science.gov (United States)

    Bedin, L. R.; Piotto, G.; Anderson, J.; King, I. R.; Cassisi, S.; Momany, Y.

    Recent, high precision photometry of Omega Centauri, the biggest Galactic globular cluster, has been obtained with Hubble Space Telescope (HST). The color magnitude diagram reveals an unexpected bifurcation of colors in the main sequence (MS). The newly found double MS, the multiple turnoffs and subgiant branches, and other sequences discovered in the past along the red giant branch of this cluster add up to a fascinating but frustrating puzzle. Among the possible explanations for the blue main sequence an anomalous overabundance of helium is suggested. The hypothesis will be tested with a set of FLAMES@VLT data we have recently obtained (ESO DDT program), and with forthcoming ACS@HST images. Based on observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by AURA, Inc., under NASA contract NAS 5-26555.

  4. Heuristics for multiobjective multiple sequence alignment.

    Science.gov (United States)

    Abbasi, Maryam; Paquete, Luís; Pereira, Francisco B

    2016-07-15

    Aligning multiple sequences arises in many tasks in Bioinformatics. However, the alignments produced by the current software packages are highly dependent on the parameters setting, such as the relative importance of opening gaps with respect to the increase of similarity. Choosing only one parameter setting may provide an undesirable bias in further steps of the analysis and give too simplistic interpretations. In this work, we reformulate multiple sequence alignment from a multiobjective point of view. The goal is to generate several sequence alignments that represent a trade-off between maximizing the substitution score and minimizing the number of indels/gaps in the sum-of-pairs score function. This trade-off gives to the practitioner further information about the similarity of the sequences, from which she could analyse and choose the most plausible alignment. We introduce several heuristic approaches, based on local search procedures, that compute a set of sequence alignments, which are representative of the trade-off between the two objectives (substitution score and indels). Several algorithm design options are discussed and analysed, with particular emphasis on the influence of the starting alignment and neighborhood search definitions on the overall performance. A perturbation technique is proposed to improve the local search, which provides a wide range of high-quality alignments. The proposed approach is tested experimentally on a wide range of instances. We performed several experiments with sequences obtained from the benchmark database BAliBASE 3.0. To evaluate the quality of the results, we calculate the hypervolume indicator of the set of score vectors returned by the algorithms. The results obtained allow us to identify reasonably good choices of parameters for our approach. Further, we compared our method in terms of correctly aligned pairs ratio and columns correctly aligned ratio with respect to reference alignments. Experimental results show

  5. Image correlation method for DNA sequence alignment.

    Science.gov (United States)

    Curilem Saldías, Millaray; Villarroel Sassarini, Felipe; Muñoz Poblete, Carlos; Vargas Vásquez, Asticio; Maureira Butler, Iván

    2012-01-01

    The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment.

  6. Dynamic programming algorithms for biological sequence comparison.

    Science.gov (United States)

    Pearson, W R; Miller, W

    1992-01-01

    Efficient dynamic programming algorithms are available for a broad class of protein and DNA sequence comparison problems. These algorithms require computer time proportional to the product of the lengths of the two sequences being compared [O(N2)] but require memory space proportional only to the sum of these lengths [O(N)]. Although the requirement for O(N2) time limits use of the algorithms to the largest computers when searching protein and DNA sequence databases, many other applications of these algorithms, such as calculation of distances for evolutionary trees and comparison of a new sequence to a library of sequence profiles, are well within the capabilities of desktop computers. In particular, the results of library searches with rapid searching programs, such as FASTA or BLAST, should be confirmed by performing a rigorous optimal alignment. Whereas rapid methods do not overlook significant sequence similarities, FASTA limits the number of gaps that can be inserted into an alignment, so that a rigorous alignment may extend the alignment substantially in some cases. BLAST does not allow gaps in the local regions that it reports; a calculation that allows gaps is very likely to extend the alignment substantially. Although a Monte Carlo evaluation of the statistical significance of a similarity score with a rigorous algorithm is much slower than the heuristic approach used by the RDF2 program, the dynamic programming approach should take less than 1 hr on a 386-based PC or desktop Unix workstation. For descriptive purposes, we have limited our discussion to methods for calculating similarity scores and distances that use gap penalties of the form g = rk. Nevertheless, programs for the more general case (g = q+rk) are readily available. Versions of these programs that run either on Unix workstations, IBM-PC class computers, or the Macintosh can be obtained from either of the authors.

