Dual Sequence Research Articles

An Out-of-frame Overlapping Reading Frame in the Ataxin-1 Coding Sequence Encodes a Novel Ataxin-1 Interacting Protein

Spinocerebellar ataxia type 1 is an autosomal dominant cerebellar ataxia associated with the expansion of a polyglutamine tract within the ataxin-1 (ATXN1) protein. Recent studies suggest that understanding the normal function of ATXN1 in cellular processes is essential to decipher the pathogenesis mechanisms in spinocerebellar ataxia type 1. We found an alternative translation initiation ATG codon in the +3 reading frame of human ATXN1 starting 30 nucleotides downstream of the initiation codon for ATXN1 and ending at nucleotide 587. This novel overlapping open reading frame (ORF) encodes a 21-kDa polypeptide termed Alt-ATXN1 (Alternative ATXN1) with a completely different amino acid sequence from ATXN1. We introduced a hemagglutinin tag in-frame with Alt-ATXN1 in ATXN1 cDNA and showed in cell culture the co-expression of both ATXN1 and Alt-ATXN1. Remarkably, Alt-ATXN1 colocalized and interacted with ATXN1 in nuclear inclusions. In contrast, in the absence of ATXN1 expression, Alt-ATXN1 displays a homogenous nucleoplasmic distribution. Alt-ATXN1 interacts with poly(A)(+) RNA, and its nuclear localization is dependent on RNA transcription. Polyclonal antibodies raised against Alt-ATXN1 confirmed the expression of Alt-ATXN1 in human cerebellum expressing ATXN1. These results demonstrate that human ATXN1 gene is a dual coding sequence and that ATXN1 interacts with and controls the subcellular distribution of Alt-ATXN1.

Assessment of cardiac volumes using an isotropic whole‐heart dual cardiac phase sequence in pediatric patients

To evaluate the accuracy of a three-dimensional dual phase (3D DP) whole-heart technique for cardiac volumetric assessment in pediatric patients with cardiac abnormalities. The institutional approved this study, and informed consent was obtained from patients or their guardians. This prospective study involved 31 pediatric patients (mean age, 7.9 years; range, 15 days to 15 years) for the assessment of cardiac abnormalities using cardiovascular MR. A standard protocol was performed for assessing cardiac anatomy and function. For evaluating the 3D DP technique, statistical comparison with a 2D cine multi-slice technique (2D steady-state free-precession [SSFP]) was performed using linear regression, intraclass correlation coefficient, and Bland Altman plots. Left (LV) and right (RV) ventricular cardiac volumes obtained with the 3D DP technique were in strong agreement with those obtained with the 2D SSFP technique for small and large ventricular volumes. The intraclass correlation coefficients (ICC) between both techniques were 0.992 for the LV end-diastolic volume (EDV), 0.983 for the LV end-systolic volume (ESV), 0.952 for the LV-systolic volume (SV), 0.992 for the RV-EDV, 0.992 for the RV-ESV, 0.928 for the RV-SV. Interobserver analysis indicated good reproducibility for both the 2D SSFP and the 3D DP techniques. The 3D DP technique provides as accurate cardiac volumes as the 2D SSFP technique in the pediatric population, but with the added benefits of easier data acquisition and detailed anatomical information of the whole heart and great vessels in a single free-breathing scan.

Feasibility of MR perfusion-weighted imaging by use of a time-spatial labeling inversion pulse

Perfusion-weighted imaging (PWI) by use of arterial spin labeling (ASL) has been introduced to the clinical setting. However, it is not widely available because it requires specialized pulse sequences. Imaging using a time-spatial labeling inversion pulse (time-SLIP), which is a magnetic resonance angiography (MRA) technique that is based on ASL, can be used in various situations. In this study, we examined the feasibility of time-SLIP PWI. Two types of time-SLIP sequences were evaluated: (1) a single inversion recovery (IR) pulse sequence, which is the same as that used in conventional time-SLIP MRA except for the timing of data acquisition, and (2) a dual IR pulse sequence, where a second, non-selective, IR pulse was added during the inflow time to suppress background signals. Subtraction processing is performed between the "on" and "off" settings of the first IR pulse (time-SLIP tag) to obtain PWI. The average signal intensity was measured in a uniform phantom as the residual of the background, and in five healthy subjects as the perfusion signal. The average signal-to-noise ratio (SNR) was also measured in the five subjects. All imaging was performed with a 1.5-T MR scanner. Images using the dual IR method showed lower background signals and higher perfusion signals compared with images using the single IR method. However, the SNR was lower in images with the dual IR method. These results demonstrate that a time-SLIP, which is an MRA method, can be used for obtaining cerebral PWI simply by adjusting the imaging parameters.

