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The effect of misclassification errors on case mix measurement.

Case mix systems have been implemented for hospital reimbursement and performance measurement across Europe and North America. Case mix categorizes patients into discrete groups based on clinical information obtained from patient charts in an attempt to identify clinical or cost difference amongst these groups. The diagnosis related group (DRG) case mix system is the most common methodology, with variants adopted in many countries. External validation studies of coding quality have confirmed that widespread variability exists between originally recorded diagnoses and re-abstracted clinical information. DRG assignment errors in hospitals that share patient level cost data for the purpose of establishing cost weights affects cost weight accuracy. The purpose of this study is to estimate bias in cost weights due to measurement error of reported clinical information. DRG assignment error rates are simulated based on recent clinical re-abstraction study results. Our simulation study estimates that 47% of cost weights representing the least severe cases are over weight by 10%, while 32% of cost weights representing the most severe cases are under weight by 10%. Applying the simulated weights to a cross-section of hospitals, we find that teaching hospitals tend to be under weight. Since inaccurate cost weights challenges the ability of case mix systems to accurately reflect patient mix and may lead to potential distortions in hospital funding, bias in hospital case mix measurement highlights the role clinical data quality plays in hospital funding in countries that use DRG-type case mix systems. Quality of clinical information should be carefully considered from hospitals that contribute financial data for establishing cost weights.

Diagnosis-Related Groups↗

Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data.

The uncovering of protein-RNA interactions enables a deeper understanding of RNA processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP) technologies such as antibody-barcoded eCLIP (ABC) dramatically increase the throughput of mapping RNA binding protein (RBP) binding sites. However, multiplex CLIP datasets are multivariate, and each RBP suffers non-uniform signal-to-noise ratio. To address this, we developed Mudskipper, a versatile computational suite comprising two components: a Dirichlet multinomial mixture model to account for the multivariate nature of ABC datasets and a softmasking approach that identifies and removes non-specific protein-RNA interactions in RBPs with low signal-to-noise ratio. Mudskipper demonstrates superior precision and recall over existing tools on multiplex datasets and supports analysis of repetitive elements and small non-coding RNAs. Our findings unravel splicing outcomes and variant-associated disruptions, enabling higher-throughput investigations into diseases and regulation mediated by RBPs.

RNA-Binding Proteins↗

Mutation screening of the muscarinic m2 and m3 receptor genes in asthmatics, outgrow subjects, and normal controls.

Muscarinic receptors are important in the development of airway hyperresponsiveness. In some patients with asthma and in animal models of hyperreactivity, functional abnormalities in these receptors are suggested to contribute to disease. Here, we have screened for single nucleotide polymorphisms in the coding region of human muscarinic m2 and m3 receptor genes using direct fluorescence sequencing. DNA samples from 102 current asthmatics and 58 who had outgrown asthma ("outgrow" patients) were compared with 70 random non-asthmatic controls. A mutation characterized by a single base substitution (A1050G, Ser350Ser) was identified in the muscarinic m2 receptor gene. This polymorphism was common and was represented in all three groups studied. In contrast, in the m3 receptor coding region examined, we found a very rare nucleotide variant (C261T, Ile87Ile), identified in only one of the 230 samples genotyped. Therefore, neither A1050G in the m2 receptor nor C261T in the m3 receptor is likely to be functionally significant for airway hyperresponsiveness in asthma. Our data suggest that both the m2 and m3 receptor genes are highly conserved, and no significant genetic mutations are related to their possible functional changes in human asthma.

Asthma↗

Recombinant human fibrinogen and sulfation of the gamma' chain.

Human fibrinogen and the homodimeric gamma'-chain-containing variant have been expressed in BHK cells using cDNAs coding for the alpha, beta, and gamma (or gamma') chains. The fibrinogens were secreted at levels greater than 4 micrograms (mg of total cell protein)-1 day-1 and were biologically active in clotting assays. Recombinant fibrinogen containing the gamma' chain incorporated 35SO4 into its chains during biosynthesis, while no incorporation occurred in the protein containing the gamma chain. The identity of the sulfated gamma' chain was verified by its ability to form dimers during clotting. In addition, carboxypeptidase Y digestion of the recombinant fibrinogen containing the gamma' chain released 96% of the 35S label from the sulfated chain, and the radioactive material was identified as tyrosine O-sulfate. These results clarify previous findings of the sulfation of tyrosine in human fibrinogen.