  7. Exome Sequencing in Suspected Monogenic Dyslipidemias

    Science.gov (United States)

    Stitziel, Nathan O.; Peloso, Gina M.; Abifadel, Marianne; Cefalu, Angelo B.; Fouchier, Sigrid; Motazacker, M. Mahdi; Tada, Hayato; Larach, Daniel B.; Awan, Zuhier; Haller, Jorge F.; Pullinger, Clive R.; Varret, Mathilde; Rabès, Jean-Pierre; Noto, Davide; Tarugi, Patrizia; Kawashiri, Masa-aki; Nohara, Atsushi; Yamagishi, Masakazu; Risman, Marjorie; Deo, Rahul; Ruel, Isabelle; Shendure, Jay; Nickerson, Deborah A.; Wilson, James G.; Rich, Stephen S.; Gupta, Namrata; Farlow, Deborah N.; Neale, Benjamin M.; Daly, Mark J.; Kane, John P.; Freeman, Mason W.; Genest, Jacques; Rader, Daniel J.; Mabuchi, Hiroshi; Kastelein, John J.P.; Hovingh, G. Kees; Averna, Maurizio R.; Gabriel, Stacey; Boileau, Catherine; Kathiresan, Sekar

    2015-01-01

    Background Exome sequencing is a promising tool for gene mapping in Mendelian disorders. We utilized this technique in an attempt to identify novel genes underlying monogenic dyslipidemias. Methods and Results We performed exome sequencing on 213 selected family members from 41 kindreds with suspected Mendelian inheritance of extreme levels of low-density lipoprotein (LDL) cholesterol (after candidate gene sequencing excluded known genetic causes for high LDL cholesterol families) or high-density lipoprotein (HDL) cholesterol. We used standard analytic approaches to identify candidate variants and also assigned a polygenic score to each individual in order to account for their burden of common genetic variants known to influence lipid levels. In nine families, we identified likely pathogenic variants in known lipid genes (ABCA1, APOB, APOE, LDLR, LIPA, and PCSK9); however, we were unable to identify obvious genetic etiologies in the remaining 32 families despite follow-up analyses. We identified three factors that limited novel gene discovery: (1) imperfect sequencing coverage across the exome hid potentially causal variants; (2) large numbers of shared rare alleles within families obfuscated causal variant identification; and (3) individuals from 15% of families carried a significant burden of common lipid-related alleles, suggesting complex inheritance can masquerade as monogenic disease. Conclusions We identified the genetic basis of disease in nine of 41 families; however, none of these represented novel gene discoveries. Our results highlight the promise and limitations of exome sequencing as a discovery technique in suspected monogenic dyslipidemias. Considering the confounders identified may inform the design of future exome sequencing studies. PMID:25632026

  8. Frequency Selective Filtering of the Modulation Spectrum and its Impact on Consonant Identification

    DEFF Research Database (Denmark)

    Christiansen, Thomas Ulrich; Greenberg, Steven

    2009-01-01

    The spectro-temporal coding of Danish consonants was investigated using an information-theoretic approach. Listeners were asked to identify eleven different consonants spoken in a CV[l] syllable context (where C refers to the initial consonant, V refers to one of three vowels, [I, a, u], and [l] ...... of information-theoretic analysis can be used to delineate those parts of the speech signal of greatest importance for encoding phonetic features associated with intelligibility and speech understanding....

