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PubMed2000

Medical communication: do our patients understand?

The objective of this study was to determine emergency department (ED) patient's understanding of common medical terms used by health care providers (HCP). Consecutive patients over 18 years of age having nonurgent conditions were recruited from the EDs of an urban and a suburban hospital between the hours of 7 a.m. and 11 p.m. Patients were asked whether six pairs of terms had the same or different meaning and scored on the number of correct answers (maximum score 6). Multiple linear regression analysis was used to assess possible relationships between test scores and age, sex, hospital site, highest education level, and predicted household income (determined from zip code). Two hundred forty-nine patients (130 men/119 women) ranging in age from 18 to 87 years old (mean = 39.4, SD = 14.9) were enrolled on the study. The mean number of correct responses was 2.8 (SD = 1.2). The percentage of patients that did not recognize analogous terms was 79% for bleeding versus hemorrhage, 78% for broken versus fractured bone, 74% for heart attack versus myocardial infarction, and 38% for stitches versus sutures. The percentage that did not recognize nonanalogous terms was 37% for diarrhea versus loose stools, and 10% for cast versus splint. Regression analysis (R2 = .13) revealed a significant positive independent relationship between test score and age (P < .024), education (P < .001), and suburban hospital site (P < .004). Predicted income had a significant relationship with test score (P < .001); however, this was no longer significant when controlled for the confounding influence of age, education and hospital site. Medical terminology is often poorly understood, especially by young, urban, poorly educated patients. Emergency health care providers should remember that even commonly used medical terminology should be carefully explained to their patients.

Adolescent↗
PubMed1993

The herpes simplex virus type 2 UL3 open reading frame encodes a nuclear localizing phosphoprotein.

The herpes simplex virus type 2 (HSV-2, strain 333) UL3 open reading frame (ORF) codes for a protein with a predicted molecular weight of 29,681. Comparisons of the UL3, strain 333 ORF show essentially complete amino acid identity with HSV-2 (strain HG52) and a 75% amino acid identity with HSV type 1 (strain 17). To characterize the expression of this gene, a hydrophilic region of the HSV-2 UL3 gene was cloned into a bacterial expression vector. The resulting fusion protein was used to generate antibodies in rabbits. In vitro translation of HSV-2-derived mRNA followed by immunoprecipitation with the rabbit antisera reveals a major 28,000-Da protein as judged by SDS-polyacrylamide gel electrophoresis. This is consistent with the predicted molecular weight of an unmodified UL3 protein. Pulse-labeling of infected cells, with [35S]methionine, followed by immunoprecipitation and electrophoretic analysis reveals three distinct bands of 28,000, 30,500, and 33,000 Da. Labeling infected cells with [32P]orthophosphate shows that the 30,500- and the 33,000-Da species are post-translationally phosphorylated. The 30,500-Da species can be converted to the 28,000-Da species with alkaline phosphatase treatment. Interestingly, the 33,000-Da species is resistant to this treatment. Immunohistochemical analysis of infected cells reveals that the UL3 protein has a perinuclear location early in infection and at later times becomes associated with the nucleus as discrete particles. A mutant of HSV, which has a major deletion of the UL3 coding region does not show any immunohistochemical staining with the UL3 antisera. The wild-type virus-infected cell staining pattern remains the same subsequent to DNAse and RNAse treatment, indicating that the UL3 protein product is not directly associated with nucleic acid.

Amino Acid Sequence↗
PubMed1998

Cloning and characterization of the dnaK heat shock operon of the marine bacterium Vibrio harveyi.