Simulation tool for the prediction of compound dependence of CW-photoacoustic-based sensor using dual optical excitation

Towards the development of a sensor dedicated to noninvasive and continuous blood glucose level monitoring, we developed a protocol called optical power balance shift (OPBS) based on a continuous-wave photoacoustic technique using a dual wavelength excitation sequence. In order to optimize the sensor response, we showed, using an analytical model, that the OPBS response depends exclusively on the absorption coefficients at the two wavelengths. Then, using a standard near-infrared spectrophotometer, we measured the absorption coefficient of water as well as the fractional absorption coefficient relative to glucose and albumin concentrations and temperature. We then plotted the OPBS-based sensor response for the three aforementioned parameters covering all the possible combinations of the two wavelengths from 1300 to 2500nm. Despite overall similar tendencies, the responses exhibit highs and lows at optical pairs specific to each compound, which allow potential improvement of measurement specificity to one compound in particular by choosing the appropriate pair of optical wavelengths. The good agreement between the model and experimental results for the 1610/1382-nm combination validates the approach.

Abstract LB-68: Identification of circulating HPV DNA in urine with a dual sequence capture approach.

Abstract HPV testing is increasingly used for cervical cancer screening in conjunction with cervical cytology. Privacy, cultural, and infrastructure issues challenge the effective implementation of HPV testing in cervical cancer screening. The detection of circulating HPV DNA from urine can be useful for cervical cancer screening. We captured and sequenced the HPV genome after isolating HPV Transrenal DNA (HPV-TrDNA) and then developed a qPCR-based HPV-TrDNA assay to quantify high risk HPV TrDNA. HPV TrDNA molecules are relatively short, fragmented, pieces of circulating DNA (less than 250 nucleotides) that get filtered by the kidneys and can be isolated from urine. Methods: We adsorbed cell-free nucelic acids from urine samples (10mL) of 41 women with 23 LGL and 18 HGL cervical lesions and 31 women with normal cytology on a Q-Sepharose resin followed by a silica-based method. A custom-designed pool of HPV-specific dual sequence capture probes was used for library amplification and target selection (Roche/NimbleGen SeqCap EZ Choice Library). A pre-capture amplification of the library was performed with ligation-mediated PCR (LM-PCR) using primers complementary to the adaptors, followed by two rounds of hybridization to the HPV-specific SeqCap EZ Choice Library. Amplified captured DNA from HPV infected cell lines, HeLa (HPV 18), CSCC7 (HPV16), and HPV TrDNA samples from premalignant cervical lesions were processed for multiplexed sequencing on the GS Junior system (Roche). Following completion of the pyrosequencing run, signal processing was performed, followed by detailed analyses. For the SYBR green qPCR assay we amplified an HPV E1 region common to thirteen high-risk HPV types for cervical cancer. Results: We isolated TrDNA from 10mL of urine samples. The mean concentration, total amount, and 260/280 ratio of isolated TrDNA was 34.2 ng/ul;1ug and 1.7 for premalignant samples and 17.2 ng/ul; 0.5ug; and 1.4 for normal samples. The total number of Pass Filter sequence reads was 100,428, the total number of bases over 41 million and the read length average was 130.3 bp. Most reads (91.63%) mapped to the reference HPV sequences, with the total number of mapped base pairs over 36 million (88%). The number of fully mapped reads was 14,899 (14.84%), and the number of partially mapped reads was 70,686 (88.17%). The average coverage of reference sequences was 78% for HPV 18 in the CSCC7 DNA, 86% for HPV 16 in HeLa DNA, as well as, 100% for HPV 18 and 96% for HPV 16 in TrDNA samples. The average Ct value for Pre-Capture LM-PCR DNAs was 35.74. The average Ct value for Post-Capture LM-PCR DNAs was 19.73; therefore the Delta Ct value was 16.01. Based on an estimated efficiency for the assay, the approximate fold enrichment was greater than 12,000. Conclusions: We demonstrated that the HPV genome can be assembled from HPV TrDNA. We are also the first to show that circulating high risk HPV TrDNA can be quantified using SYBR green qPCR assay after dual sequence capture of the HPV genome. Citation Format: Rafael E. Guerrero-Preston, Anne Jedlicka, Teresa Diaz-Montes, Josefina Romaguera, Juan C. Roa, David Sidransky. Identification of circulating HPV DNA in urine with a dual sequence capture approach. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-68. doi:10.1158/1538-7445.AM2013-LB-68