  9. Percutaneous high-frequency selective rhizotomy in the trigeminal neuralgia therapy in multiple sclerosis

    Directory of Open Access Journals (Sweden)

    V. M. Tyurnikov

    2012-01-01

    Full Text Available Trigeminal neuralgia is a rare symptom of multiple sclerosis affecting the disability. Multiple sclerosis related trigeminal neuralgia has been attributed to a demyelinating lesion in the pons. When the adequate pain drug-relieve therapy is not possible or when the patient becomes refractory to the treatment or can not continue pharmacological treatment because of the side effects, surgical intervention, including percutaneous radiofrequency rhizotomy is being discussed. Literature review and the data upon the efficiency and safety of this neurosurgical treatment in 16 patients with multiple sclerosis have been analyzed. Percutaneous radiofrequency rhizotomy has been proved to be a safe, reproducible and effective method of the symptomatic surgical treatment of trigeminal neuralgia in patients with multiple sclerosis in cases of the intolerance/inefficiency of the pharmacological therapy.

  10. Frequency Selective Filtering of the Modulation Spectrum and its Impact on Consonant Identification

    DEFF Research Database (Denmark)

    Christiansen, Thomas Ulrich; Greenberg, Steven

    2005-01-01

    The spectro-temporal coding of Danish consonants was investigated using an information-theoretic approach. Listeners were asked to identify eleven different consonants spoken in a CV[l] syllable context (where C refers to the initial consonant, V refers to one of three vowels, [I, a, u], and [l] ....... In addition, the analysis provides a means to associate specific portions of the modulation spectrum with phonetic feature properties. Such analyses indicate that: (1) Accurate, robust decoding of place-of-articulation information requires broadband cross-spectral integration (2) Place......-of-articulation information is associated most closely with the modulation spectrum above 6 Hz, with the most significant contribution coming from the region above 12 Hz. (3) Place-of-articulation information is crucial for accurate consonant recognition. Hence, consonant decoding requires cross-spectral integration...

  11. Online Optimal Switching Frequency Selection for Grid-Connected Voltage Source Inverters

    Directory of Open Access Journals (Sweden)

    Saher Albatran

    2017-12-01

    Full Text Available Enhancing the performance of the voltage source inverters (VSIs without changing the hardware structure has recently acquired an increased amount of interest. In this study, an optimization algorithm, enhancing the quality of the output power and the efficiency of three-phase grid connected VSIs is proposed. Towards that end, the proposed algorithm varies the switching frequency (fsw to maintain the best balance between switching losses of the insulated-gate-bipolar-transistor (IGBT power module as well as the output power quality under all loading conditions, including the ambient temperature effect. Since there is a contradiction with these two measures in relation to the switching frequency, the theory of multi-objective optimization is employed. The proposed algorithm is executed on the platform of Altera® DE2-115 field-programmable-gate-array (FPGA in which the optimal value of the switching frequency is determined online without the need for heavy offline calculations and/or lookup tables. With adopting the proposed algorithm, there is an improvement in the VSI efficiency without degrading the output power quality. Therefore, the proposed algorithm enhances the lifetime of the IGBT power module because of reduced variations in the module’s junction temperature. An experimental prototype is built, and experimental tests are conducted for the verification of the viability of the proposed algorithm.

  12. Performance Analysis of OFDM in Frequency Selective, Slowly Fading Nakagami Channels

    National Research Council Canada - National Science Library

    Count, Patrick

    2001-01-01

    ...) as the modulation technique of choice. Given the incredible growth in the industry as manifest by the seemingly infinite demand for wireless products and services and the accompanying need for superior performance of these systems...

  13. A 31 GHz Survey of Low-Frequency Selected Radio Sources

    Science.gov (United States)

    Mason, B. S.; Weintraub, L.; Sievers, J.; Bond, J. R.; Myers, S. T.; Pearson, T. J.; Readhead, A. C. S.; Shepherd, M. C.

