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 235 records · Page 13Linked to original sources
PubMed2002

The effect of encoding strategy on the neural correlates of memory for faces.

Encoding and recognition of unfamiliar faces in young adults were examined using positron emission tomography to determine whether different encoding strategies would lead to encoding/retrieval differences in brain activity. Three types of encoding were compared: a 'deep' task (judging pleasantness/unpleasantness), a 'shallow' task (judging right/left orientation), and an intentional learning task in which subjects were instructed to learn the faces for a subsequent memory test but were not provided with a specific strategy. Memory for all faces was tested with an old/new recognition test. A modest behavioral effect was obtained, with deeply-encoded faces being recognized more accurately than shallowly-encoded or intentionally-learned faces. Regardless of encoding strategy, encoding activated a primarily ventral system including bilateral temporal and fusiform regions and left prefrontal cortices, whereas recognition activated a primarily dorsal set of regions including right prefrontal and parietal areas. Within encoding, the type of strategy produced different brain activity patterns, with deep encoding being characterized by left amygdala and left anterior cingulate activation. There was no effect of encoding strategy on brain activity during the recognition conditions. Posterior fusiform gyrus activation was related to better recognition accuracy in those conditions encouraging perceptual strategies, whereas activity in left frontal and temporal areas correlated with better performance during the 'deep' condition. Results highlight three important aspects of face memory: (1) the effect of encoding strategy was seen only at encoding and not at recognition; (2) left inferior prefrontal cortex was engaged during encoding of faces regardless of strategy; and (3) differential activity in fusiform gyrus was found, suggesting that activity in this area is not only a result of automatic face processing but is modulated by controlled processes.

Adult↗
PubMedDate not supplied

Right prefrontal activation during encoding, but not during retrieval, in a non-verbal paired-associates task.

Brain imaging studies have shown that episodic encoding into long-term memory preferentially activates the left prefrontal cortex and retrieval activates the right prefrontal cortex. However, it is unclear to what degree verbal analysis contributes to the left prefrontal activation during encoding. The present study was designed to avoid verbal analysis during encoding by using abstract pictures and computer-generated sounds which were difficult to code verbally. Sounds and pictures were grouped into six stimulus-stimulus pairs. When the sound from a pair was presented, the subjects were instructed to recall and visualize the associated picture. After 2.0 s the associated picture and another picture appeared on the screen and the subjects were required to identify the associated picture. Feedback about the choice was then given. Regional cerebral blood flow (rCBF) was measured with [15O]butanol and positron emission tomography (PET) in 10 subjects during initial training on the paired-associates task (encoding scan) and after 35 min of training (retrieval scan). Performance during the encoding scan was 59% correct and during the retrieval scan 98% correct, with a mean reaction time of 709 ms during retrieval. The rCBF was also measured during a control condition without any instruction to encode or retrieve. Compared with retrieval, encoding showed significant activation of the posterior part of the right middle frontal gyrus, the right inferior parietal cortex, the cingulate cortex, the left inferior parietal cortex and the left inferior and middle temporal gyri. The rCBF increase during encoding was strongly correlated with the rate of encoding. Retrieval was compared with both encoding and control. In none of these comparisons was there any prefrontal activation. The lack of prefrontal activation during near-perfect performance of the retrieval task suggests that the prefrontal cortex is not necessarily active when retrieval is fast and accurate, or what might be called automatic. Encoding was not associated with more activation of the left than the right prefrontal cortex. This result presents a limitation to the generality of left prefrontal activation during episodic encoding, which has been found in several previous brain imaging studies. Differences between studies in the relative activation of left and right prefrontal cortex during encoding and retrieval might be due to differences in paradigms, the type of stimulus used, and the demand for working memory and verbal analysis.

Adult↗
PubMed1995

Semantic encoding and retrieval in the left inferior prefrontal cortex: a functional MRI study of task difficulty and process specificity.