Accurate quantitative myocardial perfusion using single cycle T1 mapping

Background Quantitative myocardial perfusion MRI depends on accurate determination of the arterial input function (AIF). Unfortunately, typical doses of contrast agent (CA) cause saturation in the AIF signal intensity at peak CA concentrations. Methods using dual boluses [1] or dual sequences [2] have been proposed to correct for this effect; however, they require additional data acquisition which complicates the imaging procedure. CA concentrations can be directly found by calculating blood and myocardial T1 values [3,4]. This method was performed in vivo and compared to the dual sequence method [2]. Methods Radial AIF correction was performed using the method described in [4]. T1 relaxation following an SR magnetization preparation and FLASH acquisition can be modeled [3]. By acquiring multiple images after a single SR and using the acquisition parameters, pixelwise T1 can be found by solving a simple non-linear data fitting exercise. Gd concentration is found using the known relaxivity of Gd CA [6]. Ten healthy volunteers underwent perfusion MRI studies on a Siemens 3T Verio system with IRB approval and written consent. Two first pass perfusion scans were

Estimation of Perilymph Enhancement after Intratympanic Administration of Gd-DTPA by Fast T1-mapping with a Dual Flip Angle 3D Spoiled Gradient Echo Sequence

Eleven patients with suspected Ménière's disease received intratympanic (IT) administration of gadolinium (gadopentetate dimeglumine; Gd) prior to acquisition of 3-dimensional (3D) fluid-attenuated inversion recovery (FLAIR), 3D real inversion recovery (IR), and fast T₁ mapping by dual flip angle 3D gradient echo (FT₁-map) imaging sequences to evaluate the degree of perilymph enhancement. Though 3-dimensional FLAIR could detect lower concentrations of gadolinium than 3D real IR, in 2 patients, poor enhancement still prevented visualization of the endolymphatic space using 3D FLAIR. We could predict poor contrast enhancement in these 2 patients using the FT₁-map technique.

Feasibility of MRI attenuation correction in cardiac FDG-PET

Background Simultaneous acquisition PET-MRI is a new technology that has the potential to significantly impact diagnostic patient care. Cardiac imaging using PET-MRI offers high signal resolution MRI images superimposed on PET metabolic functional assessment. Specifically, 18Ffluorodeoxyglucose (FDG) PET-MR has the potential to provide both anatomic scar tissue evaluation and information regarding myocardial glucose metabolism. While early brain and soft tissue data have demonstrated that PET specific uptake values (SUVs) obtained using MRI for attenuation correction (AC) are comparable to SUVs obtained using CT AC, SUV measurements of myocardial tissue have not been compared. The objective of this pilot study is to determine the reproducibility of SUVs obtained by PET imaging using an AC µ-map comprised of a dual echo VIBE Dixon MRI sequence instead of CT. Methods

An Inexact Modified Subgradient Algorithm for Primal-Dual Problems via Augmented Lagrangians

We consider a primal optimization problem in a reflexive Banach space and a duality scheme via generalized augmented Lagrangians. For solving the dual problem (in a Hilbert space), we introduce and analyze a new parameterized Inexact Modified Subgradient (IMSg) algorithm. The IMSg generates a primal-dual sequence, and we focus on two simple new choices of the stepsize. We prove that every weak accumulation point of the primal sequence is a primal solution and the dual sequence converges weakly to a dual solution, as long as the dual optimal set is nonempty. Moreover, we establish primal convergence even when the dual optimal set is empty. Our second choice of the stepsize gives rise to a variant of IMSg which has finite termination.