    2009-10-01

    The 100 m Robert C. Byrd Green Bank Telescope and the 40 m Owens Valley Radio Observatory telescope have been used to conduct a 31 GHz survey of 3165 known extragalactic radio sources over 143 deg2 of the sky. Target sources were selected from the NRAO VLA Sky Survey in fields observed by the Cosmic Background Imager (CBI); most are extragalactic active galactic nuclei (AGNs) with 1.4 GHz flux densities of 3-10 mJy. The resulting 31 GHz catalogs are presented in full online. Using a maximum-likelihood analysis to obtain an unbiased estimate of the distribution of the 1.4-31 GHz spectral indices of these sources, we find a mean 31-1.4 GHz flux ratio of 0.110 ± 0.003 corresponding to a spectral index of α = -0.71 ± 0.01 (S ν vprop να) 9.0% ± 0.8% of sources have α > - 0.5 and 1.2% ± 0.2% have α > 0. By combining this spectral-index distribution with 1.4 GHz source counts, we predict 31 GHz source counts in the range 1 mJy S 31) = (16.7 ± 1.7) deg-2(S 31/1 mJy)-0.80±0.07. We also assess the contribution of mJy-level (S 1.4 GHz < 3.4 mJy) radio sources to the 31 GHz cosmic microwave background power spectrum, finding a mean power of ell(ell + 1)C src ell/(2π) = 44 ± 14 μK2 and a 95% upper limit of 80 μK2 at ell = 2500. Including an estimated contribution of 12 μK2 from the population of sources responsible for the turn-up in counts below S 1.4 GHz = 1 mJy, this amounts to 21% ± 7% of what is needed to explain the CBI high-ell excess signal, 275 ± 63 μK2. These results are consistent with other measurements of the 31 GHz point-source foreground.

  14. Design, Development, and Testing of a Network Frequency Selection Service (NFSS)

    Science.gov (United States)

    1994-02-14

    mercial simulation software (Sim++), word processor ( FrameMaker ), editor (Gnu Emacs), software ver- sion control (Revision Control System (RCS)), system...of FrameMaker ".mif" files. When viewed using FrameMaker or a PostScript reader, each page of results appears as two columns by four rows of graphics

  15. Autonomous generator based on Ni-Mn-Ga microactuator as a frequency selective element

    Directory of Open Access Journals (Sweden)

    Barandiaran J.M.

    2013-01-01

    Full Text Available In this work, we suggest the temperature-induced resistivity change at the martensitic transformation in the Ni-Mn-Ga ferromagnetic shape memory alloy as a driving mechanism enabling periodic signal generation. We demonstrated its practical importance by a design of the prototype of a low-frequency autonomous generator. A prominent feature of this new generator is a control of its frequency by the external magnetic field.

  16. Effects of cochlear compression and frequency selectivity on pitch discrimination of complex tones with unresolved harmonics

    DEFF Research Database (Denmark)

    Bianchi, Federica; Fereczkowski, Michal; Zaar, Johannes

    2015-01-01

    Physiological studies have shown that noise-induced sensorineural hearing loss (SNHL) enhances the amplitude of envelope coding in auditory-nerve fibers. As pitch coding of unresolved complex tones is assumed to rely on temporal envelope coding mechanisms, this study investigated...... for the RP condition. Overall, these findings suggest that both reduced cochlear compression and auditory filter broadening alter the envelope representation of unresolved complex tones, leading to changes in pitch-discrimination performance....... pitchdiscrimination performance in listeners with SNHL. Pitch-discrimination thresholds were obtained in 14 normal-hearing (NH) and 10 hearingimpaired (HI) listeners for sine-phase (SP) and random-phase (RP) unresolved complex tones. The HI listeners performed, on average, similarly as the NH listeners in the SP...

  17. Noise-based frequency offset modulation in wideband frequency-selective fading channels

    NARCIS (Netherlands)

    Meijerink, Arjan; Cotton, S.L.; Bentum, Marinus Jan; Scanlon, W.G.

    2009-01-01

    A frequency offset modulation scheme using wideband noise carriers is considered. The main advantage of such a scheme is that it enables fast receiver synchronization without channel adaptation, while providing robustness to multipath fading and in-band interference. This is important for low-power

  18. Hyper-spectral frequency selection for the classification of vegetation diseases

    OpenAIRE

    Dijkstra, Klaas; van de Loosdrecht, Jaap; Schomaker, Lambert; Wiering, Marco

    2017-01-01

    Reducing the use of pesticides by early visual detection of diseases in precision agriculture is important. Because of the color similarity between potato-plant diseases, narrow band hyper-spectral imaging is required. Payload constraints on unmanned aerial vehicles require reduc- tion of spectral bands. Therefore, we present a methodology for per-patch classification combined with hyper-spectral band selection. In controlled experiments performed on a set of individual leaves, we measure the...

