Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Predictive coding”

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 1,747 records · Page 97Linked to original sources

Risk factors associated with recidivism among extrafamilial child molesters.

This study examined the predictive efficacy of 10 rationally derived, archivally coded variables for assessing reoffense risk among extrafamilial child molesters. Follow-up data on 111 child molesters who were discharged from the Massachusetts Treatment Center between 1960 and 1984 were used. Degree of sexual preoccupation with children, paraphilias, and number of prior sexual offenses predicted sexual recidivism. Juvenile and adult antisocial behavior, paraphilias, and low amount of contact with children predicted nonsexual victim-involved and violent recidivism. Area under the receiver-operating characteristic curves in all three analyses indicated discrimination that was substantially better than chance, ranging from .73 to .79.

Adult↗

Cloning, characterization, and possible origin of the Prevotella loescheii dnaK homolog.

Heat shock proteins play an important role in bacterial survival and response to environmental stress. We cloned the Prevotella loescheii HSP70 homolog (dnaK) and characterized the coding sequence, regulatory regions, and evolutionary relationships to other bacteria. Predicted proteins encoded by the P. loescheii dnaK homolog (open reading frame ORF-1) and two downstream coding regions, ORF-2 and ORF-3, are highly homologous to the proteins encoded by ORF-4 (dnaK), ORF-5, and ORF-6 from the dnaK region of Porphyromonas gingivalis. The dnaK promoter resembles other HSP (heat shock protein) promoters. Alignment of the predicted protein encoded by ORF-2 showed significant homology to the Bacteroides fragilis tnpA gene from the transposon Tn4555, whereas the ORF-3 protein showed homology to B. fragilis transposase (Tn5220) and integrase (Tn4555) proteins. This suggests a transposition-like event may be responsible for transfer of these genes between Porphyromonas and Prevotella.

Amino Acid Sequence↗

Three novel lossless image compression schemes for medical image archiving and telemedicine.

In this article, three novel lossless image compression schemes, hybrid predictive/vector quantization lossless image coding (HPVQ), shape-adaptive differential pulse code modulation (DPCM) (SADPCM), and shape-VQ-based hybrid ADPCM/DCT (ADPCMDCT) are introduced. All are based on the lossy coder, VQ. However, VQ is used in these new schemes as a tool to improve the decorrelation efficiency of those traditional lossless predictive coders such as DPCM, adaptive DPCM (ADPCM), and multiplicative autoregressive coding (MAR). A new kind of VQ, shape-VQ, is also introduced in this article. It provides predictive coders useful information regarding the shape characters of image block. These enhance the performance of predictive coders in the context of lossless coding. Simulation results of the proposed coders applied in lossless medical image compression are presented. Some leading lossless techniques such as DPCM, hierarchical interfold (HINT), CALIC, and the standard lossless JPEG are included in the tests. Promising results show that all these three methods are good candidates for lossless medical image compression.

Computer Storage Devices↗

Morbidity and mortality following bone marrow transplantation: predictive utility of pre-BMT affective functioning, compliance, and social support stability.

This study investigated the utility of 3 pretransplant psychological variables (affective functioning, compliance, social support stability) in predicting subsequent bone marrow transplantation (BMT) health outcomes. The pre-BMT psychological evaluations of 92 BMT recipients were coded along the specified psychological dimensions and used to predict post-BMT survival status and health-related quality of life. Data analyses showed that, in addition to medical risk status (low) and quality of the marrow graft (histocompatible), higher levels of pre-BMT affective functioning and social support stability significantly predicted survival status (i.e., alive) and higher levels of quality of life. These findings have important implications for the role of psychological assessment prior to BMT and the need for interventions designed to enhance psychological functioning and subsequent health outcomes following BMT.

Journal Article↗

Aromatase mRNA in the extragonadal tissues of chickens with the henny-feathering trait is derived from a distinctive promoter structure that contains a segment of a retroviral long terminal repeat. Functional organization of the Sebright, Leghorn, and Campine aromatase genes.