Prefrontal cortical function was examined during semantic encoding and repetition priming using functional magnetic resonance imaging (fMRI), a noninvasive technique for localizing regional changes in blood oxygenation, a correlate of neural activity. Words studied in a semantic (deep) encoding condition were better remembered than words studied in both easier and more difficult nonsemantic (shallow) encoding conditions, with difficulty indexed by response time. The left inferior prefrontal cortex (LIPC) (Brodmann's areas 45, 46, 47) showed increased activation during semantic encoding relative to nonsemantic encoding regardless of the relative difficulty of the nonsemantic encoding task. Therefore, LIPC activation appears to be related to semantic encoding and not task difficulty. Semantic encoding decisions are performed faster the second time words are presented. This represents semantic repetition priming, a facilitation in semantic processing for previously encoded words that is not dependent on intentional recollection. The same LIPC area activated during semantic encoding showed decreased activation during repeated semantic encoding relative to initial semantic encoding of the same words. This decrease in activation during repeated encoding was process specific; it occurred when words were semantically reprocessed but not when words were nonsemantically reprocessed. The results were apparent in both individual and averaged functional maps. These findings suggest that the LIPC is part of a semantic executive system that contributes to the on-line retrieval of semantic information.

Adolescent↗
PubMed2006

Motor brain regions are involved in the encoding of delayed intentions: a fMRI study.

In studies of prospective memory, recall of the content of delayed intentions is normally excellent, probably because they contain actions that have to be enacted at a later time. Action words encoded for later enactment are more accessible from memory than those encoded for later verbal report [Freeman, J.E., and Ellis, J.A. 2003a. The representation of delayed intentions: A prospective subject-performed task? Journal of Experimental Psychology: Learning, Memory, and Cognition, 29, 976-992.]. As this higher assessibility is lost when the intended actions have to be enacted during encoding, or when a motor interference task is introduced concurrent to intention encoding, Freeman and Ellis suggested that the advantage of to-be-enacted actions is due to additional preparatory motor operations during encoding. Accordingly, in a fMRI study with 10 healthy young participants, we investigated whether motor brain regions are differentially activated during verbal encoding of actions for later enactment with the right hand in contrast to verbal encoding of actions for later verbal report. We included an additional condition of verbal encoding of abstract verbs for later verbal report to investigate whether the semantic motor information inherent in action verbs in contrast to abstract verbs activates motor brain regions different from those involved in the verbal encoding of actions for later enactment. Differential activation for the verbal encoding of to-be-enacted actions in contrast to to-be-reported actions was found in brain regions known to be involved in covert motor preparation for hand movements, i.e. the postcentral gyrus, the precuneus, the dorsal and ventral premotor cortex, the posterior middle temporal gyrus and the inferior parietal lobule. There was no overlap between these brain regions and those differentially activated during the verbal encoding of actions in contrast to abstract verbs for later verbal report. Consequently, the results of this fMRI study suggest the presence of preparatory motor operations during the encoding of delayed intentions requiring a future motor response, which cannot be attributed to semantic information inherent to action verbs.

Adult↗
PubMed1995

Differential biochemical regulation of the URA7- and URA8-encoded CTP synthetases from Saccharomyces cerevisiae.

The URA7- and URA8-encoded CTP synthetases (EC 6.3.4.2, UTP:ammonia ligase (ADP-forming) are functionally overlapping enzymes responsible for the biosynthesis of CTP in the yeast Saccharomyces cerevisiae. URA8-encoded CTP synthetase was purified to apparent homogeneity by ammonium sulfate fractionation of the cytosolic fraction followed by chromatography with Q-Sepharose, Affi-Gel Blue, Mono Q, and Superose 6. The subunit molecular mass (67 kDa) of purified URA8-encoded CTP synthetase was in good agreement with the predicted size of the URA8 gene product. Antibodies raised against a fusion protein constructed from the coding sequences of the URA8 gene and expressed in Escherichia coli reacted with purified URA8-encoded CTP synthetase. Native URA8-encoded CTP synthetase existed as a dimer which oligomerized to a tetramer in the presence of its substrates UTP and ATP. Maximum URA8-encoded CTP synthetase activity was dependent on Mg2+ ions (Ka = 2.4 mM) and 2-mercaptoethanol at the pH optimum of 7.5. The enzyme followed saturation kinetics toward UTP (Km = 74 microM), ATP (Km = 22 microM), and glutamine (Km = 0.14 mM). GTP stimulated (Ka = 26 microM) URA8-encoded CTP synthetase activity 12-fold. CTP potently inhibited (IC50 = 85 microM) URA8-encoded CTP synthetase activity and, in addition, caused the dependence of activity toward UTP to become cooperative. The URA8-encoded CTP synthetase and the previously purified URA7-encoded CTP synthetase differed significantly with respect to several biochemical properties including turnover number, pH optimum, substrate dependences, and sensitivity to inhibition by CTP. The URA7-encoded CTP synthetase mRNA was 2-fold more abundant when compared with URA8-encoded CTP synthetase mRNA. Both CTP synthetase isoforms were maximally expressed in the exponential phase of growth.

