Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “ENCODE”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 631 records · Page 35Linked to original sources

Interpretation of flow encoding and quantification in MRI: time domain versus frequency domain.

The traditional approach to flow effects in MRI is based on the gradient moment expansion. Recently, we have presented an alternative description by using linear response theory: the distortions of the velocity waveform induced by the gradient waveforms were analyzed in the frequency domain on the basis of the transfer function. In the present paper, we perform an analysis of flow encoding and quantification in the time domain, on the basis of the impulse response. The analysis shows that flow encoding should be interpreted as a weighted averaging process. Instantaneous flow encoding is determined by the centroid of the impulse response, but care should be taken regarding the physical meaning of the instant of encoding. The relationship of this approach to the frequency domain and gradient moment expansion approaches is clarified. By way of example, some interesting applications are investigated: asymmetrical phase encoding gradients to minimize misregistration and oscillating read-out gradients for flow quantification. A variety of new applications are expected to derive from the combination of both the time and frequency domains.

Magnetic Resonance Imaging↗

Non-Fourier encoding with multiple spin echoes.

The advantages and limitations of multiple spin-echo sequences for non-Fourier encoding are investigated. Complications caused by improper encoding of alternate magnetization pathways due to imperfect refocusing pulses are analyzed. It is shown that mirror image ghosts result if the encoding RF pulse matrix is real-valued. These ghosts can be avoided as long as the rows of the RF pulse matrix are conjugate symmetric, which implies that spatial profiles are real valued. Non-Fourier encoding using bases derived from wavelet, Hadamard, and other real-valued orthogonal functions does not result in a mirror ghost artifact. A RARE sequence for non-Fourier encoding has been implemented on a clinical imaging system and successfully applied for brain imaging.

Artifacts↗

Wavelet encoding for improved SNR and retrospective slice thickness adjustment.

A method to encode the slice-select direction in magnetic resonance imaging through the use of a discrete wavelet transform is presented. The paper reports the first implementation of wavelet encoding using the Haar basis. Theoretically, the signal-to-noise ratio (SNR) for two levels of wavelet encoding is expected to be approximately 1.6 times higher than for conventional multislice imaging in which each slice is excited separately. A slightly lower SNR is encountered experimentally because of slice interference. The design of radiofrequency (RF) pulses to excite slices approximating Haar wavelet basis functions is discussed. Wavelet encoding also provides an efficient method for balancing slice thickness and SNR after an image has been acquired. The experiments have been conducted at 1.5 Tesla. Wavelet encoding of slices should be especially suitable for low-field MRI, in which the SNR is lower and the characteristically lower T1 values favor the use of shorter TR, which sometimes forces the slices to be acquired in multiple passes.

Algorithms↗

GRASE imaging at 3 Tesla with template interactive phase-encoding.

A new method for ordering the phase-encoding gradient is proposed, and an application for short effective TE gradient- and spin-echo (GRASE) imaging is demonstrated. The proposed method calculates the phase-encoding order from the signal decay of a template scan (hence "template interactive phase-encoding" or TIPE). Computer simulations are used to compare the point spread functions of different phase-encoding orders giving short effective echo times (kb centric GRASE, centric GRASE, centric TIPE). The conventional centric phase-encoding order is also considered for GRASE. The conventional centric method is sensitive to both amplitude and phase modulation of the signal in k-space. The centric TIPE method gives the least amplitude modulation artifacts but is vulnerable to phase artifacts. The TIPE experiment was implemented on a 3 Tesla system. To the best of our knowledge, we present the first in vivo GRASE images at this field strength.

Artifacts↗

Accelerating MR diffusion tensor imaging via filtered reduced-encoding projection-reconstruction.

