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PubMed2001

Accuracy of external cause of injury codes reported in Washington State hospital discharge records.

OBJECTIVE: To evaluate the accuracy of external cause of injury codes (E codes) reported in computerized hospital discharge records. METHODS: All civilian hospitals in Washington State submit computerized data for each hospital discharge to a file maintained by the Department of Health. In 1996, 32 hospitals accounted for 80% of the injury related discharges in this file; from these hospitals, we sampled 1,260 computerized records for injured patients in a stratified, but random, manner. An expert coder then visited the 32 study hospitals, reviewed the medical records that corresponded to each computerized record, and assigned an E code for that hospitalization. The computerized E code information was compared with codes provided by the expert reviewer. RESULTS: The incidence of hospitalization for injury based upon computerized hospital discharge data was very similar to that based upon chart review: incidence rate ratio 1.0 (95% confidence interval 1.00 to 1.02). Computerized hospital discharge data correctly ranked injuries in regard to both mechanism and intent. Overall agreement on coding was 87% for mechanism of injury, 95% for intent of injury, and 66% for the complete E code. The sensitivity of computerized hospital discharge data for identification of falls, motor vehicle traffic injuries, poisonings, and firearm injuries was 91% or better. The predictive value positive of coding for these four categories of injury ranged from 88% for motor vehicle traffic injuries to 94% for poisonings. The amount of agreement for intent coding ranged from 84% for firearm injuries to 99% for falls. Agreement on coding of the complete E code ranged from 57% for firearm injuries to 72% for poisonings. CONCLUSIONS: Computerized hospital discharge data can be used with confidence to determine how many injuries are treated in a hospital setting and the relative magnitude of various categories of injury. E codes reported in hospital discharge data are a reliable source of information on the types of information most often used for injury related analyses and priority setting. The detail codes (complete E codes) reported in hospital discharge codes are less reliable and must be used with caution.

Forms and Records Control↗
PubMed2002

Monte Carlo dose calculations in homogeneous media and at interfaces: a comparison between GEPTS, EGSnrc, MCNP, and measurements.

Three Monte Carlo photon/electron transport codes (GEPTS, EGSnrc, and MCNP) are bench-marked against dose measurements in homogeneous (both low- and high-Z) media as well as at interfaces. A brief overview on physical models used by each code for photon and electron (positron) transport is given. Absolute calorimetric dose measurements for 0.5 and 1 MeV electron beams incident on homogeneous and multilayer media are compared with the predictions of the three codes. Comparison with dose measurements in two-layer media exposed to a 60Co gamma source is also performed. In addition, comparisons between the codes (including the EGS4 code) are done for (a) 0.05 to 10 MeV electron beams and positron point sources in lead, (b) high-energy photons (10 and 20 MeV) irradiating a multilayer phantom (water/steel/air), and (c) simulation of a 90Sr/90Y brachytherapy source. A good agreement is observed between the calorimetric electron dose measurements and predictions of GEPTS and EGSnrc in both homogeneous and multilayer media. MCNP outputs are found to be dependent on the energy-indexing method (Default/ITS style). This dependence is significant in homogeneous media as well as at interfaces. MCNP(ITS) fits more closely the experimental data than MCNP(DEF), except for the case of Be. At low energy (0.05 and 0.1 MeV), MCNP(ITS) dose distributions in lead show higher maximums in comparison with GEPTS and EGSnrc. EGS4 produces too penetrating electron-dose distributions in high-Z media, especially at low energy (<0.1 MeV). For positrons, differences between GEPTS and EGSnrc are observed in lead because GEPTS distinguishes positrons from electrons for both elastic multiple scattering and bremsstrahlung emission models. For the 60Co source, a quite good agreement between calculations and measurements is observed with regards to the experimental uncertainty. For the other cases (10 and 20 MeV photon sources and the 90Sr/90Y beta source), a good agreement is found between the three codes. In conclusion, differences between GEPTS and EGSnrc results are found to be very small for almost all media and energies studied. MCNP results depend significantly on the electron energy-indexing method.

Algorithms↗
PubMed2001

Cloning of a metallothionein gene and characterization of two other cDNA sequences in the Pacific oyster Crassostrea gigas (CgMT1).