Base Sequence↗
PubMed2001

Depth of processing effects on neural correlates of memory encoding: relationship between findings from across- and within-task comparisons.

Neuroimaging studies have implicated the prefrontal cortex and medial temporal areas in the successful encoding of verbal material into episodic memory. The present study used event-related functional MRI to investigate whether the brain areas associated with successful episodic encoding of words in a semantic study task are a subset of those demonstrating depth of processing effects. In addition, we tested whether the brain areas associated with successful episodic encoding differ depending on the nature of the study task. At study, 15 volunteers were cued to make either animacy or alphabetical decisions about words. A recognition memory test including confidence judgements followed after a delay of 15 min. Prefrontal and medial temporal regions showed greater functional MRI activations for semantically encoded words relative to alphabetically encoded words. Two of these regions (left anterior hippocampus and left ventral inferior frontal gyrus) showed greater activation for semantically encoded words that were subsequently recognized confidently. However, other regions (left posterior hippocampus and right inferior frontal cortex) demonstrated subsequent memory effects, but not effects of depth of processing. Successful memory for alphabetically encoded words was also associated with greater activation in the left anterior hippocampus and left ventral inferior frontal gyrus. The findings suggest that episodic encoding for words in a semantic study task involves a subset of the regions activated by deep relative to shallow processing. The data provide little evidence that successful episodic encoding during a shallow study task depends upon regions different from those that support the encoding of deeply studied words. Instead, the findings suggest that successful episodic encoding during a shallow study task relies on a subset of the regions engaged during successful encoding in a deep task.

Acoustic Stimulation↗
PubMed1988

Age differences in encoding specificity.

In two experiments (one under full attention, the other under divided attention), old and young adults were presented with a cued recall task in an encoding specificity paradigm. Targets and associated cues were either pictures or matched words, and there was either a strong or weak semantic relationship between targets and cues. Additionally, cues presented at recall were either the same as or different from those presented at encoding, resulting in four encoding cue--retrieval cue combinations: (a) strong encoding cue and (same) strong retrieval cue; (b) weak encoding cue and (same) weak retrieval cue; (c) weak encoding cue and (different) strong retrieval cue; (d) strong encoding cue and (different) weak retrieval cue. For the most part, the results revealed strong encoding specificity effects for both age groups, as both old and young participants recalled more when the same cues were presented at encoding and retrieval than when different cues were presented. However, when elderly participants received verbal cues under divided attention conditions, evidence for general encoding rather than encoding specificity occurred. Results are discussed in terms of both the encoding specificity principle as well as a more process-oriented interpretation.

Aged↗
PubMed2003

Effects of encoding style, expectation of retrieval mode, and retrieval style on memory for action phrases.

The purpose of this study was to examine the effects of encoding style, expectation of retrieval mode, and retrieval style on memory for action phrases using the recall test and the source-monitoring test. In Exp. 1, the subjects were asked to memorize action phrases with a variety of encoding styles (verbal, performance, imaging), expectation of retrieval mode (to-be-remembered, to-be-performed, to-be-forgotten), and retrieval style (verbal, enacted). Analysis showed that memory for action phrases was affected by processes of encoding, i.e., type of encoding and expectation of retrieval at encoding, rather than retrieval. Also, action phrases, which were either acted out, or in which performance was imaged, or where enacting was expected later at the encoding phase, were recalled better. These results were replicated in Exp. 2, in which subjects were asked to identify the source of memories at the time of the recall test. However, results of the source-monitoring test in Exp. 1 which required, following the recall test, that participants recall as many of the test-expectation condition of action phrases as possible, showed that source memory for phrases enacted at encoding was weaker than for those in which performance was imaged or expected later but not enacted at encoding. Since, in Exp. 2, source memory for enacted items at encoding was maintained at a relatively high level, it is suggested that source memory for enacted action phrases at encoding might decay rapidly. In addition, a robust directed forgetting effect was observed in verbal and imaging encoding but not in performance encoding.