  19. Least-squares reverse time migration of marine data with frequency-selection encoding

    KAUST Repository

    Dai, Wei; Huang, Yunsong; Schuster, Gerard T.

    2013-01-01

    The phase-encoding technique can sometimes increase the efficiency of the least-squares reverse time migration (LSRTM) by more than one order of magnitude. However, traditional random encoding functions require all the encoded shots to share

  20. Performance Analysis of OFDM in Frequency Selective, Slowly Fading Nakagami Channels

    National Research Council Canada - National Science Library

    Count, Patrick

    2001-01-01

    In an effort to offer faster, more reliable wireless communications services to the public, many wireless standardization committees have, in recent years, adopted Orthogonal Frequency Division Multiplexing (OFDM...

  1. Predicting the effect of relaxation during frequency-selective adiabatic pulses

    Science.gov (United States)

    Pfaff, Annalise R.; McKee, Cailyn E.; Woelk, Klaus

    2017-11-01

    Adiabatic half and full passages are invaluable for achieving uniform, B1-insensitive excitation or inversion of macroscopic magnetization across a well-defined range of NMR frequencies. To accomplish narrow frequency ranges with adiabatic pulses (computer-calculated data with experimental results demonstrates that, in non-viscous, small-molecule fluids, it is possible to model magnetization and relaxation by considering standard T1 and T2 relaxation in the traditional rotating frame. The proposed model is aimed at performance optimizations of applications in which these pulses are employed. It differs from previous reports which focused on short high-power adiabatic pulses and relaxation that is governed by dipole-dipole interactions, cross polarization, or chemical exchange.

  2. Tuning In to Sound: Frequency-Selective Attentional Filter in Human Primary Auditory Cortex

    Science.gov (United States)

    Da Costa, Sandra; van der Zwaag, Wietske; Miller, Lee M.; Clarke, Stephanie

    2013-01-01

    Cocktail parties, busy streets, and other noisy environments pose a difficult challenge to the auditory system: how to focus attention on selected sounds while ignoring others? Neurons of primary auditory cortex, many of which are sharply tuned to sound frequency, could help solve this problem by filtering selected sound information based on frequency-content. To investigate whether this occurs, we used high-resolution fMRI at 7 tesla to map the fine-scale frequency-tuning (1.5 mm isotropic resolution) of primary auditory areas A1 and R in six human participants. Then, in a selective attention experiment, participants heard low (250 Hz)- and high (4000 Hz)-frequency streams of tones presented at the same time (dual-stream) and were instructed to focus attention onto one stream versus the other, switching back and forth every 30 s. Attention to low-frequency tones enhanced neural responses within low-frequency-tuned voxels relative to high, and when attention switched the pattern quickly reversed. Thus, like a radio, human primary auditory cortex is able to tune into attended frequency channels and can switch channels on demand. PMID:23365225

  3. The Quasar Fraction in Low-Frequency Selected Complete Samples and Implications for Unified Schemes

    Science.gov (United States)