Metallothionein (MT) genes encode essential metal-binding proteins involved in metallic homeostasis and detoxification in living organisms. Here, we describe the structure of the first Pacific oyster Crassostrea gigas metallothionein (CgMT1) gene and the sequences of two other MT cDNA. The CgMT1 gene sequence contains three coding exons plus a 5' entirely non-coding exon, and the predicted protein contains 21 cysteine residues organized in Cys-X-Cys motifs as classically described for MTs. The three cDNA sequences present few substitutions in either coding sequence or UTRs. Induction of these MT-mRNA in heavy metal-treated oysters (i.e. cadmium) was confirmed by Northern blot analysis and RT-PCR and suggests a potential specific tissue expression rate. Southern blot analysis suggested the presence of multiple CgMT genes, and allowed the detection of restriction fragment length polymorphisms (RFLPs). Although the CgMT1 coding sequence showed 30-73% nucleotide identities with known sequences in other mollusks, it included the specific motif Cys-X-Cys-X(3)-Cys-Thr-Gly-X-X-X-Cys-X-Cys-X(5)-Cys-X-Cys-Lys found in Mollusk family 2. Marine bivalves are commonly used as pollution bioindicators, thus the development of genetic markers based on CgMT1 polymorphism will allow a monitoring of heavy metal exposure in anthropogenically disturbed ecosystems.

Amino Acid Sequence↗
PubMed1981

Isolation and Mapping of Small Cauliflower Mosaic Virus DNA Fragments Active as Promoters in Escherichia coli.

Small EcoRI(*) fragments of cauliflower mosiac virus DNA (strain CM4-184), which act as promoters for the tetracycline resistance gene on the promoter probe plasmid pBRH4 in Escherichia coli, have been isolated and mapped on the viral genome. Two regions of the viral genome contain DNA sequences with promoter activity in E. coli. Two independent cloned fragments from one region direct a high level of tetracycline resistance (up to 38 mug of tetracycline per ml). Two independent fragments from the second region of the viral genome also direct tetracycline resistance, but at lower levels. The activity of the two fragments with the strongest promoter activity in E. coli may direct transcription of the viral genome in a clockwise direction. This is consistent with the direction of transcription predicted from sequence analysis of the viral DNA (Franck et al., Cell 21: 285-294, 1980). One of these fragments maps at the start of a large open translational reading frame which is predicted to contain the coding sequence for the viral coat protein. Each promoter-active fragment is located in the 5'-terminal portion of one of the six open reading frames predicted from the DNA sequence.

Journal Article↗
PubMed2002

Identifying patient preoperative risk factors and postoperative adverse events in administrative databases: results from the Department of Veterans Affairs National Surgical Quality Improvement Program.

BACKGROUND: The Department of Veterans Affairs (DVA) National Surgical Quality Improvement Program (NSQIP) employs trained nurse data collectors to prospectively gather preoperative patient characteristics and 30-day postoperative outcomes for most major operations in 123 DVA hospitals to provide risk-adjusted outcomes to centers as quality indicators. It has been suggested that routine hospital discharge abstracts contain the same information and would provide accurate and complete data at much lower cost. STUDY DESIGN: With preoperative risks and 30-day outcomes recorded by trained data collectors as criteria standards, ICD-9-CM hospital discharge diagnosis codes in the Patient Treatment File (PTF) were tested for sensitivity and positive predictive value. ICD-9-CM codes for 61 preoperative patient characteristics and 21 postoperative adverse events were identified. RESULTS: Moderately good ICD-9-CM matches of descriptions were found for 37 NSQIP preoperative patient characteristics (61%); good data were available from other automated sources for another 15 (25%). ICD-9-CM coding was available for only 13 (45%) of the top 29 predictor variables. In only three (23%) was sensitivity and in only four (31%) was positive predictive value greater than 0.500. There were ICD-9-CM matches for all 21 NSQIP postoperative adverse events; multiple matches were appropriate for most. Postoperative occurrence was implied in only 41%; same breadth of clinical description in only 23%. In only four (7%) was sensitivity and only two (4%) was positive predictive value greater than 0.500. CONCLUSION: Sensitivity and positive predictive value of administrative data in comparison to NSQIP data were poor. We cannot recommend substitution of administrative data for NSQIP data methods.