Cognition↗
PubMed1997

Improvement of protein secondary structure prediction using binary word encoding.

We propose a binary word encoding to improve the protein secondary structure prediction. A binary word encoding encodes a local amino acid sequence to a binary word, which consists of 0 or 1. We use an encoding function to map an amino acid to 0 or 1. Using the binary word encoding, we can statistically extract the multiresidue information, which depends on more than one residue. We combine the binary word encoding with the GOR method, its modified version, which shows better accuracy, and the neural network method. The binary word encoding improves the accuracy of GOR by 2.8%. We obtain similar improvement when we combine this with the modified GOR method and the neural network method. When we use multiple sequence alignment data, the binary word encoding similarly improves the accuracy. The accuracy of our best combined method is 68.2%. In this paper, we only show improvement of the GOR and neural network method, we cannot say that the encoding improves the other methods. But the improvement by the encoding suggests that the multiresidue interaction affects the formation of secondary structure. In addition, we find that the optimal encoding function obtained by the simulated annealing method relates to nonpolarity. This means that nonpolarity is important to the multiresidue interaction.

Amino Acid Sequence↗
PubMed2001

Left temporal and temporoparietal brain activity depends on depth of word encoding: a magnetoencephalographic study in healthy young subjects.

Using a 143-channel whole-head magnetoencephalograph (MEG) we recorded the temporal changes of brain activity from 26 healthy young subjects (14 females) related to shallow perceptual and deep semantic word encoding. During subsequent recognition tests, the subjects had to recognize the previously encoded words which were interspersed with new words. The resulting mean memory performances across all subjects clearly mirrored the different levels of encoding. The grand averaged event-related fields (ERFs) associated with perceptual and semantic word encoding differed significantly between 200 and 550 ms after stimulus onset mainly over left superior temporal and left superior parietal sensors. Semantic encoding elicited higher brain activity than perceptual encoding. Source localization procedures revealed that neural populations of the left temporal and temporoparietal brain areas showed different activity strengths across the whole group of subjects depending on depth of word encoding. We suggest that the higher brain activity associated with deep encoding as compared to shallow encoding was due to the involvement of more neural systems during the processing of visually presented words. Deep encoding required more energy than shallow encoding but for all that led to a better memory performance.

Adult↗
PubMed2002

Evidence for cortical encoding specificity in episodic memory: memory-induced re-activation of picture processing areas.

Functional magnetic resonance imaging (fMRI) was used to examine whether neural pathways used to encode pictures into memory were re-activated during retrieval of those memories. At encoding, subjects semantically classified common objects presented as pictures or words. At retrieval, subjects performed yes/no recognition memory judgments on words that had been encoded as pictures or as words. The retrieval test probed memory for the encoded item, but not memory for the modality of the encoded item (picture/word). Results revealed that a subset of the brain regions involved specifically in encoding of pictures were also engaged during recognition memory for the encoded pictures. Specifically, encoding of pictures relative to words engaged bilateral extrastriate visual cortex, namely fusiform, lingual, middle occipital, and inferior temporal gyri (Broadman area (BA) 18/19/37). Recognition memory judgments about words that were encoded as pictures relative to those that were encoded as words activated fusiform and inferior temporal gyri primarily in the left hemisphere. Thus, cortical areas originally involved in perception of a visual experience become part of the long-term memory trace for that experience. These findings suggest a neural basis for encoding specificity and transfer appropriate processing in human memory.

Adult↗
PubMed1997

Cardiac nuclear encoded cytochrome c oxidase subunits are decreased with copper restriction but not iron restriction: gene expression, protein synthesis and heat shock protein aspects.

