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At least 127 records · Page 7Linked to original sources
PubMed2000

Variation in modes and rates of evolution in nuclear and mitochondrial ribosomal DNA in the mushroom genus Amanita (Agaricales, Basidiomycota): phylogenetic implications.

Modes and rates of molecular evolution, and congruence and combinability for phylogenetic reconstruction, of portions of the nuclear large ribosomal subunit (nLSU-rDNA) and mitochondrial small subunit (mtSSU-rDNA) genes were investigated in the mushroom genus Amanita. The AT content was higher in the mtSSU-rDNA than in the nLSU-rDNA. A transition bias in which AT substitutions were as frequent as transitions was present in the mtSSU-rDNA but not in the nLSU-rDNA. Among-sites rate variation in nucleotide substitutions at variable sites was present in the nLSU-rDNA but not in the mtSSU-rDNA. Likelihood ratio tests indicated very different models of evolution for the two molecules. A molecular clock could be rejected for both data sets. Rates of molecular evolution in the two molecules were uncoupled: faster evolutionary rates in the mtSSU-rDNA and nLSU-rDNA were not observed for the same taxa. In separate phylogenetic analyses, the nLSU-rDNA data set had higher phylogenetic resolution. The partition homogeneity test and statistical bootstrap support for branches indicated absence of conflict in the phylogenetic signal in the two data sets; however, tree topologies produced from the separate data sets were not congruent. Heterogeneity in modes and rates of evolution in the two molecules pose difficulties for a combined analysis of the two data sets: the use of equally weighted parsimony is not fully satisfactory when rate heterogeneity is present, and it is impractical to determine a model for maximum-likelihood analysis that fits simultaneously two heterogeneous data sets. Overall topologies produced from either the separated or the combined analyses using various tree reconstruction methods were identical for nearly all statistically significant branches.

Amanita↗
PubMed2005

Characterization of human control region sequences of the African American SWGDAM forensic mtDNA data set.

The scientific working group on DNA analysis Methods (SWGDAM) mitochondrial DNA (mtDNA) population data set is used to infer the relative rarity of control region mtDNA profiles obtained from evidence samples and of profiles used for identification of missing persons. In this study, the African American haplogroup patterns in the SWGDAM data were analyzed in a phylogenetic context to determine relevant single nucleotide polymorphisms (SNPs) and to describe haplogroup distributions for Africans observed in these data sets. Over 200 SNPs (n=217) were observed in the African American data set (n=1148). These SNPs ranged from having 1-39 changes in the phylogenetic tree, with sites 152 and 16519 being the most variable. On average there were 5.8 changes for a character on the tree. The most variable sites (with 19 or more changes each) observed included 16093, 16129, 16189, 16311, 16362, 16519, 146, 150, 152, 189, and 195. These rapidly changing sites are consistent with other published analyses. Only 34 SNPs are needed to identify all clusters containing 10 or more individuals in the African American data set. The results show that the African American SWGDAM mtDNA data set contains variation consistent with that described in continental African populations. Thirteen of the 18 haplogroups previously observed in African populations were observed and include: L1a, L1b, L1c, L2a, L2b, L2c, L3b, L3d, L3e1, L3e2, L3e3, L3e4 and L3f. Haplogroup L2a is the most commonly observed cluster (18.8%) in the African American data set. The next most common haplogroups in the African American data set include the clusters L1c (11.0%), L1b (9.1%), L3e2 (9.0%) and L3b (8.1%). Approximately 8% of the haplogroups observed within African Americans were common in European Caucasians or East Asians; these were H (n=32), J (n=4), K (n=5), T (n=2), U5 (n=6), U6 (n=9 also known from North Africa), A (n=12), B (n=7), C (n=4), and M (n=16), respectively. The European Caucasian and East Asian haplogroups are expected due to admixture between individuals with recent ancestry in Western Eurasia and sub-Saharan Africa. The genetic characterization of these relevant data sets is fully consistent with other published mtDNA genetic variation. The sequence diversity observed in this data set makes it a valuable tool for forensic applications.

Black People↗
PubMed2000

Differentiation of newly described antarctic bacterial isolates related to Roseobacter species based on 16S-23S rDNA internal transcribed spacer sequences.