We cloned the DNA region of the Vibrio harveyi chromosome containing the heat shock genes dnaK and dnaJ and sequenced them. These genes are arranged in the chromosome in the order dnaK-dnaJ, as in other proteobacteria of the alpha and gamma subdivisions. The dnaK gene is 1923 nucleotides in length and codes for a protein of 640 amino acid residues, with a predicted molecular mass of 69,076 Da and 81.2% similarity to the DnaK protein of Escherichia coli. The V. harveyi dnaJ gene has a coding sequence of 1158 nucleotides. The predicted DnaJ protein contains 385 amino acids, its calculated molecular mass is 41,619 Da and it has 74.7% similarity to the DnaJ protein of E. coli. Northern hybridization experiments with RNA from V. harveyi cells and a DNA probe carrying both the dnaK and dnaJ genes showed a single, heat-inducible transcript, indicating that these genes form an operon. Primer extension analysis revealed five heat-inducible transcriptional start sites upstream of the dnaK gene, two of which (T1 and T4) are preceded by sequences typical of the E. coli heat shock promoters recognized by the sigma 32 (sigma32) factor. Location of these promoters is highly similar to that of the E. coli dnaK promoters. No transcriptional start sites were detected upstream of the dnaJ gene. The V. harveyi dnaKJ operon cloned in a plasmid in E. coli cells was transcribed in a sigma32 dependent manner and the size of the transcript, the kinetics of transcription, and the transcriptional start sites were as in V. harveyi cells. This indicates a high conservation of the transcriptional heat shock regulatory elements between E. coli and V. harveyi, both belonging to the gamma subdivision of proteobacteria. We tested the ability of the cloned dnaKJ genes to complement E. coli dnaK and dnaJ mutants and found that V. harveyi DnaJ restored a thermoresistant phenotype to dnaJ mutants and enabled lambda phage to grow in the mutant cells. V. harveyi DnaK did not suppress the thermosensitivity of dnaK mutants but complemented the dnaK deletion mutant with respect to growth of lambda phage. V. harveyi DnaK, in contrast to DnaJ, failed to modulate the heat shock response in E. coli. Our results suggest that the DnaK chaperone may be more species specific than the DnaJ chaperone.

Amino Acid Sequence↗
PubMed1992

Examination of potato virus X proteins synthesized in infected tobacco plants.

Nucleotide sequence analysis of potato virus X (PVX) genomic RNA predicts five open reading frames (ORFs). Previous analysis of total RNAs from PVX-infected leaf tissue suggested that six subgenomic RNAs are synthesized during infection. However, the proteins encoded by the genomic RNA, the subgenomic RNAs, or the predicted ORFs have not been identified in vivo. To characterize the coding properties of the viral RNA, particularly to determine whether the five predicted ORFs function in vivo, total protein extracts prepared from PVX-infected leaf tissue were analyzed by using antibodies raised against virus-specific synthetic peptides and against the virus capsid protein. Dot blot analyses showed that these antibodies reacted to PVX-infected extracts, indicating in vivo expression of the five predicted ORFs. In addition, Western blot (immunoblot) analysis of the extracts showed that ORF 1, 2, 3, and 4 peptide antisera and coat protein antiserum detect predominantly a single protein.

Amino Acid Sequence↗
PubMed2001

An energy budget for signaling in the grey matter of the brain.

Anatomic and physiologic data are used to analyze the energy expenditure on different components of excitatory signaling in the grey matter of rodent brain. Action potentials and postsynaptic effects of glutamate are predicted to consume much of the energy (47% and 34%, respectively), with the resting potential consuming a smaller amount (13%), and glutamate recycling using only 3%. Energy usage depends strongly on action potential rate--an increase in activity of 1 action potential/cortical neuron/s will raise oxygen consumption by 145 mL/100 g grey matter/h. The energy expended on signaling is a large fraction of the total energy used by the brain; this favors the use of energy efficient neural codes and wiring patterns. Our estimates of energy usage predict the use of distributed codes, with <or=15% of neurons simultaneously active, to reduce energy consumption and allow greater computing power from a fixed number of neurons. Functional magnetic resonance imaging signals are likely to be dominated by changes in energy usage associated with synaptic currents and action potential propagation.

Action Potentials↗
PubMed1991

The protein structure code: what is its present status?