Generation of attenuation map for MR-based attenuation correction of PET data in the head area employing 3D short echo time MR imaging

Attenuation correction is a crucial step to get accurate quantification of Positron Emission Tomography (PET) data. An attenuation map to provide attenuation coefficients at 511keV can be generated using Magnetic Resonance Images (MRI). One of the main steps involved in MR-based attenuation correction (MRAC) of PET data is to separate bone from air. Low signal intensity of bone in conventional MRI makes it difficult to separate bone from air in the head area, while their attenuation coefficients are very different. In literature, several groups proposed ultrashort echo-time (UTE) sequences to differentiate bone from air [4,5,7], because these sequences are capable of imaging tissues with short T2⁎ relaxation time, such as cortical bone; however, they are difficult to use, expensive and time-consuming. Employing short echo-time (STE) MRI in combination with long echo-time (LTE) MRI, and along with high performance image processing algorithms is a good substitute for UTE-based PET attenuation correction; they are widely available, easy to use, inexpensive and much faster than UTE pulse sequences. In this work, we propose the use of STE sequences along with LTE ones, as well as a dedicated image processing method to differentiate bone from air cavities in the head area by creating contrast between the tissues. Attenuation coefficients at 511kev, relying on literature [5], will then be assigned to the voxels. Acquisition was performed on a clinical 3T Tim Trio scanner (Siemens Medical Solution, Erlangen, Germany), employing a dual echo sequence. To achieve an optimized protocol with the best result for discrimination of bone and air, two types of acquisitions were performed, with and without fat suppression; the acquisition parameters were as follows: TE=1.21/5ms, TR=5/17, FA=30, and TE=1.12/3.16ms, TR=5/5, FA=12 for non-fat-suppressed and fat-suppressed protocol, respectively. Contrast enhancement and tissue segmentation were applied as processing steps, to successfully classify voxels into bone, air and soft tissue classes, yielding accuracy, sensitivity and specificity of 88%, 77% and 94%, for non-fat suppressed acquisition, respectively. This method could potentially be as an efficient method for generation of attenuation map in 511keV for MR-based attenuation correction of PET data in clinical PET/MR applications with mixed air and bone signals.

Part 1

Development of a dual-tuned proton/sodium radiofrequency (RF) coil for magnetic resonance imaging (MRI) of the rabbit spine and quantification of sodium concentration in intervertebral discs. To develop the dual-tuned proton/sodium MRI of rabbit lumbar spine to investigate proteoglycan matrix content and intervertebral disc degeneration (IDD). IDD is a common chronic condition that may lead to back pain, limited activity, and disability. Early-stage IDD involves the loss of proteoglycan matrix and water content in the disc. Sodium MRI is a promising noninvasive technique for quantitative measurement of proteoglycan changes associated with IDD. The combined structural (proton) and biochemical (sodium) MRI facilitates the investigation of morphological and molecular changes associated with degeneration of discs. Multichannel dual-tuned proton/sodium transceiver RF coil of the rabbit spine was developed and optimized at 3T human scanner-8 channels allocated for the sodium coil and 4 channels for the proton coil. High-resolution anatomy proton images of the discs were acquired using turbo spin echo and dual echo steady state sequence. Sodium concentration of the discs was quantified from sodium magnetic resonance (MR) images that were calibrated for signal attenuation because of RF field inhomogeneity, sodium MR relaxation times, and disc thickness. Twelve rabbits (~1-yr old, female, 5.2 ± 0.4 kg) were used for measuring disc sodium concentration. High-resolution in vivo proton and sodium MR images of rabbit discs (≤2-mm thickness) were successfully obtained using an in-house dual-tuned proton/sodium RF coil at 3T. The total acquisition time for each set of images was approximately 40 minutes. Sodium concentration of normal rabbit lumbar discs was measured at 269.7 ± 6.3 mM, and this measurement was highly reproducible, with 5.3% of coefficient of variation. Sodium concentrations of rabbit lumbar discs were reliably measured using our newly developed dual-tuned multichannel proton/sodium RF coil at 3T.