Hearts from rats fed a copper-deficient (Cu-) diet have decreased levels of nuclear-encoded peptides of cytochrome c oxidase (CCO). Studies were conducted to determine whether iron deficiency would lead to a similar finding, whether mRNA transcripts and the chaperonin heat shock proteins (HSP) 60 and 70 from hearts of Cu- rats were decreased as compared with copper-adequate controls and whether synthesis of mitochondrial and nuclear encoded peptides differed as affected by diet copper. In study 1, weanling rats were assigned to one of three groups (n = 6 in each group): (1) control copper and iron adequate fed rats; (2) Cu- rats and (3) iron-deficient (Fe-) rats. Western blotting of nonmyofibrillar cardiac proteins revealed that the nuclear encoded peptides of CCO from the Cu- rats were markedly decreased as compared with control and Fe- rats. Mitochondrial encoded subunits did not appear to differ by treatment groups. Iron-deficient rats had similar nuclear encoded peptide levels as those of controls. In study 2, mRNA transcripts from Cu- (n = 4) and control copper adequate (n = 4) rats did not appear to differ for subunits II and IV, which correspond to mitochondrial and nuclear encoded subunits, respectively. In study 3, levels of HSP 60 and 70 from hearts of Cu- rats (n = 3) did not differ from Cu+ rats (n = 3). In study 4, infusion of 3H-(4,5)-leucine into the hearts of Cu+ and Cu- rats suggested there was no difference in synthesis of the nuclear encoded peptides by copper status and some indication there was enhanced breakdown of the nuclear encoded peptides among the Cu- rats. As expected, more isotope was incorporated into the mitochondria of Cu- rats than Cu+ rats. These results demonstrate an independent effect of copper upon the apparent decrease in the nuclear encoded subunits of CCO, the effect of copper upon the CCO subunits is probably post-transcriptional and that translocation of the nuclear encoded subunits from the ribosomes to the mitochondria via the chaperonin proteins is not a primary defect in explaining these observations in hearts from Cu- rats and synthesis of the nuclear encoded subunits of CCO in not impaired in copper deficiency.

Actins↗
PubMed1994

Self-mobilization and organization of the genes encoding the toluene metabolic pathway of Pseudomonas mendocina KR1.

The toluene metabolic pathway of Pseudomonas mendocina KR1 is chromosomally encoded, but the pathway could be transferred by conjugation from strain KR1 to the chromosome of P. aeruginosa or P. putida. Such transconjugants utilized toluene, p-cresol, and p-hydroxybenzaldehyde. However, transconjugants were unable to further transfer toluene genes to other recipients unless Pseudomonas sex factor R68.45 was present in trans. Although the genes encoding the upper pathway for toluene metabolism in P. mendocina KR1 are sufficiently linked to permit their coordinate mobilization, they were found to be encoded in three independently regulated units: one encoding toluene-4-monooxygenase, a second encoding p-cresol methylhydroxylase and p-hydroxybenzaldehyde dehydrogenase, and a third encoding p-hydroxybenzoate hydroxylase. The last two regulatory units were cloned from the chromosome of a P. aeruginosa transconjugant onto a plasmid designated pRO1999. Analysis of pRO1999 showed that genes encoding p-cresol methylhydroxylase and p-hydroxybenzaldehyde dehydrogenase are organized as an operon; the gene encoding p-hydroxybenzaldehyde dehydrogenase is transcribed first, and this is followed by transcription of the gene encoding p-cresol methylhydroxylase. This operon is regulated by a positively acting regulator. The P. mendocina KR1 gene encoding p-hydroxybenzoate hydroxylase was linked to, but independently regulated from, the genes encoding toluene-4-monooxygenase, p-cresol methylhydroxylase, and p-hydroxybenzaldehyde dehydrogenase.

4-Hydroxybenzoate-3-Monooxygenase↗
PubMed1992

Comparative distribution of messenger RNAs encoding glutamic acid decarboxylases (Mr 65,000 and Mr 67,000) in the basal ganglia of the rat.