Benchmarking↗
PubMed1994

Antiviral drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase occur in specific RNA structural regions.

A statistically significant correlation exists between the locations of drug resistance mutations (DRMs) observed for various reverse transcriptase inhibitors and features of the secondary structure predicted for the RNA coding for human immunodeficiency virus type 1 reverse transcriptase. The known DRMs map onto "unstable" bases, which are predominantly nonhelical regions (i.e., loops, bulges, and bends) of the predicted RNA secondary structure, whereas codons for the key conserved residues of polymerase sequence motifs map onto "stable" paired bases involved in helical regions. On the basis of these results, we hypothesize that the secondary structure of the RNA template (in this case, the reverse transcriptase gene itself) may be a previously unrecognized factor contributing to base misincorporation errors during reverse transcription and that, rather than being randomly distributed, mutations are more likely to occur in specific regions of the genome. The results suggest that these "mutation-prone" regions can be predicted by using a standard algorithm for RNA secondary structure.

Antiviral Agents↗
PubMed2001

Identification of a region in glycoprotein IIIa involved in subunit association with glycoprotein IIb: further lessons from Iraqi-Jewish Glanzmann thrombasthenia.

The most frequent mutation causing Glanzmann thrombasthenia in Iraqi-Jews (IJ-1) is an 11-bp deletion in exon 13 of the glycoprotein (GP) IIIa gene. This deletion predicts a frameshift that results in the elimination of the C406-C655 disulfide bond and a premature termination codon shortly before the transmembrane domain. To determine the contribution of each of these alterations to the thrombasthenic phenotype, Chinese hamster ovary or baby hamster kidney cells were cotransfected with normal GPIIb complementary DNA (cDNA) and the following GPIIIa cDNAs: normal, cDNA bearing IJ-1 mutation, 2011T>A mutated cDNA predicting C655S (single-letter amino acid codes) substitution, and 2019A>T mutated cDNA predicting Stop657. Elimination of the C406-C655 disulfide bond by C655S substitution did not affect GPIIb/IIIa surface expression or binding of the transfected cells to immobilized fibrinogen, whereas elimination of the transmembrane and cytoplasmic domains in IJ-1 and Stop657 mutants prevented both surface expression and binding of the transfected cells to immobilized fibrinogen. Immunohistochemical staining and immunoprecipitation demonstrated that the elimination of amino acids 657-762 in IJ-1 and Stop657 prevented intracellular GPIIb/IIIa complex formation, and differential immunofluorescence staining of GPIIIa and cellular organelles suggested that the truncated uncomplexed GPIIIa protein was retained in the endoplasmic reticulum. Because the use of GPIIIa Stop693 and normal GPIIb cDNAs yielded GPIIb/IIIa complex formation, though with lower efficiency, it is suggested that amino acids 657-692 of GPIIIa are essential for the intracellular association of GPIIb and GPIIIa. (Blood. 2001;98:1063-1069)

Animals↗
PubMed2005

Ventral pallidal neurons code incentive motivation: amplification by mesolimbic sensitization and amphetamine.

Neurons in ventral pallidum fire to reward and its predictive cues. We tested mesolimbic activation effects on neural reward coding. Rats learned that a Pavlovian conditioned stimulus (CS+1 tone) predicted a second conditioned stimulus (CS+2 feeder click) followed by an unconditioned stimulus (UCS sucrose reward). Some rats were sensitized to amphetamine after training. Electrophysiological activity of ventral pallidal neurons to stimuli was later recorded under the influence of vehicle or acute amphetamine injection. Both sensitization and acute amphetamine increased ventral pallidum firing at CS+2 (population code and rate code). There were no changes at CS+1 and minimal changes to UCS. With a new 'Profile Analysis', we show that mesolimbic activation by sensitization/amphetamine incrementally shifted neuronal firing profiles away from prediction signal coding (maximal at CS+1) and toward incentive coding (maximal at CS+2), without changing hedonic impact coding (maximal at UCS). This pattern suggests mesolimbic activation specifically amplifies a motivational transform of CS+ predictive information into incentive salience coded by ventral pallidal neurons. Our results support incentive-sensitization predictions and suggest why cues temporally proximal to drug presentation may precipitate cue-triggered relapse in human addicts.