MR diffusion tensor imaging (DTI) is a promising tool for characterizing the microstructure of ordered tissues. However, its practical applications are hampered by relatively low signal-to-noise-ratio and spatial and temporal resolution. Reduced-encoding imaging (REI) via k-space sharing with constrained reconstruction has previously been shown to be effective for accelerating DTI, although the implementation was based on rectilinear k-space sampling. Due to the intrinsic oversampling of central k-space and allowance for isotropic downsampling, projection-reconstruction (PR) imaging may be better suited for REI. In this study, regularization procedures, including radial filtering and baseline signal correction to adequately reconstruct reduced encoded PR imaging data, are investigated. The proposed filtered reduced-encoding projection-reconstruction (FREPR) technique is applied to DTI tissue fiber orientation and fractional anisotropy (FA) measurements. Results show that FREPR offers improved reconstructions of the reduced encoded images and on an equal total scan-time basis provides more accurate fiber orientation and FA measurements compared to rectilinear k-space sampling-based REI methods or a control experiment consisting of only fully encoded images. These findings suggest a potentially significant role of FREPR in accelerating repeated imaging and improving the data acquisition-time efficiency of DTI experiments.

Computer Simulation↗

In-plane velocity encoding with coherent steady-state imaging.

Standard phase-contrast flow quantification (PC-FQ) using radiofrequency (RF) spoiled steady-state (SS) incoherent gradient-echo sequences have a relatively low signal-to-noise ratio (SNR). Unspoiled SS coherent (SSC) gradient-echo sequences have a higher intrinsic SNR and are T2/T1 weighted so that blood has a relatively large signal compared to other tissues. An SSC sequence that was modified to allow in-plane velocity encoding is presented. Velocity encoding was achieved by inverting the readout gradients. This offers the benefit that there is no resultant increase in repetition time (TR), which avoids increased sensitivity to off-resonance artifacts when conventional velocity-encoding methods using separate velocity-encoding gradients are extended to SSC sequences. The results of standard PC-FQ and the new method from in vitro experiments of constant and sinusoidal flow, and in vivo imaging of the carotid artery were compared. Vector field maps and paths obtained from particle-tracking calculations based on the velocity-encoded images were used to visualize the velocity data. The technique has the potential to increase the precision of PC-FQ measurements.

Algorithms↗

Bunched phase encoding (BPE): a new fast data acquisition method in MRI.

A new fast data acquisition method, "Bunched Phase Encoding" (BPE), is presented. In conventional rectilinear data acquisition, only a readout gradient (and no phase encoding gradient) is applied when k-space data are acquired. Reduction of the number of phase encoding lines by increasing the phase encoding step size often leads to aliasing artifacts. Papoulis's generalized sampling theory asserts that in some cases aliasing artifact-free signals can be reconstructed even if the Nyquist criterion is violated in some regions of the Fourier domain. In this study, Papoulis's theoretical construct is exploited to reduce the number of acquired phase encoding lines. To achieve this, k-space data are sampled along a "zigzag" trajectory during each readout; samples are acquired at a sampling frequency higher than that of the normal rectilinear acquisition. The total number of TR cycles and, hence, the total scan time can be reduced. The resultant signal-to-noise ratio (SNR) often varies across the reconstructed image when using the BPE technique, and the image SNR depends on the reconstruction method. This work is comparable to a gradient based version of parallel imaging. Evidence suggests it may serve as the basis for new opportunities for fast data acquisition in MRI.

Image Interpretation, Computer-Assisted↗

Tissue-specific stability of nuclear- and mitochondrially encoded mRNAs.

Steady-state levels of mRNAs encoding mitochondrial proteins are drastically different among tissues. We evaluated tissue-specific variations in mRNA stability by comparing rates of mRNA decay in liver, heart, and muscle following the inhibition of transcription. Rates of decline of the mRNAs encoding delta-aminolevulinate synthase (ALAs), cytochrome c oxidase subunit VIc (nuclear-encoded), and subunit III (mitochondrially encoded) in heart, liver, and muscle for 6 h following transcription inhibition with actinomycin D or ethidium bromide were measured. Subunit VIc mRNA levels were least stable in liver (t1/2 = 2.4 h), slightly greater in heart (t1/2 = 3.3 h), and very stable in skeletal muscle. Similarly, ALAs mRNA exhibited a t1/2 of 41 min in liver, but this was markedly increased to approximately 11-14 h in heart and skeletal muscle. In contrast, subunit III was least stable in heart (t1/2 = 2.1 h), somewhat more stable in liver (t1/2 = 3.8 h), but no decline in subunit III mRNA levels occurred in muscle following the inhibition of transcription. Thus, muscle, heart, and liver possess tissue-specific mechanisms which control the stability of mRNAs encoding mitochondrial proteins. In addition, the coordinated expression of subunit III and VIc mRNAs is different tissues is partly due to parallel rates of mRNA turnover. This suggests the presence of intra- and extramitochondrial factors within a tissue which regulate the stability of specific mRNAs in a similar manner.