Glutamic acid decarboxylase, the enzyme required for GABA synthesis, exists as distinct isoforms, which have recently been found to be encoded by different genes. The relative expression of messenger RNAs encoding two isoforms of glutamic acid decarboxylase (Mr 67,000 and Mr 65,000) was measured at the single-cell level in neurons of the rat basal ganglia with in situ hybridization histochemistry. Both messenger RNAs were expressed in neurons of the striatum, pallidum, and substantia nigra pars reticulata, but marked differences in the relative level of labelling were observed with the two probes. In striatum, efferent neurons were more densely labelled for the messenger RNA encoding glutamic acid decarboxylase (Mr 65,000) than for the messenger RNA encoding glutamic acid decarboxylase (Mr 67,000), whereas the reverse was observed for GABA-ergic interneurons. Neurons of the entopeduncular nucleus were much more densely labelled for messenger RNA encoding glutamic acid decarboxylase (Mr 65,000) than for messenger RNA encoding glutamic acid decarboxylase (Mr 67,000). In addition, labelling for messenger RNA encoding glutamic acid decarboxylase (Mr 65,000) was higher in the entopeduncular nucleus (internal pallidum) than in the globus pallidus (external pallidum), a structure which expressed similar levels of both mRNAs. In contrast to neurons of the internal pallidum, efferent neurons of the substantia nigra pars reticulata expressed slightly more messenger RNA encoding glutamic acid decarboxylase (Mr 67,000) than that encoding the other isoform of the enzyme. The results suggest a differential expression of the messenger RNAs encoding the two isoforms of glutamic acid decarboxylase in subpopulations of basal ganglia neurons in rats.

Animals↗
PubMed2003

Encoding of novel picture pairs activates the perirhinal cortex: an fMRI study.

It is well established in nonhuman primates that the medial temporal lobe (MTL) structures, the hippocampus and the entorhinal and perirhinal cortices, are necessary for declarative memory encoding. In humans, the neuropathological and neuropsychological changes in early Alzheimer's disease (AD) further support a role for the rhinal cortex in the consolidation of new events into long-term memory. Little is known, however, regarding the function of the rhinal cortex in humans in vivo. To examine the participation of the interconnected MTL structures as well as the whole-brain network of activated brain areas in visual associative long-term memory, functional magnetic resonance imaging (fMRI) was used to determine the brain regions that are activated during encoding and retrieval of paired pictures in 12 young control subjects. The most striking finding in the MTL activation pattern was the consistent activation of the perirhinal cortex in the encoding-baseline and encoding-retrieval comparisons with a strict statistical threshold (P < 0.00001). In contrast, no perirhinal cortex activation was detected in the retrieval-baseline or retrieval-encoding comparisons even with a low statistical threshold (P < 0.05). The location of the perirhinal activation area was in the transentorhinal part of the perirhinal cortex, in the medial bank of the collateral sulcus. The hippocampus and the more posterior parahippocampal gyrus were activated in both encoding and retrieval conditions. During the encoding processing, MTL activations were more consistent and the hippocampal activation area located more anteriorly than during retrieval. The frontal, parietal, temporal, and occipital association cortices were also activated in the encoding-baseline and retrieval-baseline comparisons. The data suggest that encoding, but not retrieval, of novel picture pairs activates the perirhinal cortex. To our knowledge, this is the first fMRI study reporting encoding activation in this transentorhinal part of the perirhinal cortex, the site of the very earliest neuropathological changes in AD.

Adult↗
PubMed2001

Comparison of gradient encoding schemes for diffusion-tensor MRI.

The accuracy of single diffusion tensor MRI (DT-MRI) measurements depends upon the encoding scheme used. In this study, the diffusion tensor accuracy of several strategies for DT-MRI encoding are compared. The encoding strategies are based upon heuristic, numerically optimized, and regular polyhedra schemes. The criteria for numerical optimization include the minimum tensor variance (MV), minimum force (MF), minimum potential energy (ME), and minimum condition number. The regular polyhedra scheme includes variations of the icosahedron. Analytical comparisons and Monte Carlo simulations show that the icosahedron scheme is optimum for six encoding directions. The MV, MF, and ME solutions for six directions are functionally equivalent to the icosahedron scheme. Two commonly used heuristic DT-MRI encoding schemes with six directions, which are based upon the geometric landmarks of a cube (vertices, edge centers, and face centers), are found to be suboptimal. For more than six encoding directions, many methods are able to generate a set of equivalent optimum encoding directions including the regular polyhedra, and the ME, MF and MV numerical optimization solutions. For seven directions, a previously described heuristic encoding scheme (tetrahedral plus x, y, z) was also found to be optimum. This study indicates that there is no significant advantage to using more than six encoding directions as long as an optimum encoding is used for six directions. Future DT-MRI studies are necessary to validate these observations. J. Magn. Reson. Imaging 2001;13:769-780.