Algorithms↗
PubMed1993

Characterization and sequence analysis of a small cryptic plasmid from Lactobacillus curvatus LTH683 and its use for construction of new Lactobacillus cloning vectors.

Lactobacillus curvatus LTH683, a strain originally isolated from raw sausage, contains the single cryptic plasmid called pLC2. The sequence and genetic organization of the complete 2489-bp plasmid pLC2 was determined and used as the basis for construction of a series of vectors useful in Lactobacillus strains. The major parts of pLC2 nucleotide sequence could be aligned with other plasmids from gram-positive bacteria replicating by a rolling circle mechanism of replication (RCR). Direct evidence for a RCR mechanism was obtained by showing the accumulation of single-stranded plasmid intermediates in the presence of rifampicin. Three protein-coding sequences could be predicted and the corresponding proteins were detected after in vitro transcription/translation of pLC2 plasmid DNA. ORFs 1 and 3 showed minor homologies to plasmids of gram-positive bacteria. The replication protein coded by ORF2 and its corresponding target sequence, the plus origin, were similar to replication regions of other gram-positive bacteria plasmids like pLS1, pWV01, and pE194. Upstream of the ori+ site, in a noncoding region, which was nonessential for replication, strong homology to other Lactobacillus plasmids like pC30i1, pLP1, pLJ1, and pLAB1000 could be detected. A palindromic sequence predicted to be the minus origin of replication was localized there. Small vectors (3213 bp) suitable for cloning in lactobacilli were constructed based on a 1635-bp DNA fragment of pLC2, containing the region necessary for replication, marked with the chloramphenicol resistance gene and a multiple cloning site.

Amino Acid Sequence↗
PubMed2005

A nineteen-year cohort study on the relationship of electrocardiographic findings to all cause mortality among subjects in the national survey on circulatory disorders, NIPPON DATA80.

BACKGROUND: Electrocardiogram (ECG) is one of the most popular tools for daily clinics and health checkup, and has been used for the National Survey on Circulatory Disorders to assess the health status in Japanese people. The meaningfulness to predict mortality from all causes among people with ECG abnormality is to be clarified using national samples. METHODS: ECG findings recorded among 9,638 subjects for National Survey on Circulatory Disorders 1980 in Japan, were classified using the Minnesota Codes (mc). Their relationships to all cause mortality over 19 years were examined using Cox proportional hazard models adjusting for sex, age, systolic blood pressure, blood glucose, and smoking habits. RESULTS: Subjects with abnormal Q-QS findings showed significantly high hazard ratios ( 3.71(mc1-1) and 1.57 (mc1-3)) for mortality to the subjects who were free from any major ECG findings. Hazard ratios were 1.37 (mc2-1) to 4.16 (mc2-5) for axis deviation, and 1.34 (mc3-1) to 1.35 (mc3-3) for left high R waves. Those were 1.63 (mc4-3) to 2.59 (mc4-1) for ST depression, and 1.54 (mc5-3) to 2.33 (mc5-1) for T abnormality. The lower the second number of the Minnesota Codes was, the higher hazard ratio was observed in the Q-QS, ST, T codes. The hazard ratios of junction-type ST depression (mc4-4), and low T waves (mc5-4, 5-5) were not significant. CONCLUSIONS: ECG findings defined by the Minnesota Codes were useful to predict the risk for mortality from all causes even after adjusting for the other major risk factors, and the results supported a usefulness of the ECG for health check-ups.

Adult↗
PubMed2001

Computerized assessment of complications after colorectal surgery: is it valid?