The henny-feathering trait is an autosomal dominant mutation that causes the expression of aromatase activity and accumulation of aromatase mRNA in extragonadal tissues of chickens. The current studies establish that the aromatase gene is not amplified and is organized similarly in control (Leghorn) and henny-feathered (Sebright and Campine) birds. Nucleotide sequence analysis of the nine coding exons of the aromatase gene reveals that the predicted amino acid sequence is identical in all three strains. We, therefore, characterized the genomic DNA segments flanking the coding segment of the Sebright, Leghorn, and Campine aromatase genes. The site of transcription initiation utilized in the ovary of all three strains is located approximately 147 nucleotides upstream of the initiator methionine. In addition to aromatase mRNA derived from this common ovarian promoter, another species of aromatase mRNA is present in Sebright and Campine ovary and is the only type detected in Sebright fibroblasts. cDNA copies of this second species of aromatase mRNA contain a unique 5' terminus, suggesting that a second promoter controls extragonadal aromatase expression in birds that carry the henny-feathering trait. Nucleotide sequence analysis of this 5' terminus indicates that this segment is derived from a retroviral long terminal repeat.

Amino Acid Sequence↗

Validity of stroke diagnosis on hospital discharge records in Saskatchewan, Canada: implications for stroke surveillance.

This study examines the validity of the diagnosis of stroke on hospital discharge records in Saskatchewan, Canada. In total, 1,494 records with a discharge diagnosis of 'stroke' or a 'stroke-related condition' were reviewed. The clinical algorithm of the 1980 USA National Survey of Stroke was considered the 'gold standard'. The positive predictive value of a primary diagnosis of stroke in the tertiary-care hospitals was about 90%. In community hospitals the majority of stroke cases were coded as ICD9 436 in which the positive predictive value was 78%. The variation between regions would limit the use of hospital discharge data for stroke surveillance.

Cerebrovascular Disorders↗

Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus.

MOTIVATION: The recent outbreak of severe acute respiratory syndrome (SARS) caused by SARS coronavirus (SARS-CoV) has necessitated an in-depth molecular understanding of the virus to identify new drug targets. The availability of complete genome sequence of several strains of SARS virus provides the possibility of identification of protein-coding genes and defining their functions. Computational approach to identify protein-coding genes and their putative functions will help in designing experimental protocols. RESULTS: In this paper, a novel analysis of SARS genome using gene prediction method GeneDecipher developed in our laboratory has been presented. Each of the 18 newly sequenced SARS-CoV genomes has been analyzed using GeneDecipher. In addition to polyprotein 1ab(1), polyprotein 1a and the four genes coding for major structural proteins spike (S), small envelope (E), membrane (M) and nucleocapsid (N), six to eight additional proteins have been predicted depending upon the strain analyzed. Their lengths range between 61 and 274 amino acids. Our method also suggests that polyprotein 1ab, polyprotein 1a, S, M and N are proteins of viral origin and others are of prokaryotic. Putative functions of all predicted protein-coding genes have been suggested using conserved peptides present in their open reading frames. AVAILABILITY: Detailed results of GeneDecipher analysis of all the 18 strains of SARS-CoV genomes are available at http://www.igib.res.in/sarsanalysis.html

Algorithms↗

Sequence analysis of the fiber genomic region of a porcine adenovirus predicts a novel fiber protein.

The complete nucleotide sequence of the putative fiber protein of a porcine adenovirus isolate, NADC-1, was determined. The coding sequence for the fiber protein was found to be 2112 nucleotides, predicting a 703 amino acid protein with a calculated molecular mass of 76,681 Da. The coding sequence is located between 86 and 92.5 map units. A polyadenylation signal was found 44 bases downstream of the stop codon. Northern hybridization analysis identified a band at 2.4 kb, which likely includes the primary transcript plus a tripartite leader (typically found with adenovirus transcripts) and a polyA(+) tail. The predicted NADC-1 fiber protein was found to have a tail domain comparable in size and sequence to most adenovirus fiber proteins, a comparatively short shaft region, and a head region that was more than twice as large as that of other adenovirus fiber proteins. Each of the three structural domains (tail, shaft, and head) of the predicted NADC-1 fiber protein was found to be most similar to the corresponding domain of a different mammalian adenovirus. The NADC-1 fiber head contained an RGD sequence, a motif that is found in the penton protein of other adenoviruses. Furthermore, the predicted amino acid sequence of the C-terminal half of the NADC-1 fiber head has significant homology to S-lectin proteins, a characteristic not shared with other adenovirus fiber proteins. Thus the predicted amino acid sequence of the NADC-1 fiber head is unique among adenoviruses for which the sequence of the fiber protein is known.