A dual echo approach to motion correction for functional connectivity studies

The effect of subject head movement on functional connectivity as measured by BOLD (blood oxygen level dependent) fMRI was investigated; movement mainly introduced increases in connectivity into the dataset. The effect of movement on connectivity is an important consideration when comparing patients suffering from neurological conditions to healthy controls, since it is well known that patients affected by such conditions are prone to move more in the scanner than healthy subjects. A method of motion correction utilising a dual echo EPI sequence is described. The first echo is acquired soon after the slice excitation (TE(1)=10 ms) when BOLD contrast is low and the MR signal is mainly sensitive to movement related effects, while the second echo is acquired at an echo time (TE(2)=30 ms) at which the MR signal is sensitive to both BOLD and movement related effects. To correct for additional signal variance introduced by subject movement, the second echo image is divided by the first echo image at each time point across the length of the scan. This procedure is easy to implement and requires no extra scan time. This method proved superior to the standard means of correction whereby realignment parameters and their first order derivatives are used as covariates of no interest in a linear regression model.

Extension of Shift-Invariant Systems in L 2(ℝ) to Frames

In this article, we show that any shift-invariant Bessel sequence with an at most countable number of generators can be extended to a tight frame for its closed linear span by adding another shift-invariant system with at most the same number of generators. We show that in general this result is optimal, by providing examples where it is impossible to obtain a tight frame by adding a smaller number of generators. An alternative construction (which avoids the technical complication of extracting the square root of a positive operator) yields an extension of the given Bessel sequence to a pair of dual frame sequences.

Quantum dot-enhanced detection of dual short RNA sequences via one-step template-dependent surface hybridization

A novel multiplexed method for short RNA detection is reported that employs a design strategy in which capture and reporter probes anneal to each other in the presence of a short RNA target via the formation of a stable three-component complex. Quantum dots (QDs) functionalized with reporter DNA are thus specifically bound onto a capture probe-modified 96-well plate by one-step hybridization for simple RNA detection. In comparison with conventional organic dye-modified reporter probes, the use of reporter DNA-modified QD conjugates increase the melting temperature and lead to the detection of short RNA without the need for a ligation reaction. Moreover, QD properties allow multiple short RNA sequences to be simultaneously determined via rapid and simple one-step hybridization, as exemplified herein. The present results clearly demonstrate that this new strategy can be used to detect dual-short RNA sequence at concentrations of 10pM in 100μL.

Dual Inversion-Recovery MR Imaging Sequence for Reduced Blood Signal on Late Gadolinium-enhanced Images of Myocardial Scar

To investigate whether a dual inversion-recovery (IR) prepulse improves scar-to-blood contrast and expert confidence and consistency at late gadolinium-enhanced magnetic resonance (MR) imaging of myocardial scar compared with the standard IR technique at 3.0 T. The study was approved by the local ethics committee, and all patients provided written informed consent. Twelve men (mean age±standard deviation, 63 years±8) with known myocardial scar underwent MR imaging 10, 20, and 30 minutes after administration of 0.2 mmol/kg gadobutrol with a standard and dual IR sequence. Contrast-to-noise ratios (CNRs) were measured by using region-of-interest analysis, and data were compared with the analysis of variance test. Two experts measured scar size and transmurality, and data were compared with the Student t test and Bland-Altman test. Experts assigned confidence scores for scar detection and transmurality, which were compared with a Wilcoxon matched-pairs signed rank test. Patient data showed improved scar-to-blood CNR for the dual IR technique compared with the standard IR technique at all time points (P<.05). For images obtained 20 minutes after contrast material administration, the dual IR sequence provided higher confidence scores for scar detection and transmurality assessment (P<.05) and resulted in more consistent assessment of scar size and transmurality between readers compared with the IR sequence (P<.05). In this preliminary patient study, the dual IR prepulse improved contrast, scar visualization, and expert confidence and reduced expert differences in transmurality and scar size assessment compared with the standard IR technique.

Polynomial sequences associated with the classical linear functionals

This work in mainly devoted to the study of polynomial sequences, not necessarily orthogonal, defined by integral powers of certain first order differential operators in deep connection to the classical polynomials of Hermite, Laguerre, Bessel and Jacobi. This connection is streamed from the canonical element of their dual sequences. Meanwhile new Rodrigues-type formulas for the Hermite and Bessel polynomials are achieved.