Artifacts↗
PubMed1998

Applicability and efficiency of near-optimal spatial encoding for dynamically adaptive MRI.

Adaptive near-optimal MRI spatial encoding entails, for the acquisition of each image update in a dynamic series, the computation of encodes in the form of a linear algebra-derived orthogonal basis set determined from an image estimate. The origins of adaptive encoding relevant to MRI are reviewed. Sources of error of this approach are identified from the linear algebraic perspective where MRI data acquisition is viewed as the projection of information from the field-of-view onto the encoding basis set. The definitions of ideal and non-ideal encoding follow, with nonideal encoding characterized by the principal angles between two vector spaces. An analysis of the distribution of principal angles is introduced and applied in several example cases to quantitatively describe the suitability of a basis set derived from a specific image estimate for the spatial encoding of a given field-of-view. The robustness of adaptive near-optimal spatial encoding for dynamic MRI is favorably shown by results computed using singular value decomposition encoding that simulates specific instances of worst case data acquisition when all objects have changed or new objects have appeared in the field-of-view. The mathematical analysis and simulations presented clarify the applicability and efficiency of adaptively determined near-optimal spatial encoding throughout a range of circumstances as may typically occur during use of dynamic MRI.

Brain↗
PubMed1996

Sequence and organization of genes encoding enzymes involved in pyruvate metabolism in Mycoplasma capricolum.

The region of the genome of Mycoplasma capricolum upstream of the portion encompassing the genes for Enzymes I and IIAglc of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) was cloned and sequenced. Examination of the sequence revealed open reading frames corresponding to numerous genes involved with the oxidation of pyruvate. The deduced gene organization is naox (encoding NADH oxidase)-lplA (encoding lipoate-protein ligase)-odpA (encoding pyruvate dehydrogenase EI alpha)-odpB (encoding pyruvate dehydrogenase EI beta)-odp2(encoding pyruvate dehydrogenase EII)-dldH (encoding dihydrolipoamide dehydrogenase)-pta (encoding phosphotransacetylase)-ack (encoding acetate kinase)-orfA (an unknown open reading frame)-kdtB-ptsI-crr. Analysis of the DNA sequence suggests that the naox and lplA genes are part of a single operon, odpA and odpB constitute an additional operon, odp2 and dldH a third operon, and pta and ack an additional transcription unit. Phylogenetic analyses of the protein products of the odpA and odpB genes indicate that they are most similar to the corresponding proteins from Mycoplasma genitalium, Acholeplasma laidlawii, and Gram-positive organisms. The product of the odp2 gene contains a single lipoyl domain, as is the case with the corresponding proteins from M. genitalium and numerous other organisms. An evolutionary tree places the M. capricolum odp2 gene product in close relationship to the corresponding proteins from A. laidlawii and M.genitalium. The dldH gene encodes an unusual form of dihydrolipoamide dehydrogenase that contains an aminoterminal extension corresponding to a lipoyl domain, a property shared by the corresponding proteins from Alcaligenes eutrophus and Clostridium magnum. Aside from that feature, the protein is related phylogenetically to the corresponding proteins from A. laidlawii and M. genitalium. The phosphotransacetylase from M. capricolum is related most closely to the corresponding protein from M. genitalium and is distinguished easily from the enzymes from Escherichia coli and Haemophilus influenzae by the absence of the characteristic amino-terminal extension. The acetate kinase from M. capricolum is related evolutionarily to the homologous enzyme from M. genitalium. Map position comparisons of genes encoding proteins involved with pyruvate metabolism show that, whereas all the genes are clustered in M. capricolum, they are scattered in M. genitalium.

Acetate Kinase↗