Current methods of prediction of protein conformation are reviewed and the algorithms on which they rely are presented. For non-homologous proteins and after cross-validation the reported methods exhibit a probability index, i.e. the per cent of correctly predicted residues per predicted residues, of 63-65% with a standard deviation of the order of 7% for three conformational states--helix, beta-strand and coil. This present limitation in the accuracy of predictions that use only the information of the local sequence can be related essentially to the effect of long-range interactions specific for each protein family. The methods based on sequence similarity can improve the accuracy of prediction by expressing explicitly the homology of the protein to be predicted with proteins in the database. In these circumstances the probability index can reach 87% with a standard deviation of 6.6%. This property can be used for modeling homologous proteins by aiding in amino acid sequence alignments. The prediction of the tertiary structure of a protein is still limited to the case of modeling a structure based on the known three-dimensional structure of a homologous protein.

Algorithms↗
PubMed1994

Cloning, characterization and construction of htrA and htrA-like mutants of Brucella abortus and their survival in BALB/c mice.

A genomic library of Brucella abortus S2308 was screened for expression of recombinant proteins recognized by sera from mice and from cattle infected with B. abortus. A positive clone, BA1, expressing a 50 kDa peptide was recognized by both sera. Plasmid pBA1, isolated from BA1, was shown by restriction enzyme digestion to possess a 1.9 kb insert. The nucleotide sequence of the pBA1 insert revealed an open reading frame with of 1539 bases with a coding capacity of 513 amino acids and a predicted molecular weight of 50,992. The predicted amino acid sequence showed 37% identity to E. coli HtrA, a temperature inducible serine protease. A second B. abortus htrA gene, designated htrA-like, was identified on a different cloned fragment that also encoded B. abortus recA. The nucleotide sequence of the htrA-like gene revealed an open reading frame of 1422 nucleotides with a coding capacity of 474 amino acids and a predicted molecular weight of 50,155. The deduced amino acid sequence of the htrA-like gene showed 42% and 36% identity with B. abortus and E. coli HtrAs respectively. Western blotting of E. coli lysate containing the htrA-like gene was not recognized by sera from B. abortus-infected cattle or mice. B. abortus htrA but not htrA-like relieved the temperature sensitive phenotype and permitted growth of an E. coli htrA mutant at 42 degrees C. B. abortus htrA and htrA-like mutants were constructed and their survival and growth in BALB/c mice was compared to the parental strain S2308.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed2026

Whole-genome sequencing implicates rare, low-frequency and structural non-coding variation at the SCN5A locus in Brugada syndrome.

Brugada syndrome (BrS) is an inherited cardiac condition characterized by a hallmark ECG pattern and an increased risk of sudden cardiac death. Central to the aetiology of BrS, the SCN5A region harbours both common non-coding risk variants and rare coding variants that are causative in approximately 20% of patients. However, rare non-coding genetic variation in this region remains largely unexplored. Here, we used whole-genome sequencing (WGS) of 752 European-ancestry BrS cases and 1,827 ancestry-matched controls to identify BrS-associated rare non-coding genetic variation at the SCN5A locus. Sliding-window and cis-regulatory element (CRE)-based rare-variant aggregate testing implicated three conserved CREs, including a dense aggregation of case singleton variants within a 178 bp enhancer in intron 17 of SCN5A which replicated in an independent BrS cohort. Prioritised BrS-associated rare and low-frequency non-coding variants within these elements were predicted to alter cardiac transcription factor motifs, and altered CRE activity in hiPSC-CM luciferase assays or were associated with BrS-relevant ECG endophenotypes in the UK Biobank. Single-variant analysis across the region identified a Bonferroni-significant five-fold case-enriched low-frequency variant within a known CRE in intron 1 of SCN5A, which replicated, was associated with slower cardiac conduction in the UK Biobank and accounted for part of the BrS GWAS signal at this locus. Structural variant analyses identified a 10.5 kb deletion upstream of SCN5A in a BrS case that encompassed a cardiac CRE and reduced sodium current density in a hiPSC-CM model, as well as a 6 kb BrS-enriched retrotransposon insertion in SCN5A that appeared to underlie part of the GWAS signal in this region. Together, these findings implicate rare and low-frequency non-coding variation at the SCN5A locus in BrS susceptibility and demonstrate the value of targeted WGS analysis of key disease loci.