    Willott, Chris J.; Rawlings, Steve; Blundell, Katherine M.; Lacy, Mark

    2000-01-01

    Low-frequency radio surveys are ideal for selecting orientation-independent samples of extragalactic sources because the sample members are selected by virtue of their isotropic steep-spectrum extended emission. We use the new 7C Redshift Survey along with the brighter 3CRR and 6C samples to investigate the fraction of objects with observed broad emission lines - the 'quasar fraction' - as a function of redshift and of radio and narrow emission line luminosity. We find that the quasar fraction is more strongly dependent upon luminosity (both narrow line and radio) than it is on redshift. Above a narrow [OII] emission line luminosity of log(base 10) (L(sub [OII])/W) approximately > 35 [or radio luminosity log(base 10) (L(sub 151)/ W/Hz.sr) approximately > 26.5], the quasar fraction is virtually independent of redshift and luminosity; this is consistent with a simple unified scheme with an obscuring torus with a half-opening angle theta(sub trans) approximately equal 53 deg. For objects with less luminous narrow lines, the quasar fraction is lower. We show that this is not due to the difficulty of detecting lower-luminosity broad emission lines in a less luminous, but otherwise similar, quasar population. We discuss evidence which supports at least two probable physical causes for the drop in quasar fraction at low luminosity: (i) a gradual decrease in theta(sub trans) and/or a gradual increase in the fraction of lightly-reddened (0 approximately quasar luminosity; and (ii) the emergence of a distinct second population of low luminosity radio sources which, like M8T, lack a well-fed quasar nucleus and may well lack a thick obscuring torus.

  4. Frequency Selection for Multi-frequency Acoustic Measurement of Suspended Sediment

    Science.gov (United States)

    Chen, X.; HO, H.; Fu, X.

    2017-12-01

    Multi-frequency acoustic measurement of suspended sediment has found successful applications in marine and fluvial environments. Difficult challenges remain in regard to improving its effectiveness and efficiency when applied to high concentrations and wide size distributions in rivers. We performed a multi-frequency acoustic scattering experiment in a cylindrical tank with a suspension of natural sands. The sands range from 50 to 600 μm in diameter with a lognormal size distribution. The bulk concentration of suspended sediment varied from 1.0 to 12.0 g/L. We found that the commonly used linear relationship between the intensity of acoustic backscatter and suspended sediment concentration holds only at sufficiently low concentrations, for instance below 3.0 g/L. It fails at a critical value of concentration that depends on measurement frequency and the distance between the transducer and the target point. Instead, an exponential relationship was found to work satisfactorily throughout the entire range of concentration. The coefficient and exponent of the exponential function changed, however, with the measuring frequency and distance. Considering the increased complexity of inverting the concentration values when an exponential relationship prevails, we further analyzed the relationship between measurement error and measuring frequency. It was also found that the inversion error may be effectively controlled within 5% if the frequency is properly set. Compared with concentration, grain size was found to heavily affect the selection of optimum frequency. A regression relationship for optimum frequency versus grain size was developed based on the experimental results.

  5. Relation between derived-band auditory brainstem response latencies and behavioral frequency selectivity

    DEFF Research Database (Denmark)

    Strelcyk, Olaf; Christoforidis, Dimitrios; Dau, Torsten

    2009-01-01

    response times. For the same listeners, auditory-filter bandwidths at 2 kHz were estimated using a behavioral notched-noise masking paradigm. Generally, shorter derived-band latencies were observed for the HI than for the NH listeners. Only at low click sensation levels, prolonged latencies were obtained...

  6. Frequency-Selective Signal Sensing with Sub-Nyquist Uniform Sampling Scheme

    DEFF Research Database (Denmark)

    Pierzchlewski, Jacek; Arildsen, Thomas

    2015-01-01

    In this paper the authors discuss a problem of acquisition and reconstruction of a signal polluted by adjacent- channel interference. The authors propose a method to find a sub-Nyquist uniform sampling pattern which allows for correct reconstruction of selected frequencies. The method is inspired...... by the Restricted Isometry Property, which is known from the field of compressed sensing. Then, compressed sensing is used to successfully reconstruct a wanted signal even if some of the uniform samples were randomly lost, e. g. due to ADC saturation. An experiment which tests the proposed method in practice...

  7. Least-squares Migration and Full Waveform Inversion with Multisource Frequency Selection

    KAUST Repository

    Huang, Yunsong

    2013-01-01

    , with the same advantages of computational efficiency and storage savings. In the Finite-Difference Time-Domain (FDTD) method, to mitigate spectral leakage due to delayed onsets of sine waves detected at receivers, I double the simulation time and retain only

  8. Crack recognition on vertical rotors by means of frequency selective vibration monitoring

    International Nuclear Information System (INIS)

    Nink, A.; Stoelben, H.