The 16S-23S rDNA internal transcribed spacer (ITS) of Roseobacter denitrificans, Roseobacter litoralis, Ruegeria algicola and strains of the recently described species Antarctobacter heliothermus and Roseovarius tolerans were analysed in order to examine DNA sequence variations and to draw conclusions about inter- and intraspecific relationships. A. heliothermus included four strains with an ITS fragment length of 1092 bp. Roseovarius tolerans was described on the basis of eight strains. Five of these harboured two ITS fragments of different lengths (959 and about 1100 bp), while the others had one fragment of either 1083 bp (two strains) or 1165 bp (one strain). ITS lengths of the related species Roseobacter denitrificans, Roseobacter litoralis and Ruegeria algicola were found to be 980, 984 and 1158 bp, respectively. Phylogenetic analyses of the DNA sequences allowed species affiliation of strains with sequence length differences of > 200 bp and recognition of relationships based on a well-supported ITS tree. The strains of A. heliothermus and Roseovarius tolerans each formed a monophyletic branch and they were separated from each other by Ruegeria algicola. This species was now clearly separated from Roseobacter denitrificans and Roseobacter litoralis, which corresponded to the new genus affiliation of Ruegeria algicola. These data were additionally supported by analyses of the structure, relative position and order of genes for tRNA(Ile) and tRNA(Ala) found within the ITS of each strain. Comparative DNA sequence analyses of ITS and 16S rDNA revealed limitations, on species and strain levels, with respect to the phylogenetic resolution of the 16S rDNA due to the limited number of informative (variable) sites, while ITS sequence analyses provided more variable and sufficiently conserved positions to discriminate between strains and to reconstruct their taxonomic relationships.

Alphaproteobacteria↗
PubMed2001

A molecular topology approach to predicting pesticide pollution of groundwater.

Various models have proposed methods for the discrimination of polluting and nonpolluting compounds on the basis of simple parameters, typically adsorption and degradation constants. However, such attempts are prone to site variability and measurement error to the extent that compounds cannot be reliably classified nor the chemistry of pollution extrapolated from them. Using observations of pesticide occurrence in U.S. groundwater it is possible to show that polluting from nonpolluting compounds can be distinguished purely on the basis of molecular topology. Topological parameters can be derived without measurement error or site-specific variability. A logistic regression model has been developed which explains 97% of the variation in the data, with 86% of the variation being explained by the rule that a compound will be found in groundwater if 6 chi Pv < 0.55. Where 6 chi p is the sixth-order molecular path connectivity. One group of compounds cannot be classified by this rule and prediction requires reference to higher order connectivity parameters. The use of molecular approaches for understanding pollution at the molecular level and their application to agrochemical development and risk assessment is discussed.

Agriculture↗
PubMed2025

Molecular Epidemiology of Coxsackievirus A10 Associated With Hand, Foot and Mouth Disease From 2021 to 2024 in Shenzhen, China.

The study aimed to investigate epidemiological profile and molecular characteristics of coxsackievirus A10 (CVA10) associated with hand, foot and mouth disease (HFMD) in Shenzhen, China and comparatively analyze genomes of CVA10 strains related to differential clinical phenotypes. A total of 3170 clinical specimens collected between 2021 and 2024 were examined for CVA10 using real-time RT-PCR. Complete VP1 sequences and near-complete genome sequences of CVA10 were determined by RT-PCR methods and sequencing. Sequences were analyzed using a series of bioinformatics programs. Two (33.33%) out of 6 severe cases were infected with CVA10. The detection rate of CVA10 associated with mild HFMD ranged from 1.21% to 6.11% in 2021-2024, with an overall detection rate of 3.73%. There was no significant difference in the infection rate of CVA10 between males and females or different age groups. The CVA10 infections mainly occurred in Spring (March to May) and Summer (June to August) in Shenzhen. Of the 74 VP1 sequences determined, 71 (95.95%) of them were detected in the sub-genotype C2, 3 (4.05%) were assigned to the genotype D. Genomic sequence analysis indicated that the genotype D of CVA10 of this study derived from genetic recombination between CVA10 and CVA16 in 3A-3D coding region (nucleotide position: 5075-6896). Different variable sites were observed in the two CVA10 strains associated with different severe complications when compared to CVA10 strains associated with mild diseases. In conclusion, CVA10 associated with HFMD circulated at a low level in Shenzhen in 2021-2024, with C2 as the predominant genotype. Recombinant genotype D of CVA10 was introduced first to Shenzhen in 2024. The study emphasizes the importance of continuous molecular surveillance of CVA10.

Humans↗
PubMed1996

Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences.