Amino Acid Sequence↗

Predictors of reading skill development in children with early cochlear implantation.

OBJECTIVE: The present study sought to document the word reading and comprehension levels attained by children who were implanted by 5 yr of age. It was hypothesized that the improved speech perception abilities acquired with cochlear implantation would promote phonological coding skills and facilitate the acquisition of beginning reading skills. DESIGN: Three subtests from diagnostic reading assessment batteries standardized on hearing children were administered to 181 children between 8 yr 0 mo and 9 yr 11 mo of age who had 4 to 6 yr of implant experience. In addition, a battery of processing measures was administered including a lexical decision task, a rhyme task and the digit span subtest of the Wechsler Intelligence Scale for Children. RESULTS: Over half of the children scored within the average range for their age compared with the normative data for hearing children. Reading competence was associated with higher nonverbal intelligence, higher family socio-economic status, female gender and later onset of deafness (between birth and 36 mo). After variance due to these child and family characteristics was removed, reading competence was associated with mainstream educational placement, use of an updated implant speech processor with a wide dynamic range, and speech processing characteristics that included longer memory span and use of phonological coding strategies. Reading outcome was most highly predicted by linguistic competence and, secondarily, by speech production skill. CONCLUSION: Children who experience severe to profound deafness early in their development have a better prognosis for normal literacy development than ever before. To the extent that use of a cochlear implant is associated with greater use of phonological coding strategies for decoding print, longer working memory spans for short-term storage of phonemes, words and sentences and accelerated language development for reading comprehension, it should have a facilitative effect on the acquisition of literacy.

Canada↗

Noninvasive field measurement of low-frequency ultrasonic transducers operating in sealed vessels.

This paper describes a noninvasive technique utilizing the acousto-optic effect, laser interferometry, and tomographic principles that have been implemented to measure the acoustic fields generated by low-frequency ultrasonic transducers operating into sealed, water-loaded vessels commonly used in industrial processing applications. A customized scanning frame, incorporating both linear and rotational stages, has been developed to facilitate manipulation of the laser head and vessel under evaluation. First, transmitted pressure profiles in air are predicted from surface displacement data acquired directly by laser measurement of the vibrating aperture. These profiles were then used to verify the measured fields obtained via conventional tomographic scanning procedures, coupled with laser interferometry, applied within a draft-proof scanning facility under free-field conditions. Next, the finite element code PZF(lex) was employed for the prediction of pressure fields within cylindrical cell configurations. Finally, precise manipulation of the laser firing angle and position was implemented in order to compensate for the effects of refraction at the cell wall boundaries, and to re-establish the projections required for the reconstruction algorithm. The experimental results demonstrate good corroboration with the PZF(lex) predictions, validating its application of ultrasound as a virtual prototyping tool for the design of high power ultrasonic test vessels.

Equipment Design↗

Using amino acid patterns to accurately predict translation initiation sites.

The translation initiation site (TIS) prediction problem is about how to correctly identify TIS in mRNA, cDNA, or other types of genomic sequences. High prediction accuracy can be helpful in a better understanding of protein coding from nucleotide sequences. This is an important step in genomic analysis to determine protein coding from nucleotide sequences. In this paper, we present an in silico method to predict translation initiation sites in vertebrate cDNA or mRNA sequences. This method consists of three sequential steps as follows. In the first step, candidate features are generated using k-gram amino acid patterns. In the second step, a small number of top-ranked features are selected by an entropy-based algorithm. In the third step, a classification model is built to recognize true TISs by applying support vector machines or ensembles of decision trees to the selected features. We have tested our method on several independent data sets, including two public ones and our own extracted sequences. The experimental results achieved are better than those reported previously using the same data sets. Our high accuracy not only demonstrates the feasibility of our method, but also indicates that there might be "amino acid" patterns around TIS in cDNA and mRNA sequences.