Journal Article↗
PubMed2000

Cloning of the murine Krit1 cDNA reveals novel mammalian 5' coding exons.

Human KRIT1 (Krev interaction trapped 1), a defective gene product in cerebral cavernous malformation, was cloned from a HeLa cell cDNA library by virtue of its interaction with Krev/rap1A, a small ras-family GTPase. We have now characterized the full-length cDNA for the murine orthologue that encodes a predicted protein of 736 amino acids, 207 amino acids longer than the previously reported human protein. 5' Rapid amplification of cDNA ends analysis of mouse mRNA demonstrated a single transcriptional start site. The putative initiator codon was found within a context that conformed well to the Kozak consensus sequence and was preceded by an in-frame termination codon. BLAST analysis revealed that conceptual translation of a fragment of human genomic DNA upstream of the 5' end of the reported KRIT1 coding sequence predicts extension of the human open reading frame by 207 codons with 95% amino acid identity between the novel putative human and murine amino termini. This block of coding sequence was divided among four exons that are flanked by consensus splice site sequences. The extreme evolutionary conservation of this region, including a putative nuclear localization signal, indicates functional importance. These data have immediate relevance to mutation screening efforts in cerebral cavernous malformation and may contribute to our understanding of the normal biology of KRIT1 and the pathogenesis of this disorder.

Amino Acid Sequence↗
PubMed1986

Structure of the RESA gene of Plasmodium falciparum.

We have determined the nucleotide sequence of the gene encoding the ring-infected erythrocyte surface antigen (RESA) of Plasmodium falciparum, an antigen that has been shown to confer protective immunity on monkeys. The sequence has enabled us to predict the structure of the RESA gene and the amino acid sequence of its protein product. The gene consists of two exons with a short intron located near the 5' end of the coding region. A hydrophobic amino acid segment predicted for the 3' end of exon 1 is consistent with the possibility that exon 1 encodes trafficking signal sequences. We show that restriction fragment length polymorphisms can be used to define two different alleles of RESA, represented by isolates FC27 and NF7, and compare the FC27 sequence with that of a long cDNA clone from NF7 described previously.

Amino Acid Sequence↗
PubMed2005

[Italian national register of major coronary events: attack rates and fatality in different areas of the country].

BACKGROUND: The national register is a monitoring surveillance system of fatal and non-fatal events in the general population aged 35-74 years; it was launched in Italy at the end of the 1990's with the aim of estimating the occurrence and fatality of coronary events in different geographical areas of the country. METHODS: Two sources of information were used to assess current events: death certificates and hospital discharge diagnosis registers. Once the events were identified through the International Classification for Diseases-ICD9 codes and the duration of the event, the number of current events in each single area was multiplied for the positive predictive value of each specific mortality or discharge code derived from suspected events validated by applying the MONICA Project diagnostic criteria. The attack rate was calculated as the mean value of a 2-year period, dividing the average number of estimated events by the average resident population; case fatality was calculated at 28 days from admission as fatal to total event ratio. RESULTS: Attack rates are higher in men than in women: mean age-adjusted (Italian population 1998) attack rate of all areas was 33.9 per 10,000 men and 9.1 per 10,000 women; age-adjusted 28-day case fatality was higher in women (35.5%) than in men (27.3%). Statistically significant geographical differences in comparison with the mean attack rate of all areas were found both in men and women. Case fatality rates result significantly heterogeneous when compared among areas in men but not in women. CONCLUSIONS: Results show that there still exist some differences in the geographic distribution of attack rate and fatality of coronary events which seem to be independent of the North-South gradient. These data show the feasibility of implementing a population-based register, essential for cardiovascular disease surveillance.

Adult↗
PubMed2001

Characterization of a proteasome alpha-chain from Giardia lamblia.