Amino Acid Sequence↗

Expression vectors for studying cytoskeletal proteins in Dictyostelium discoideum.

We generated and tested a set of cloning vectors designed to facilitate the production, purification and visualization of proteins in Dictyostelium discoideum. The vectors are derived from the Dictyostelium-E. coli shuttle vector pDXA-3H (6.1 kb), which carries the origin of replication of the Dd high-copy-number plasmid, Ddp2, a high-copy-number E. coli plasmid origin of replication, an act6 promoter driven G418 resistance cassette, the bacterial ampicillin resistance gene and an expression cassette. The new cloning vectors carry expression cassettes consisting of the strong constitutive actin-15 promoter, a translation start followed by a multiple cloning site, sequences for the addition of purification or visualization tags, and Dictyostelium polyadenylation and termination signals. Vectors designed to facilitate protein visualization in living Dictyostelium cells contain either coding sequences for the cyan (CFP) or yellow (YFP) variants of green fluorescent protein (GFP). Versions of the vectors for the production of N- and C-terminal fusions with the fluorescent proteins were generated. To facilitate protein purification, vectors for the production of glutathione-S-transferase (GST) fusion proteins and Strep- or FLAG-affinity-tagged proteins were generated. Additionally, a vector for the production of His8-tagged proteins was generated, which has the G418-resistance cassette replaced by a hygromycin resistance cassette.

Amino Acid Sequence↗

Multiple D2 dopamine receptors produced by alternative RNA splicing.

Dopamine receptor belong to a large class of neurotransmitter and hormone receptors that are linked to their signal transduction pathways through guanine nucleotide binding regulatory proteins (G proteins). Pharmacological, biochemical and physiological criteria have been used to define two subcategories of dopamine receptors referred to as D1 and D2. D1 receptors activate adenylyl cyclase and are coupled with the Gs regulatory protein. By contrast, activation of D2 receptors results in various responses including inhibition of adenylyl cyclase, inhibition of phosphatidylinositol turnover, increase in K+ channel activity and inhibition of Ca2+ mobilization. The G protein(s) linking the D2 receptors to these responses have not been identified, although D2 receptors have been shown to both copurify and functionally reconstitute with both Gi and Go related proteins. The diversity of responses elicited by D2-receptor activation could reflect the existence of multiple D2 receptor subtypes, the identification of which is facilitated by the recent cloning of a complementary DNA encoding a rat D2 receptor. This receptor exhibits considerable amino-acid homology with other members of the G protein-coupled receptor superfamily. Here we report the identification and cloning of a cDNA encoding an RNA splice variant of the rat D2 receptor cDNA. This cDNA codes for a receptor isoform which is predominantly expressed in the brain and contains an additional 29 amino acids in the third cytoplasmic loop, a region believed to be involved in G protein coupling.

Amino Acid Sequence↗

Association of the Val158Met catechol O-methyltransferase genetic polymorphism with panic disorder.

Genetic as well as clinical data suggest that catechol O-methyltransferase (COMT) is involved in multiple complex psychiatric conditions. Recent studies have described an association between the Val158Met COMT polymorphism and panic disorder. Other recent investigations provide evidence that there are other loci within or nearby the COMT gene that may contribute to the susceptibility to panic disorder. To further evaluate the influence of the Val158Met COMT polymorphism in panic disorder we genotyped this marker in the coding region of the COMT gene and two additional variants (rs737865 and rs165599) in the 5' and the 3' region, respectively, in two independent Canadian samples: 121 nuclear families, and 89 cases with matched controls. In the nuclear families, significant transmission disequilibrium for the valine allele was observed between the alleles of the Val158Met COMT polymorphism and panic disorder (p<0.01). A significant excess of the valine allele was found in analysis of the case-control sample (p<0.01). This effect was mainly derived from the subgroup of females. This finding, including the female effect, replicates earlier results in studies of the Val158Met polymorphism in panic disorder. No significant results were found for the other two markers. These results support the hypothesis that the valine allele of the Val158Met COMT polymorphism or a nearby locus is involved in the etiopathogenesis of panic disorder.