    1990-01-01

    Shaft cracks on primary coolant pumps in pressurized water reactors have led to intensive vibration monitoring, in particular of vertically arranged rotors. However, the interpretation of shaft vibrations with respect to crack recognition proved to be very difficult. Appropriate experimental approaches resulted in an improved interpretation base. The article describes both the problems related to primary coolant pumps and first experimental experience gained from tests on a pre-cracked vertical rotor. Differential vectors of rotational speed harmonics provide an optimum description of the effect of a crack on shaft vibration. Diagnostics can be supported by observing the vectors, while purposefully changing axial loads. (orig.) [de

  9. Radio frequency selective addressing of localized atoms in a periodic potential

    International Nuclear Information System (INIS)

    Ott, H.; De Mirandes, E.; Ferlaino, F.; Roati, G.; Tuerck, V.; Modugno, G.; Inguscio, M.

    2004-01-01

    We study the localization and addressability of ultracold atoms in a combined parabolic and periodic potential. Such a potential supports the existence of localized stationary states and we show that applying a radio frequency field allows us to selectively address atoms in these states. This method is used to measure the energy and momentum distribution of the atoms in the localized states. We also discuss possible extensions of this scheme to address and manipulate atoms in single lattice sites

  10. The evolutionary sequence: origin and emergences

    Science.gov (United States)

    Fox, S. W.

    1986-01-01

    The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects.

  11. The computational linguistics of biological sequences

    Energy Technology Data Exchange (ETDEWEB)

    Searls, D. [Univ. of Pennsylvania, Philadelphia, PA (United States)

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Protein sequences are analogous in many respects, particularly their folding behavior. Proteins have a much richer variety of interactions, but in theory the same linguistic principles could come to bear in describing dependencies between distant residues that arise by virtue of three-dimensional structure. This tutorial will concentrate on nucleic acid sequences.

  12. Applications of High Throughput Nucleotide Sequencing

    DEFF Research Database (Denmark)

    Waage, Johannes Eichler

    equally large demands in data handling, analysis and interpretation, perhaps defining the modern challenge of the computational biologist of the post-genomic era. The first part of this thesis consists of a general introduction to the history, common terms and challenges of next generation sequencing......-sequencing, a study of the effects on alternative RNA splicing of KO of the nonsense mediated RNA decay system in Mus, using digital gene expression and a custom-built exon-exon junction mapping pipeline is presented (article I). Evolved from this work, a Bioconductor package, spliceR, for classifying alternative...

  13. Digital image sequence processing, compression, and analysis

    CERN Document Server

    Reed, Todd R

    2004-01-01

    IntroductionTodd R. ReedCONTENT-BASED IMAGE SEQUENCE REPRESENTATIONPedro M. Q. Aguiar, Radu S. Jasinschi, José M. F. Moura, andCharnchai PluempitiwiriyawejTHE COMPUTATION OF MOTIONChristoph Stiller, Sören Kammel, Jan Horn, and Thao DangMOTION ANALYSIS AND DISPLACEMENT ESTIMATION IN THE FREQUENCY DOMAINLuca Lucchese and Guido Maria CortelazzoQUALITY OF SERVICE ASSESSMENT IN NEW GENERATION WIRELESS VIDEO COMMUNICATIONSGaetano GiuntaERROR CONCEALMENT IN DIGITAL VIDEOFrancesco G.B. De NataleIMAGE SEQUENCE RESTORATION: A WIDER PERSPECTIVEAnil KokaramVIDEO SUMMARIZATIONCuneyt M. Taskiran and Edward

  14. Output-Sensitive Pattern Extraction in Sequences

    DEFF Research Database (Denmark)

    Grossi, Roberto; Menconi, Giulia; Pisanti, Nadia

    2014-01-01

    Genomic Analysis, Plagiarism Detection, Data Mining, Intrusion Detection, Spam Fighting and Time Series Analysis are just some examples of applications where extraction of recurring patterns in sequences of objects is one of the main computational challenges. Several notions of patterns exist...... or extend them causes a loss of significant information (where the number of occurrences changes). Output-sensitive algorithms have been proposed to enumerate and list these patterns, taking polynomial time O(nc) per pattern for constant c > 1, which is impractical for massive sequences of very large length...