To begin to characterize the components of the 20S proteasome of Giardia lamblia, we have cloned a genomic sequence encoding an alpha-chain (type alpha3/C9, predicted size 244 amino acid residues). Southern analysis indicated that a single gene codes for this protein, and a Northern blot exhibited a single signal at 850 nt. An antiserum against a C-terminal fragment of the alpha-chain expressed in Escherichia coli reacted with a single protein band of Mr 27,000 that was present at constant levels in trophozoites and encysting cells. On a 2D blot of the purified 20S proteasome, we identified the cross-reacting component as a single protein of IEP 6.0, in agreement with the IEP predicted by the coding sequence. Our data confirm that the G. lamblia 20S proteasome is typically eukaryotic in containing a set of diverged alpha-subunits.

Amino Acid Sequence↗
PubMed1993

Mitochondrial RNA abundance in differentiating human colonic epithelial tumor cells estimated through use of a mitochondrial genome map.

We describe a procedure for quantification of mitochondrial (mt) RNA present in total RNA extracts of HT-29 human colonic adenocarcinoma cells grown under conditions for rapid growth (25 mM glucose) or differentiation (25 mM trehalose or 5 mM butyrate). Purified mt DNA was fragmented into specific coding regions using restriction endonuclease sites predicted from HeLa cell mt DNA sequence and probed with either 32P-labelled mt DNA or cDNA made from total RNA of HT-29 or HeLa cells. The amounts of probe that hybridized to various gene-encoded mt DNA fragments or RNA were quantified by laser densitometry. Use of 13 restriction endonucleases revealed that most if not all the mt DNA of HT-29 and K562 leukemic cells was comparable in size to that of HeLa cells. Relative levels of mt RNA from rapidly growing HT-29 and HeLa cells were lower than those measured for differentiated HT-29 cells induced by either trehalose or butyrate. In rapidly growing HT-29 cells and HeLa cells, the highest levels of specific mt RNAs were those encoded by mt DNA sequences immediately flanking the nested promoters and the heavy-strand replication origin (OH). Expression patterns of specific mt RNAs from HT-29 cells treated with butyrate and with trehalose were similar, but not identical. In either case, the mt RNAs that increased the most were those coded by mt DNA sequences located downstream from the light-strand replication origin (OL), suggesting a novel pattern of expression not seen before.

Butyrates↗
PubMedDate not supplied

Addition patterns in carbon allotropes: independence numbers and d-codes in the Klein and related graphs.

The problem of predicting stoichiometries and patterns of chemical addition to a carbon framework, subject solely to the restriction that each addend excludes neighboring sites up to some distance d, is equivalent to determination of d-codes of a graph, and for d = 2 to determination of maximum independent sets. Sizes, symmetries, and numbers of d-codes are found for the all-heptagon Klein graph (prototype for "plumber's nightmare" carbon) and for three related graphs. The independence number of the Klein graph is 23, which increases to 24 for a related, but sterically relaxed, all-heptagon network with the same number of vertices and modified adjacencies. Expansion of the Klein graph and its relaxed analogue by insertion of hexagonal faces to form leapfrog graphs also allows all heptagons to achieve their maximum of 3 addends. Consideration of the pi system that is the complement of the addition pattern imposes a closed-shell requirement on the adjacency spectrum, which typically reduces the size of acceptable independent sets. The closed-shell independence numbers of the Klein graph and its relaxed analogue are 18 and 20, respectively.

Journal Article↗
PubMedDate not supplied

Experimental and theoretical energy and angular dependencies of scattered radiation in the mammography energy range.

Predicted scatter characteristics from a Monte Carlo code have been compared to an experiment for a 4.0-cm-thick acrylic resin (Plexiglas) phantom and 27.3-keV radiation. The results show generally good agreement, except that in the scattered spectra the predictions appear to underestimate the proportion of photons in the low-energy tail of the scattered radiation. The angular dependency of the energy-integrated scattered radiation fluence is in excellent agreement with the predictions.

Mammography↗
PubMed2005

Dopamine D1 receptors involved in locomotor activity and accumbens neural responses to prediction of reward associated with place.