Animals↗

The "neurothekeoma": immunohistochemical analysis distinguishes the true nerve sheath myxoma from its mimics.

In contrast with the myxoid variant of neurothekeoma (nerve sheath myxoma), evidence of neurosustentacular (NS) differentiation in the so-called cellular and mixed (intermediate) variants of neurothekeoma remains controversial. In this study, we selected 22 tumors coded as neurothekeoma or nerve sheath myxoma from the Soft Tissue Registry of the AFIP. Each tumor was histologically subtyped as either a myxoid/hypocellular neurothekeoma (MN) (N = 11) or as a "cellular" or "mixed" (intermediate) neurothekeoma variant (C&MV) (n = 11) and analyzed immunohistochemically. The MNs were composed of small, cytologically bland cells arranged in a loose cellular network or in files within highly myxomatous nodules delineated by dense collagen. The tumors showed clear-cut evidence of NS differentiation by exhibiting consistent immunoreactivity for S-100 protein (11 of 11 cases) and low-affinity nerve growth factor receptor, p75(NGFR), (NGFR) (10 of 10), and variable reactivity for glial fibrillary acidic protein (GFAP) (10 of 11) and CD57 (Leu-7) (5 of 9). They also showed pericellular collagen type IV (CIV) expression (9 of 9), scattered intralesional CD34-positive spindled cells (10 of 10), epithelial membrane antigen (EMA)-positive spindled cells located within the adjacent dense collagen (8 of 11), and immunoreactivity for alpha-smooth muscle actin (SMA) (3 of 10) and calponin (4 of 9). In 4 cases, scattered intralesional neuraxons were detected by the Bodian histochemical method or immunohistochemically with anti-neurofilament protein. The tumors had a male-to-female ratio of 6:5, a peak incidence in the 4th decade of life, and an anatomic distribution that included the upper and lower limbs and back. The C&MVs included 9 "mixed" and 2 "cellular" variants. C&MVs differed histologically from MNs by their higher cellularity and presence of larger spindled or epithelioid cells with vesicular nuclei. Immunohistochemically, the tumor cells expressed CIV (9 of 10), calponin (7 of 9), SMA (5 of 10), Leu-7 (1 of 7), S-100 protein (1 of 11), but not NGFR, GFAP, or CD34. EMA-positive spindled cells surrounded tumor fascicles in 1 case. Intralesional neuraxons were not identified. Clinically, these tumors differed from the MNs by exhibiting a male-to-female ratio of 4:7, a peak incidence in the 2nd decade, and an upper body distribution. Our results indicate that the MN shows NS differentiation and is the bona fide nerve sheath tumor, whereas the C&MVs fail to show convincing evidence of NS differentiation and probably warrant a separate classification.

Adolescent↗

Genomic signatures of dairy adaptation in Saccharomyces cerevisiae from traditional Yaghnob goat-cheese fermentation.

The growing interest in studying Saccharomyces cerevisiae strains from previously unexplored niches is greatly expanding our understanding of this yeast's ecology and evolution. While strains involved in alcoholic fermentation are the most studied, S. cerevisiae has also been isolated from milk fermentations and their products, suggesting a potential evolutionary specialization for dairy environments. These fermentations are characterized by the predominant presence of lactose, a carbon source that S. cerevisiae cannot metabolize directly but can exploit through the enzymatic activity of co-occurring microorganisms that convert lactose into fermentable substrates, such as glucose and galactose. In this study, we analyzed S. cerevisiae strains isolated from an unexplored and remote niche: traditional goat fermented milk produced by the Yaghnob people, an ethnically and geographically partly isolated population living in the Upper Zarafshan area of the Republic of Tajikistan. Comparative analyses with published S. cerevisiae genomes positioned the Yaghnob strains at the base of the phylogenetic dairy clade. These strains revealed distinctive coding sequences and strain-specific single-nucleotide variants present in all Yaghnob strains but absent from the other 1,053 strains analyzed. Further investigation of variants in key genes involved in galactose metabolism provided insights into the genomic and protein-level evolution of Yaghnob strains, uncovering unique genomic signatures of adaptation to the dairy environment.