Algorithms↗

SVMtm: support vector machines to predict transmembrane segments.

A new method has been developed for prediction of transmembrane helices using support vector machines. Different coding schemes of protein sequences were explored, and their performances were assessed by crossvalidation tests. The best performance method can predict the transmembrane helices with sensitivity of 93.4% and precision of 92.0%. For each predicted transmembrane segment, a score is given to show the strength of transmembrane signal and the prediction reliability. In particular, this method can distinguish transmembrane proteins from soluble proteins with an accuracy of approximately 99%. This method can be used to complement current transmembrane helix prediction methods and can be used for consensus analysis of entire proteomes. The predictor is located at http://genet.imb.uq.edu.au/predictors/SVMtm.

Algorithms↗

Analysis of strain-specific plasmid sequences from Coxiella burnetii.

Acute isolates of Coxiella burnetii possess a 36-kbp plasmid termed QpH1. DNA hybridizations show that QpH1 contains approximately 6-kbp region of DNA which is not present in the QpRS plasmid from chronic isolates. This QpH1-specific region of DNA contains the contiguous EcoRI fragments G, E, and D. The GED region was found to possess seven open reading frames (ORF's) coding for proteins ranging from 5.5 to 42.3 kDa in molecular mass when subcloned and expressed in vitro. Summing the predicted ORF's accounts for 95% of the GED coding potential. E. coli expression produced a stable 42.3-kDa protein from the pHIN19 subclone of GED. The ORF of the 42.3-kDa protein, termed cbhE', has been localized on GED by both in vitro transcription/translation and DNA sequencing. The cbhE' gene is estimated as 1142 bp in length with a putative promoter region of TCAACT (-35)-N16-TAAAAT (-10)-N14-AGAAGGA (Shine-Dalgarno)-N10-ATG.

Cloning, Molecular↗

Probabilistic code for DNA recognition by proteins of the EGR family.

A recognition code for protein-DNA interactions would allow for the prediction of binding sites based on protein sequence, and the identification of binding proteins for specific DNA targets. Crystallographic studies of protein-DNA complexes showed that a simple, deterministic recognition code does not exist. Here, we present a probabilistic recognition code (P-code) that assigns energies to all possible base-pair-amino acid interactions for the early growth response factor (EGR) family of zinc-finger transcription factors. The specific energy values are determined by a maximum likelihood method using examples from in vitro randomisation experiments (namely, SELEX and phage display) reported in the literature. The accuracy of the model is tested in several ways, including the ability to predict in vivo binding sites of EGR proteins and other non-EGR zinc-finger proteins, and the correlation between predicted and measured binding affinities of various EGR proteins to several different DNA sites. We also show that this model improves significantly upon the prediction capabilities of previous qualitative and quantitative models. The probabilistic code we develop uses information about the interacting positions between the protein and DNA, but we show that such information is not necessary, although it reduces the number of parameters to be determined. We also employ the assumption that the total binding energy is the sum of the energies of the individual contacts, but we describe how that assumption can be relaxed at the cost of additional parameters.

Algorithms↗

Numerical simulation of turbulent gas flames in tubes.

Computational fluid dynamics (CFD) is an emerging technique to predict possible consequences of gas explosion and it is often considered a powerful and accurate tool to obtain detailed results. However, systematic analyses of the reliability of this approach to real-scale industrial configurations are still needed. Furthermore, few experimental data are available for comparison and validation. In this work, a set of well documented experimental data related to the flame acceleration obtained within obstacle-filled tubes filled with flammable gas-air mixtures, has been simulated. In these experiments, terminal steady flame speeds corresponding to different propagation regimes were observed, thus, allowing a clear and prompt characterisation of the numerical results with respect to numerical parameters, as grid definition, geometrical parameters, as blockage ratio and to mixture parameters, as mixture reactivity. The CFD code AutoReagas was used for the simulations. Numerical predictions were compared with available experimental data and some insights into the code accuracy were determined. Computational results are satisfactory for the relatively slower turbulent deflagration regimes and became fair when choking regime is observed, whereas transition to quasi-detonation or Chapman-Jogouet (CJ) were never predicted.