  15. Value of a newly sequenced bacterial genome

    DEFF Research Database (Denmark)

    Barbosa, Eudes; Aburjaile, Flavia F; Ramos, Rommel Tj

    2014-01-01

    and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses...... heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting...

  16. Simulating efficiently the evolution of DNA sequences.

    Science.gov (United States)

    Schöniger, M; von Haeseler, A

    1995-02-01

    Two menu-driven FORTRAN programs are described that simulate the evolution of DNA sequences in accordance with a user-specified model. This general stochastic model allows for an arbitrary stationary nucleotide composition and any transition-transversion bias during the process of base substitution. In addition, the user may define any hypothetical model tree according to which a family of sequences evolves. The programs suggest the computationally most inexpensive approach to generate nucleotide substitutions. Either reproducible or non-repeatable simulations, depending on the method of initializing the pseudo-random number generator, can be performed. The corresponding options are offered by the interface menu.

  17. Final sonorant sequences in the Celje dialect

    Directory of Open Access Journals (Sweden)

    Alja Ferme

    2006-12-01

    Full Text Available In this paper I will analyse final sonorant sequencesin the Celje variety of Slovene. In §2 various definitions of a consonant cluster will be discussed and the definition needed for further development ofthe article will be provided. In §3 I will present pretheoretical arguments against treating all final sonorant sequences as consonant clusters. In addition, a seemingly special behaviour of a small group of sequences will be pointed out. The government phonology framework will be introduced in §4. In §5 the hin the given theoretical framework.

  18. Bordism, stable homotopy and adams spectral sequences

    CERN Document Server

    Kochman, Stanley O

    1996-01-01

    This book is a compilation of lecture notes that were prepared for the graduate course "Adams Spectral Sequences and Stable Homotopy Theory" given at The Fields Institute during the fall of 1995. The aim of this volume is to prepare students with a knowledge of elementary algebraic topology to study recent developments in stable homotopy theory, such as the nilpotence and periodicity theorems. Suitable as a text for an intermediate course in algebraic topology, this book provides a direct exposition of the basic concepts of bordism, characteristic classes, Adams spectral sequences, Brown-Peter

  19. Complete genome sequence of Ikoma lyssavirus.

    Science.gov (United States)

    Marston, Denise A; Ellis, Richard J; Horton, Daniel L; Kuzmin, Ivan V; Wise, Emma L; McElhinney, Lorraine M; Banyard, Ashley C; Ngeleja, Chanasa; Keyyu, Julius; Cleaveland, Sarah; Lembo, Tiziana; Rupprecht, Charles E; Fooks, Anthony R

    2012-09-01

    Lyssaviruses (family Rhabdoviridae) constitute one of the most important groups of viral zoonoses globally. All lyssaviruses cause the disease rabies, an acute progressive encephalitis for which, once symptoms occur, there is no effective cure. Currently available vaccines are highly protective against the predominantly circulating lyssavirus species. Using next-generation sequencing technologies, we have obtained the whole-genome sequence for a novel lyssavirus, Ikoma lyssavirus (IKOV), isolated from an African civet in Tanzania displaying clinical signs of rabies. Genetically, this virus is the most divergent within the genus Lyssavirus. Characterization of the genome will help to improve our understanding of lyssavirus diversity and enable investigation into vaccine-induced immunity and protection.

  20. Lacunary ideal convergence of multiple sequences

    Directory of Open Access Journals (Sweden)

    Bipan Hazarika

    2016-01-01

    Full Text Available An ideal I is a family of subsets of N×N which is closed under taking finite unions and subsets of its elements. In this article, the concept of lacunary ideal convergence of double sequences has been introduced. Also the relation between lacunary ideal convergent and lacunary Cauchy double sequences has been established. Furthermore, the notions of lacunary ideal limit point and lacunary ideal cluster points have been introduced and find the relation between these two notions. Finally, we have studied the properties such as solidity, monotonic.