Saccharomyces cerevisiae↗

Restriction map variation in the Adh region of Drosophila.

Restriction maps of a 12,000-nucleotide region containing the alcohol dehydrogenase (Adh) locus of the second chromosome of Drosophila were determined for (i) 18 independent second chromosome stocks of D. melanogaster established from several natural populations and (ii) five closely related Drosophila species. All of the detected map differences appear to lie outside the Adh coding block. Four polymorphic restriction sites and four insertion/deletion variants were identified among D. melanogaster chromosomes. The estimated heterozygosity per nucleotide site was 0.006. The relative distributions of restriction sites and insertion/deletion variations among subpopulations and species suggest that the insertion/deletion variation may be mildly deleterious.

Alcohol Dehydrogenase↗

Allelic heterogeneity at the serotonin transporter locus (SLC6A4) confers susceptibility to autism and rigid-compulsive behaviors.

Autism is a spectrum of neurodevelopmental disorders with a primarily genetic etiology exhibiting deficits in (1) development of language and (2) social relationships and (3) patterns of repetitive, restricted behaviors or interests and resistance to change. Elevated platelet serotonin (5-HT) in 20%-25% of cases and efficacy of selective 5-HT reuptake inhibitors (SSRIs) in treating anxiety, depression, and repetitive behaviors points to the 5-HT transporter (5-HTT; SERT) as a strong candidate gene. Association studies involving the functional insertion/deletion polymorphism in the promoter (5-HTTLPR) and a polymorphism in intron 2 are inconclusive, possibly because of phenotypic heterogeneity. Nonetheless, mounting evidence for genetic linkage of autism to the chromosome 17q11.2 region that harbors the SERT locus (SLC6A4) supports a genetic effect at or near this gene. We confirm recent reports of sex-biased genetic effects in 17q by showing highly significant linkage driven by families with only affected males. Association with common alleles fails to explain observed linkage; therefore, we hypothesized that preferential transmission of multiple alleles does explain it. From 120 families, most contributing to linkage at 17q11.2, we found four coding substitutions at highly conserved positions and 15 other variants in 5' noncoding and other intronic regions transmitted in families exhibiting increased rigid-compulsive behaviors. In the aggregate, these variants show significant linkage to and association with autism. Our data provide strong support for a collection of multiple, often rare, alleles at SLC6A4 as imposing risk of autism.

Alanine↗

Identification of the transcription factor ARNTL2 as a candidate gene for the type 1 diabetes locus Idd6.

The Idd6 murine type 1 diabetes locus has been shown to control diabetes by regulating the protective activity of the peripheral immune system, as demonstrated by diabetes transfer assays using splenocytes. The analysis of three novel subcongenic (NOD.C3H nonobese. C3H) diabetes strains has confirmed the presence of at least two diabetes-related genes within the 5.8 Mb Idd6 interval with the disease protection conferred by splenocyte co-transfer being located to the 700 kb Idd6.3 subregion. This subinterval contains the circadian rhythm-related transcription factor Arntl2 (Bmal2), a homologue of the type 2 diabetes-associated ARNT (HIF1beta) gene. Arntl2 exhibited a six-fold upregulation in spleens of the NOD.C3H 6.VIII congenic strain compared with the NOD control strain, strain-specific splice variants and a large number of polymorphisms in both coding and non-coding regions. Arntl2 upregulation was not associated with changes in the expression levels of other circadian genes in the spleen, but did correlate with the upregulation of the ARNT-binding motif containing Pla2g4a gene, which has recently been described as being protective for the progression of insulitis and autoimmune diabetes in the NOD mouse via regulation of the tumour necrosis factor-alpha pathway. Our studies strongly suggest that the HIFbeta-homologous Arntl2 gene is involved in the control of type 1 diabetes.