5-Aminolevulinate Synthetase↗

Neural correlates of successful and unsuccessful verbal memory encoding.

Recent neuroimaging studies suggest that episodic memory encoding involves a network of neocortical structures which may act interdependently with medial temporal lobe (mTL) structures to promote the formation of durable memories, and that activation in certain structures is modulated according to task performance. Functional magnetic resonance imaging (fMRI) was used to determine the neural structures recruited during a verbal episodic encoding task and to examine the relationship between activation during encoding and subsequent recognition memory performance across subjects. Our results show performance-correlated activation during encoding both in neocortical and medial temporal structures. Neocortical activations associated with later successful and unsuccessful recognition memory were found to differ not only in magnitude, but also in hemispheric laterality. These performance-related hemispheric effects, which have not been previously reported, may correspond to between-subject differences in encoding strategy.

Adolescent↗

Development and evaluation of a computerized admission diagnoses encoding system.

Hospital information systems designed to support the needs of health care professionals include patient data entered using both freetext and precoded storage schemes. A major disadvantage of freetext storage schemes is that data captured in this format can only be presented as is to the user for review tasks. In the view of many health care scientists, natural language understanding systems capable of identifying, extracting, and encoding information contained in freetext data may provide the necessary tools to overcome this weakness. This paper describes the development and evaluation of a such a system designed to encode freetext admission diagnoses. This system combines both semantic and syntactic linguistic analysis techniques. Evaluation results demonstrate the overall performance of this system to be reasonable, accurately encoding approximately 76% of admission diagnoses. Inefficiencies are primarily due to the inability of this system to generate encodings in roughly 15% of test cases. When encodings are produced, however, accuracy equals that of the current manual coding method. With further modification, this application can partially automate the coding process.

Algorithms↗

Trypanosoma rangeli and Trypanosoma cruzi: molecular characterization of genes encoding putative calcium-binding proteins, highly conserved in trypanosomatids.

Genes encoding a 29-kDa flagellar calcium-binding protein (F29) in Trypanosoma cruzi, strongly homologous to EF-hand calcium-binding protein-encoding genes previously reported in this parasite, were isolated by immunoscreening. F29 is encoded by a number of very similar genes, highly conserved among different T. cruzi isolates. The genes are located on a pair of homologous chromosomes, arranged in one or two clusters of tandem repeats. PCR amplification of Trypanosoma rangeli genomic DNA, using primers derived from the T. cruzi F29 sequence made it possible to isolate the homologous gene in T. rangeli, encoding a 23-kDa protein called TrCaBP. Gene sequence comparisons showed homology to EF-hand calcium-binding proteins from T. cruzi (82.8%), Trypanosoma brucei brucei (60.2%), and Entamoeba histolytica (28.4%). Northern blot analysis revealed that the TrCaBP gene is expressed in T. rangeli as a polyadenylated transcript. The TrCaBP-encoding genes are present in at least 20 copies per cell, organized in tandem arrays, on large T. rangeli chromosomes in some isolates and on two smaller ones in others. This gene, however, seems to be absent from Leishmania.

Amino Acid Sequence↗

The exon-intron organization of the human X-linked gene (FLN1) encoding actin-binding protein 280.