Gases↗

Dynamic molecular modeling of pathogenic mutations in the spectrin self-association domain.

Disruption of spectrin self-association underlies many inherited hemolytic disorders. Using dynamic modeling and energy minimization, the 3-dimensional structure of the self-association domain has been estimated in human erythrocyte spectrin and the structural consequences of 17 elliptogenic mutations determined. The predicted structure of the normal self-association domain was remarkably similar to the crystal structure of the Drosophila alpha-spectrin 14th repeat unit, despite replacement in the human sequence of over 70% of the amino acids relative to fly spectrin, including 2 prolines in the human sequence that appear in helical regions of the fly structure. The predicted structure placed all hydrophilic residues at the surface and identified 4 salt bridges, 9 hydrophobic interactions, and 4 H-bonds that stabilize the native self-association unit. Remarkably, every pathologic point mutation, including seemingly conservative substitutions such as G for A, A for V, or K for R (single-letter amino acid codes), led to conformational rearrangements in the predicted structure. The degree of structural disruption, as measured by root-mean-square deviation of the predicted backbone structure from the Drosophila structure, correlated strongly with the severity of clinical disease associated with each mutation. This approach thus enables an accurate prediction, from the primary sequence, of the clinical consequences of specific point mutations in spectrin. The 3-dimensional structure of the self-association domain derived here is likely to be accurate. It provides a powerful heuristic model for understanding how point mutations disrupt cytoskeletal function in a variety of hemolytic disorders.

Amino Acid Sequence↗

The nucleotide sequence of a rat myosin light chain 2 gene.

A rat myosin light chain 2 gene was characterized by nucleotide sequence and S1 mapping analyses. It contains seven exons separated by six introns. The corresponding mRNA is predicted to be 654 nucleotides long (excluding polyA sequences), with 5'-nontranslated, coding, and 3'-nontranslated lengths of 56, 510, and 88 nucleotides, respectively. The predicted amino acid sequence is identical to that from rabbit except that the rat sequence lacks one of two Gly residues located at positions 12 and 13 in the rabbit sequence. From the nucleotide sequence, nascent rat myosin light chain 2 is predicted to have Met Ala preceding Pro at the N-terminal end.

Amino Acid Sequence↗

The accuracy of hospital records and death certificates for acute myocardial infarction.

BACKGROUND: In Australia information on the incidence of acute myocardial infarction (AMI) is available from routinely collected morbidity and mortality data. Given that these data are used for monitoring AMI it is important to assess their quality. AIMS: This paper examines the accuracy of the hospital records and death certificates. METHODS: Morbidity and mortality data were compared with the Newcastle heart disease register which is part of the WHO MONICA Project for 1986-1991 and sensitivity and positive predictive values calculated. RESULTS: For non-fatal AMI the hospital diagnostic coding had sensitivity of 78.9% (95% confidence interval [CI] 77.1%-80.7%), and positive predictive value of 65.6% (95% CI 63.7%-67.4%). Sensitivity was higher for men than for women and decreased with increasing age. Sensitivity was higher in those with no history of either AMI or other ischaemic heart disease (IHD), higher in current smokers than ex-smokers or never smokers, and lower in those with a self-reported history of high blood pressure. Sensitivity also varied among hospitals. Positive predictive value varied only with hospital. Both sensitivity and positive predictive value were high for death certificate data--89.9% (95% CI 88.4%-91.3%) and 96.0% (95% CI 95.1%-97.0%), respectively. CONCLUSIONS: Although the mortality data appear to be quite accurate, the hospital data alone are not accurate enough to be used to estimate rates or trends of heart attacks. Additional data are required in order to determine numbers of non-fatal AMIs accurately.

Adult↗