Predicting reward is essential in learning approach behaviors. Dopaminergic activity has been implicated in reward, movement, and cognitive processes, all essential elements in learning. The nucleus accumbens (NAc) receives converging inputs from corticolimbic information-processing areas and from mesolimbic dopamine neurons originating in the ventral tegmental area. Previously, we reported that in mice, a dopamine D2 receptor knockout (D2R-KO) eliminated the prereward inhibitory response, increased place-field size of NAc neurons, and reduced locomotor activity without marked change in intracranial self-stimulation (ICSS) behavior. The present study investigated the specific contribution of dopamine D1 receptor (D1R) in mediating reward, locomotor activity, and spatial associative processes and in regulating NAc neural responses. In contrast to D2R-KO animals, here we find D1R-KO in mice selectively eliminated the prereward excitatory response and decreased place-field size of NAc neurons. Furthermore, D1R-KO impaired ICSS behavior, seriously reduced locomotor activity, and retarded acquisition of a place learning task. Thus, the present results suggest that D1R may be an important determinant in brain stimulation reward (ICSS) and participates in coding for a type of reward prediction of NAc neurons and in spatial learning.

Animals↗
PubMed2005

Identifying and distinguishing cases of parkinsonism and Parkinson's disease using ICD-9 CM codes and pharmacy data.

Administrative databases have the potential to assess quality and cost of care for parkinsonism and Parkinson's disease. However, the validity of findings is limited by our understanding of how cases are identified. Patient records listing International Classification of Diseases, Version 9, Clinical Modification (ICD-9 CM) codes for parkinsonism (n = 2,076) and dopaminergic medications (n = 2,798) were pulled from fiscal years 1999 to 2001 for patients in the Pacific Northwest Veterans Administration. Samples of these records (n = 397) and records without these ICD-9 CM codes (n = 500) were reviewed, and clinical data were extracted. The accuracy of administrative data to identify and distinguish between Parkinson's disease and parkinsonism was calculated. A total of 37.9% of parkinsonism cases were detected using pharmacy data and ICD-9 CM codes compared to 18.7% by using ICD-9 CM codes alone. The ICD-9 CM code for paralysis agitans (332.0) did not distinguish between probable Parkinson's disease and other causes of parkinsonism, whereas the ICD-9 CM code for degenerative basal ganglia disorder (333.0) predicted having secondary parkinsonism (odds ratio [OR] = 5.0) as well as dopa-responsiveness in patients without secondary parkinsonism (OR = 4.5). Administrative data are limited in the ability to identify parkinsonism. The ICD-9 CM code, 332.0, which is generally considered the code to identify Parkinson's disease, did not distinguish between parkinsonism and Parkinson's disease.

Confidence Intervals↗
PubMed2000

A cDNA encoding a nuclear hormone receptor of the steroid/thyroid hormone-receptor superfamily from the human parasitic nematode Strongyloides stercoralis.

A cDNA encoding a nuclear hormone receptor of the steroid/thyroid receptor superfamily was obtained from third-stage larvae(L3) of the parasitic roundworm Strongyloides stercoralis. A recombinant clone was isolated via screening of an S. stercoralis cDNA library with a polymerase chain reaction (PCR)-generated probe. The insert of 2,583 bp contained the complete coding sequence of the receptor homologue. The conceptually translated amino acid sequence of this open reading frame encodes a 753-amino-acid-residue protein with an apparent molecular weight of 83.6 kDa and a predicted isoelectric point (pI) of 8.52. The coding sequence is 69% AT and the noncoding sequence is 72% AT, reflecting a characteristic A/T codon bias of S. stercoralis. In this report the amino acid sequence of the S. stercoralis nuclear hormone receptor of the steroid/thyroid receptor superfamily is compared with that of nuclear hormones of Caenorhabditis elegans, human orphan nuclear receptors, and insect ecdysone receptors. The potential role of steroids in the induction of hyperinfection syndrome is also discussed.

Amino Acid Sequence↗