We have determined the exon-intron organization of the human X-linked gene (FLN1) encoding actin-binding protein 280 (filamin), a ubiquitous protein that plays an important role in the mechanochemical activities of cells through its association with actin filaments and membrane components. The gene is composed of 47 exons spanning approximately 26 kb. The first and part of the second exon are untranslated. The actin-binding domain at the N-terminus is encoded by exons 2 to 5. The 96-amino-acid repeats corresponding to the elongated rod backbone of the protein are encoded by the remaining 42 exons: size, location, and boundaries of the exons cannot be easily correlated with the repeated structure, while sequences interrupting the repeats (the two hinge segments preceding repeats 16 and 24 and the 8-amino-acid (aa) segment interrupting the 15th repeat) were encoded by separate exons, suggesting that they may be recent additions to the X-linked protein. The 8-aa segment is encoded by exon 29, which is alternatively spliced.

Amino Acid Sequence↗

cDNA cloning, chromosomal localization, and expression pattern of EPLG8, a new member of the EPLG gene family encoding ligands of EPH-related protein-tyrosine kinase receptors.

By screening a human fetal brain cDNA library under low stringency using cDNA encoding the mouse ligand of Cek5 as a probe, we have isolated a novel cDNA belonging to the EPLG gene family. This family encodes ligands of EPH-related tyrosine kinase receptors. Since the novel gene is the eighth member of the EPLG gene family, it is designated EPLG8. The deduced amino acid sequence of EPLG8 suggests that it encodes a transmembrane protein that is most related to those encoded by EPLG2 and EPLG5. We mapped the EPLG8 gene to human chromosome 17p11.2-p13.1 by PCR screening of human-rodent somatic cell hybrid panels. In the midterm fetus, EPLG8 mRNA is expressed at the highest level in brain, followed by heart, kidney, and lung. In the adult, EPLG8 mRNA expression is restricted to brain. These data suggest that LERK-8, the protein encoded by EPLG8, is important in brain development as well as in its maintenance. Moreover, since levels of EPLG8 expression were particularly high in several forebrain subregions compared to other brain subregions, LERK-8 may play a pivotal role in forebrain function.

Adult↗

cDNA cloning and genomic structure of three genes localized to human chromosome band 5q31 encoding potential nuclear proteins.

Loss of a whole chromosome 5, or a del(5q), is a recurring abnormality in malignant myeloid diseases. By cytogenetic and molecular analyses, we delineated previously a 1- to 1.5-Mb region that is deleted in all patients with a del(5q). In our efforts to identify a myeloid tumor suppressor gene within the commonly deleted segment (CDS), we have cloned and characterized the genes encoding three putative nuclear proteins, each of which contains a bipartite nuclear localization signal (NLS). In addition, C5ORF5 contains a putative rhoGAP domain at the N-terminus, C5ORF6 has a proline-rich sequence near the N-terminus, and C5ORF7 has a zinc-finger domain that partially overlaps the NLS. All three genes are ubiquitously expressed and encode novel proteins. The C5ORF5 cDNA is 5.47 kb encoding a protein of 915 amino acids (aa) with a predicted molecular mass of approximately 105 kDa. C5ORF5 has 23 exons spanning over 27 kb. The C5ORF6 transcript is 4.1 kb encoding a protein of 392 aa with a predicted molecular mass of approximately 43 kDa. C5ORF6 has 5 exons and spans approximately 11 kb. The C5ORF7 cDNA is 6.3 kb and encodes a protein of 1417 aa with a predicted molecular mass of approximately 155 kDa. C5ORF7 has 24 exons spanning approximately 64 kb. All three genes were localized to the distal half of the CDS between D5S1983 and D5S500. We evaluated each as a candidate tumor suppressor gene by the analysis of myeloid leukemia cells from patients with -5/del(5q), but no inactivating mutations were identified.

Amino Acid Sequence↗

Structural conservation of the genes encoding CaT1, CaT2, and related cation channels.