Foxj2 Expression in Rat Spinal Cord After Injury and Its Role in Inflammation

Foxj2 (forkhead box J2), a novel member of the forkhead/HNF3 family, binds DNA with a dual sequence specificity. It may play a role in maintenance and survival of developing and adult neurons. However, its expression and function in the central nervous system lesion are still unclear. In this study, we performed a spinal cord injury (SCI) model in adult Sprague-Dawley rats and investigated the dynamic changes of Foxj2 expression in the spinal cord. Western blot analysis revealed that Foxj2 was present in normal spinal cord. It gradually increased, reached a peak at day5 after SCI, and then declined during the following days. Double immunofluorescence staining revealed wide expression of Foxj2, which is detected in neurons and astrocytes. After injury, Foxj2 expression was increased predominantly in astrocytes, which highly expressed proliferating cell nuclear antigen, a marker for proliferating cells. And knockdown of Foxj2 in cultured primary astrocytes by siRNA showed that Foxj2 played an important role in lipopolysaccharide-induced inflammatory responses. These results suggested that Foxj2 may be involved in the pathophysiology of SCI, and further research is needed to have a good understanding of its function and mechanism.

Simulation Tool for the Prediction of Compound Dependence of CW-Photoacoustic-based Sensor using Dual Differential Optical Excitation

Abstract Towards the development of a sensor dedicated to noninvasive and continuous blood glucose level monitoring, we developed a protocol called optical power balance shift based on a continuous-wave photoacoustic technique using a dual differential wavelength excitation sequence. In order to optimize the sensor response, we showed using an analytical model that the OPBS response depends exclusively on the absorption coefficients at the two wavelengths. Then, using a standard near-infrared spectrophotometer, we measured the dependence of relative absorption coefficients on glucose and albumin concentrations and temperature, and built a simulation tool covering all the possible combinations of the two wavelengths from 1300 to 2500 nm. The model was validated by good agreement when compared with experimental results for the 1382/1610 nm combination.

Global Convergence of Augmented Lagrangian Methods Applied to Optimization Problems with Degenerate Constraints, Including Problems with Complementarity Constraints

We consider global convergence properties of the augmented Lagrangian methods on problems with degenerate constraints, with a special emphasis on mathematical programs with complementarity constraints (MPCC). In the general case, we show convergence to stationary points of the problem under an error bound condition for the feasible set (which is weaker than constraint qualifications), assuming that the iterates have some modest features of approximate local minimizers of the augmented Lagrangian. For MPCC, we first argue that even weak forms of general constraint qualifications that are suitable for convergence of the augmented Lagrangian methods, such as the recently proposed relaxed positive linear dependence condition, should not be expected to hold and thus special analysis is needed. We next obtain a rather complete picture, showing that, under this context's usual MPCC-linear independence constraint qualification, feasible accumulation points of the iterates are guaranteed to be C-stationary for MPCC (better than weakly stationary), but in general need not be M-stationary (hence, neither strongly stationary). However, strong stationarity is guaranteed if the generated dual sequence is bounded, which we show to be the typical numerical behavior even though the multiplier set itself is unbounded. Experiments with the ALGENCAN augmented Lagrangian solver on the MacMPEC and DEGEN collections are reported, with comparisons to the SNOPT and filterSQP implementations of the SQP method, to the MINOS implementation of the linearly constrained Lagrangian method, and to the interior-point solvers IPOPT and KNITRO. We show that ALGENCAN is a very good option if one is primarily interested in robustness and quality of computed solutions.

Dual Convergence for Penalty Algorithms in Convex Programming

Algorithms for convex programming, based on penalty methods, can be designed to have good primal convergence properties even without uniqueness of optimal solutions. Taking primal convergence for granted, in this paper we investigate the asymptotic behavior of an appropriate dual sequence obtained directly from primal iterates. First, under mild hypotheses, which include the standard Slater condition but neither strict complementarity nor second-order conditions, we show that this dual sequence is bounded and also, each cluster point belongs to the set of Karush–Kuhn–Tucker multipliers. Then we identify a general condition on the behavior of the generated primal objective values that ensures the full convergence of the dual sequence to a specific multiplier. This dual limit depends only on the particular penalty scheme used by the algorithm. Finally, we apply this approach to prove the first general dual convergence result of this kind for penalty-proximal algorithms in a nonlinear setting.