PURPOSE: Historically, complication rates after colorectal surgery have been stratified by disease process, type of operation, or anesthesia risk derived after an intensive review of the medical record. Newer computer applications purport to shorten this process and predict the probability of postoperative complications by distinguishing them from comorbidities that are commingled on uniform discharge codes. We analyzed CaduCIS software, which uses discharge codes, to determine whether its predictions of comorbidity and complications were comparable to what was interpreted on the medical record. METHODS: Two-hundred seventy patients were analyzed according to the principal and secondary diagnoses coded on discharge. Coding inaccuracies of clinical occurrences were identified by physician review of each medical record. The actual incidences of 17 common preoperative comorbidities and 11 postoperative complications were compared with those predicted by CaduCIS. RESULTS: The CaduCIS-predicted distribution of comorbidities was similar to the actual occurrences in 15 of 17 categories. The overall incidence of complications obtained by physician (actual) review was 47 percent, compared with 46 percent predicted by CaduCIS. However, there was a statistical difference between the CaduCIS-predicted and the actual complication rates in 5 of the 11 categories. The most common preoperative comorbidity and complication was cardiopulmonary (47 percent and 28 percent, respectively). CONCLUSION: The overall complication rate interpreted from the medical record (47 percent) was accurately predicted by CaduCIS (46 percent). Predictions of 5 of 11 individual complications were underestimated because of charting and coding inaccuracies, not because of computerized errors. Because uniform discharge coding of commingled comorbidity and complications is increasingly used to rapidly compute surgical outcomes, colon and rectal surgeons need to ensure compatibility of the actual and coded medical records.

Comorbidity↗
PubMed2003

Narrative electronic patient records as source of discharge diagnoses.

OBJECTIVE: To evaluate the consistency of diagnostic data extracted from narrative electronic patient record (EPR) notes compared with the data from a patient administrative system (PAS). To assess potential benefit of using EPR notes as source of diagnosis data and as basis for case identification. DESIGN: Construction of a computer algorithm to extract ICD-9 codes from narrative EPR notes. Assessment of consistency and reliability of the diagnostic codes retrieved from EPR notes and PAS. Estimation of efficiency of case identification based on data from PAS and EPR. RESULTS: Diagnosis codes were retrieved from PAS with sensitivity of 0.989 and the positive predictive value (PPV) was 0.993. Codes were retrieved from EPR with sensitivity of 0.908 and PPV of 0.990. Combining these two sources increased sensitivity to 0.999. CONCLUSION: Discharge diagnoses were easily extracted from narrative EPR notes by automatic methods. Information extracted from record notes was not significantly different from the corresponding data in PAS, but EPR was incomplete as compared with PAS. Utilizing data extracted from EPR improved case identification significantly.

Algorithms↗
PubMedDate not supplied

A predictive reinforcement model of dopamine neurons for learning approach behavior.

A neural network model of how dopamine and prefrontal cortex activity guides short- and long-term information processing within the cortico-striatal circuits during reward-related learning of approach behavior is proposed. The model predicts two types of reward-related neuronal responses generated during learning: (1) cell activity signaling errors in the prediction of the expected time of reward delivery and (2) neural activations coding for errors in the prediction of the amount and type of reward or stimulus expectancies. The former type of signal is consistent with the responses of dopaminergic neurons, while the latter signal is consistent with reward expectancy responses reported in the prefrontal cortex. It is shown that a neural network architecture that satisfies the design principles of the adaptive resonance theory of Carpenter and Grossberg (1987) can account for the dopamine responses to novelty, generalization, and discrimination of appetitive and aversive stimuli. These hypotheses are scrutinized via simulations of the model in relation to the delivery of free food outside a task, the timed contingent delivery of appetitive and aversive stimuli, and an asymmetric, instructed delay response task.

Animals↗
PubMedDate not supplied

[Emotional disorders in the mothers of children treated at a mental health center].

The aim of this research has been the detection of possible psychiatric disorders in the mothers of referred children. Also, we investigated the family history and its dynamic aspects. It was carried out from February to June of 1988. The sample is made up of 43 children (3-16 years old). Each of the mothers filled out the GHQ-28. Other variables studied were the epidemiologic ones, parental age, the DSM-III diagnostics and the severity of the pathology found in the children through the CGAS. We found that the mothers tended to be pathologic in the GHQ values; 17 children (40%) had familial antecedents and abnormal family dynamics; 11 children (26%) had a mother with a pathologic GHQ and abnormal family dynamics and psychiatric antecedents. It was suggested that these 3 factors may have a predictive value for the DSM-III-specific diagnosis different from the Code V diagnosis, that is, predictive of more severe psychopathology.