We report here the genomic structures of the genes encoding human calcium transport proteins CaT1 and CaT2, which belong to a recently identified class of highly selective calcium entry channels. The mRNA for CaT1 was expressed more abundantly than that for CaT2 in three major tissues involved in transcellular calcium transport, namely intestine, kidney, and placenta, as determined by quantitative PCR. The genes encoding CaT1 and CaT2, ECAC2 and ECAC1, respectively, are completely conserved in terms of exon size in the coding regions. They also share similar intron-exon structures with the genes encoding the closely related, nonselective cation channels VR1, VRL-1, OTRPC4 (also known as VR-OAC, Trp12, and VRL-2), and a hypothetical protein, VRL-3. We conclude that ECAC2 and ECAC1, which encode calcium selective channels, share a common ancestral gene with the genes encoding the related nonselective cation channels.

Amino Acid Sequence↗

Identification and characterization of cDNAs encoding four novel proteins that interact with translin associated factor-X.

Translin-associated factor X (TRAX) is the predominantly cytoplasmic binding partner of TB-RBP/translin in mouse testis. Four mouse testis cDNAs encoding specific TRAX-interacting proteins were isolated from a yeast two-hybrid library screen. One novel cDNA designated Tsnaxip1 (TRAX-interacting protein-1) encodes 709 amino acids. We isolated a cDNA encoding the 427 carboxy-terminal amino acids of MEA-2, a Golgi-associated, maleenhanced autoantigen; a cDNA encoding 429 amino acids with 73% homology to centrosomal Akap9; and a cDNA encoding 346 amino acids with 75% homology to SUN1, a predicted human protein that contains a SUN domain (which is present in some perinuclear proteins). Interactions were verified using in vitro synthesized fusion proteins. All four genes were expressed in the testis and enriched in germ cells. Confocal microscopy studies using green fluorescent protein fusion proteins determined that these TRAX-interacting proteins colocalize with TRAX. The data suggest that TRAX may have a function associated with perinuclear organelles during spermatogenesis.

A Kinase Anchor Proteins↗

Model-based maximum-likelihood estimation for phase- and frequency-encoded magnetic-resonance-imaging data.

A maximum-likelihood (ML)-based magnetic-resonance-imaging (MRI) reconstruction algorithm is established, based on frequency- and phase-encoded data. The model on which the ML method is based is a superposition of exponentially decaying, sinc-modulated sinusoids, arising from the basic Bloch equations for MR spectroscopy, modified to account for the distribution of resonance frequencies and phases used for spatial localization in the image field. Spatial-localizing gradients are assumed to be known linear functions of spatial coordinate position, with the x-encode (frequency) gradient applied continuously during the full duration of data collection, and the y-encode (phase) gradient applied during varying time periods before data collection. A single-voxel emitter becomes sinc-modulated in the x, y directions at rates proportional to voxel size and gradient strengths in the x-encode and y-encode directions. The full two-dimensional MRI signal becomes a superposition of sinc-modulated, exponentially decaying, single-sinusoid emitters, one for each voxel. The ML estimation of spin-density and spin-spin relaxation decay time images becomes a nonlinear least-squares optimization problem; it is solved using an iterative expectation-maximization algorithm for estimating multiple modulated sinusoids in noise. Phantom studies are presented, demonstrating the accuracy of the model and the application of the algorithm to spin-density and spin-spin relaxation decay time profiles.

Algorithms↗

Amino acid encoding schemes from protein structure alignments: multi-dimensional vectors to describe residue types.

Bioinformatic software has used various numerical encoding schemes to describe amino acid sequences. Orthogonal encoding, employing 20 numbers to describe the amino acid type of one protein residue, is often used with artificial neural network (ANN) models. However, this can increase the model complexity, thus leading to difficulty in implementation and poor performance. Here, we use ANNs to derive encoding schemes for the amino acid types from protein three-dimensional structure alignments. Each of the 20 amino acid types is characterized with a few real numbers. Our schemes are tested on the simulation of amino acid substitution matrices. These simplified schemes outperform the orthogonal encoding on small data sets. Using one of these encoding schemes, we generate a colouring scheme for the amino acids in which comparable amino acids are in similar colours. We expect it to be useful for visual inspection and manual editing of protein multiple sequence alignments.

Algorithms↗