ARNTL Transcription Factors↗

Characterization of a 2.6 kbp variable region within a class 1 integron found in an Acinetobacter baumannii strain isolated from a horse.

OBJECTIVES: A complete gene cassette contained in a class 1 integron from a multidrug-resistant (MDR) isolate of Acinetobacter baumannii cultured from a horse was characterized by molecular methods. METHODS: Template genomic DNA purified from the A. baumannii isolate was investigated by PCR. A gene cassette-associated amplicon was detected and completely characterized. RESULTS: A 2.6 kbp DNA fragment containing four gene cassettes was amplified from the MDR A. baumannii isolate. Sequence analysis showed it was similar to sequences recently reported in Klebsiella pneumoniae, Serratia marcescens and an Escherichia coli plasmid p1658/97 which conferred aminoglycoside resistance. Aminoglycoside resistance-encoding genes aacC1 and aadA1 were located within the 2.6 kbp amplicon, separated by two open reading frames (ORFs) coding for unknown products. This cassette structure (and some variants) was identified in unrelated Acinetobacter spp. from human sources, based on sequence comparisons of the current databases. CONCLUSIONS: Identification of a complete class 1 integron in an equine isolate of A. baumannii suggests that the screening of isolates from animals for these elements should be considered, as this information could influence the selection of chemotherapeutic agents.

Acinetobacter baumannii↗

Transcription initiation and RNA processing of a yeast mitochondrial tRNA gene cluster.

Expression of 5 yeast mitochondrial tRNA genes (Ala, Ile, Tyr, Asn and Metm), localized upstream from the oxil gene has been analyzed by in vitro capping using guanylyltransferase, northern hybridization and S1 nuclease mapping in the wild type and a rho-strain. The 5 tRNA sequences belong to the same transcriptional unit which is initiated 133 bp upstream from the tRNA(Ala) gene at a promoter sequence TTATAAGTA. Furthermore, a truncated tRNA(Tyr) transcript, 2 nucleotides shorter than mature tRNA(Tyr) has been found, only in the rho-strain. This minor transcript may result from secondary transcription initiation at a variant nonanucleotide sequence, ATATAAGGA, which overlaps the tRNA(Tyr) coding sequence by 3 nucleotides. The polycistronic precursor has proven to be useful in investigation of the mechanisms of tRNA processing. Maturation of this primary transcript proceeds exclusively by precise endonucleolytic cleavages at the 5' and 3'-ends of tRNA sequences.

Base Sequence↗

Molecular basis of chronic non-spherocytic haemolytic anaemia: a new G6PD variant (393 Arg----His) with abnormal KmG6P and marked in vivo instability.

More than 80 genetic variants of glucose-6-phosphate dehydrogenase (G6PD) are associated with chronic non-spherocytic haemolytic anaemia (CNSHA). In order to help clarify the molecular basis of this association, we have carried out a detailed biochemical and genetic characterization of two G6PD deficient brothers affected by CNSHA. The G6PD from the two patients has altered electrophoretic mobility, abnormally elevated Michaelis constant (Km) for G6P, and extreme instability in vivo and in vitro. By comparison with published information we found that this is a new G6PD variant which we have designated G6PD Portici. The entire coding region of the gene has been sequenced, and a single point mutation, a G----A transition, was found at position 1178 in exon X, causing a substitution of histidine for arginine at residue 393 in the polypeptide chain. By polymerase chain reaction (PCR) amplification followed by diagnostic restriction enzyme analysis and allele-specific oligonucleotide hybridization we have demonstrated the inheritance of this mutation in the patient's family. Our results support the notion of a causative link between this mutation in the G6PD gene and CNSHA. Our data, in combination with previous data in the literature, suggest that the three-dimensional structure of G6PD is such as to cause interaction in the binding of its two substrates, G6P and NADP.

Adolescent↗

Effect of polyamines on translation fidelity in vivo.