Adolescent↗
PubMed2004

Computerized coding of injury narrative data from the National Health Interview Survey.

OBJECTIVE: To investigate the accuracy of a computerized method for classifying injury narratives into external-cause-of-injury and poisoning (E-code) categories. METHODS: This study used injury narratives and corresponding E-codes assigned by experts from the 1997 and 1998 US National Health Interview Survey (NHIS). A Fuzzy Bayesian model was used to assign injury descriptions to 13 E-code categories. Sensitivity, specificity and positive predictive value were measured by comparing the computer generated codes with E-code categories assigned by experts. RESULTS: The computer program correctly classified 4695 (82.7%) of the 5677 injury narratives when multiple words were included as keywords in the model. The use of multiple-word predictors compared with using single words alone improved both the sensitivity and specificity of the computer generated codes. The program is capable of identifying and filtering out cases that would benefit most from manual coding. For example, the program could be used to code the narrative if the maximum probability of a category given the keywords in the narrative was at least 0.9. If the maximum probability was lower than 0.9 (which will be the case for approximately 33% of the narratives) the case would be filtered out for manual review. CONCLUSIONS: A computer program based on Fuzzy Bayes logic is capable of accurately categorizing cause-of-injury codes from injury narratives. The capacity to filter out certain cases for manual coding improves the utility of this process.

Forms and Records Control↗
PubMed2006

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

BACKGROUND: As part of the ENCODE Genome Annotation Assessment Project (EGASP), we developed the MARS extension to the Twinscan algorithm. MARS is designed to find human alternatively spliced transcripts that are conserved in only one or a limited number of extant species. MARS is able to use an arbitrary number of informant sequences and predicts a number of alternative transcripts at each gene locus. RESULTS: MARS uses the mouse, rat, dog, opossum, chicken, and frog genome sequences as pairwise informant sources for Twinscan and combines the resulting transcript predictions into genes based on coding (CDS) region overlap. Based on the EGASP assessment, MARS is one of the more accurate dual-genome prediction programs. Compared to the GENCODE annotation, we find that predictive sensitivity increases, while specificity decreases, as more informant species are used. MARS correctly predicts alternatively spliced transcripts for 11 of the 236 multi-exon GENCODE genes that are alternatively spliced in the coding region of their transcripts. For these genes a total of 24 correct transcripts are predicted. CONCLUSION: The MARS algorithm is able to predict alternatively spliced transcripts without the use of expressed sequence information, although the number of loci in which multiple predicted transcripts match multiple alternatively spliced transcripts in the GENCODE annotation is relatively small.

Algorithms↗
PubMed1997

Functional prediction of B. subtilis genes from their regulatory sequences.

In bacterial cells, gene expression is regulated by multiple sigma factors, each of which has its promoter specificity, according to their conditions. Thus, if we can discriminate which sigma factor binds to the upstream region of a given coding sequence, we can predict in what condition it will be expressed. In this paper, we show this approach is feasible for the analysis of Bacillus subtilis genome. Based on our collection of known promoter sequences, we prepared 8 predictors to characterize known sigma factors using the hidden Markov model and their prediction accuracies were estimated with a cross-validation test. Furthermore, we predicted the sigma-dependencies for each of 1415 candidate genes in the genome. Our prediction results are experimentally testable and seem useful for the post-sequencing project.

Bacillus subtilis↗
PubMed2003

[In silicon cloning of the human TECTB gene].

The coding sequence of the mouse Tectb and chick Tectb gene were subjected to Blastn searching against the human dbEST and Htgs in NCBI. One BAC clone sequence(GenBank: AL157786) was obtained, which shows high homology to the two genes. We predicted the exons and introns in the homologous region of AL157786 using GENSCAN, MZEF and Blast 2 sequence program, and then assembled the predicted exons into the coding sequence of the human TECTB. The open reading frame of human TECTB gene is 990 bp composed of ten exons, which encodes a protein of 329 amino acids. Human TECTB gene shows 88.1% identity in 990 bp overlap with that of the mouse Tectb gene and the predicted polypeptide shows 94.2% identity in 329 as with the mouse beta-tectorin. The TECTB gene was mapped to human chromosome 10q25 by electronic-PCR.

Amino Acid Sequence↗