Polyamines, when added to cell-free protein-synthesizing systems, have been shown either to reduce mistranslation or to increase it depending upon the composition of the reaction mixture. To study this question under conditions as natural as possible we investigated the effects of polyamines on the fidelity of protein synthesis in intact Escherichia coli bacterial cells, using strains which were auxotrophic for polyamine synthesis. Error was measured in two ways: the incorporation of [3H]histidine into coat protein of bacteriophage MS2, the gene of which does not code for histidine, and the synthesis of a basic variant of MS2 coat protein in which a lysine erroneously replaces an asparagine, causing a change in isoelectric point. We found that when cell cultures were supplemented with polyamines there was no effect on the first type of error and the second type decreased twofold. The measured errors occurred at the level of translation because their frequency increased in the presence of streptomycin and decreased in cells bearing a streptomycin-resistance mutation known to lower the occurrence of translational misreading. The average erroneous incorporation per mol coat protein in the presence of polyamines was 1.43 +/- 0.59 mmol histidine and 25-34 mmol lysine/asparagine substitution. The reason for the different effect of polyamines on the two types of error is not known but could be related to the difference between their corresponding frequencies or to codon-specific effects.

Capsid↗

Adult abdominal migraine: a new syndrome or sporadic feature of migraine headache? A case report.

Abdominal migraine is one of the variants of migraine headache typically occurring in children and coded as 1.3.2 in the revised edition of IHS classification within the group 'Childhood periodic syndromes that are commonly precursors of migraine'. The affected children frequently develop typical migraine later in their life. We report a case of a 23 years old woman affected by attacks of recurrent abdominal pain accompanied by migraine. Abdominal pain attacks started in the adolescence and persisted without headache until the patient was 21. At this time, she experienced migraine pain accompanied by nausea, photophobia and phonophobia and associated to acute abdominal pain. Neuroimaging investigations and laboratory testing excluded any underlying organic disease. Complete remission of abdominal attacks was obtained during 4-month treatment period with pizotifen. Attacks fulfil IHS diagnostic criteria for 'abdominal migraine', although of late onset. This case report suggests that 'abdominal migraine' is a migraineous disorder to be hypothesized in adult patients after having disclosed any organic disease. As reported in the literature, 'adult abdominal migraine' is a sporadic migraine subtype in adult patients and it is not to be considered as a new migraineous syndrome.

Abdominal Pain↗

Genetic polymorphisms of the human CYP2A13 gene: identification of single-nucleotide polymorphisms and functional characterization of an Arg257Cys variant.

Human cytochrome P450 2A13 (CYP2A13), which is highly efficient in the metabolic activation of a major tobacco-specific carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), may play important roles in xenobiotic toxicity and tobacco-related tumorigenesis in the respiratory tract. The aim of this study was to identify any genetic polymorphisms of the CYP2A13 gene, which may alter the metabolic capacities of the enzyme. Polymerase chain reaction (PCR) single-strand conformational polymorphism analysis was used to identify single-nucleotide polymorphisms (SNPs) in all of the exons and at the exon-intron boundaries, and PCR-restriction fragment length polymorphism analysis and DNA sequencing were used to determine the frequencies of the newly identified variant alleles in the four major ethnic groups. Blood spot DNA from more than 100 individuals was used for these analyses. Seven variant alleles were found, but only one SNP was detected in the coding region, in exon 5, leading to an Arg257Cys amino acid change. The frequencies of the Arg257Cys allele in white, black, Hispanic, and Asian individuals are 1.9%, 14.4%, 5.8%, and 7.7%, respectively. Functional analysis of the variant protein was performed following its heterologous expression. The Arg257Cys variant was 37 to 56% less active than the wild-type Arg-257 protein toward all substrates tested. With NNK, Cys-257 had higher K(m) and lower V(max) values than did Arg-257, with a >2-fold decrease in catalytic efficiency. The Arg257Cys mutation could provide some protection against xenobiotic toxicity in the respiratory tract to individuals who are homozygous for the Cys-257 allele.

Amino Acid Substitution↗