Pre-mRNA splicing in plants, while generally similar to the processes in vertebrates and yeast, is thought to involve plant specific cis-acting elements. Both monocot and dicot introns are typically strongly enriched in U nucleotides, and AU- or U-rich segments are thought to be involved in intron recognition, splice site selection, and splicing efficiency. We have applied logitlinear models to find optimal combinations of splice site variables for the purpose of separating true splice sites from a large excess of potential sites. It is shown that plant splice site prediction from sequence inspection is greatly improved when compositional contrast between exons and introns is considered in addition to degree of matching to the splice site consensus (signal quality). The best model involves subclassification of splice sites according to the identity of the base immediately upstream of the GU and AG signals and gives substantial performance gains compared with conventional profile methods.

Algorithms↗
PubMed1998

Trematode and monogenean rRNA ITS2 secondary structures support a four-domain model.

The secondary structure of rRNA internal transcribed spacer 2 is important in the process of ribosomal biogenesis. Trematode ITS sequences are poorly conserved and difficult to align for phylogenetic comparisons above a family level. If a conserved secondary structure can be identified, it can be used to guide primary sequence alignments. ITS2 sequences from 39 species were compared. These species span four orders of trematodes (Echinostomiformes, Plagiorchiformes, Strigeiformes, and Paramphistomiformes) and one monogenean (Gyrodactyliformes). The sequences vary in length from 251 to 431 bases, with an average GC content of 48%. The monogenean sequence could not be aligned with confidence to the trematodes. Above the family level trematode sequences were alignable from the 5' end for 139 bases. Secondary structure foldings predicted a four-domain model. Three folding patterns were required for the apex of domain B. The folding pattern of domains C and D varies for each family. The structures display a high GC content within stems. Bases A and U are favored in unpaired regions and variable sites cluster. This produces a mosaic of conserved and variable regions with a structural conformation resistant to change. Two conserved strings were identified, one in domain B and the other in domain C. The first site can be aligned to a processing site identified in yeast and rat. The second site has been found in plants, and structural location appears to be important. A phylogenetic tree of the trematode sequences, aligned with the aid of secondary structures, distinguishes the four recognized orders.

Animals↗
PubMed1993

The Chironomus thummi genome contains a non-LTR retrotransposon.

Nineteen recombinant phages containing DNA from the region of Balbiani ring a (BRa), which develops on chromosome IV in cells of the special lobe of the Chironomus thummi salivary gland, were isolated from a Chironomus thummi genomic library. Three of the clones contained transposable element sequences that hybridized to more than 100 sites on all four Chironomus chromosomes, including constant and variable sites. Two handogous clones, lambda 24 (which lacks the transposable element) and lambda 43 (which contains this insertion) were investigated by nucleotide sequence analysis. The complete nucleotide sequence of the 4.8 kb transposable element from Chironomus thummi (NLR1Cth) is reported here. This element contains two overlapping open reading frames of 1887 (ORF1) and 2649 bp (ORF2). Three cysteine motifs are found in the sequence of ORF1. Sequence similarity was found between ORF2 and known genes of viruses and transposable elements which encode reverse transcriptase. The NLR1Cth element has no long terminal repeats and is flanked by short direct repeats of the sequence TATCACTGACAAC. A 24 bp poly(dA) sequence was found at the 3' end of the element. Based upon its structural organization and comparative analysis of its nucleotide sequence we suggest that this NLR1Cth element belongs to the class of non-LTR retrotransposons. The genomic clone pC6.10 was previously obtained by microdissection and cloning of DNA from polytene chromosome IV of Chironomus thummi. A 2.4 kb insertion contained part of the 3' terminal region of the NLR1Cth element, but this differed in sequence from the first copy by several nucleotide substitutions and a shorter poly (dA) tract at the 3' end.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1990

A new transposable element in Chironomus thummi.

A 1.7 kb long transposable element called TECth1 was found in the 3' flanking region of a Chironomus thummi Balbiani ring gene. As shown by sequence comparison with a second copy, TECth1 is characterized by a perfect terminal inverted repeat of 17 bp flanked by a duplicated target site of 8 bp, four internal imperfect inverted repeats of 17 to 26 bp and terminal regions of about 0.25 kb with a high number of short direct repeats of the consensus sequence ACTTT or permutated and mutated forms such as TTTAC or ACTAT. The terminal inverted repeats and the 8 bp target site duplication are reminiscent of Drosophila P and hobo elements but no long open reading frame starting with ATG is present, suggesting that the two TECth1 copies studied represent deletion derivatives of a longer element coding for its own transposase. In situ hybridization revealed about 75 labelled sites distributed over all chromosomes with the Balbiani ring locus most strongly labelled. Fifty percent of the sites are specific for a given individual, and these variable sites are often heterozygous for the element.

Animals↗
PubMed2000

Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies.

Haplotype variation in 9.7 kb of genomic DNA sequence from the human lipoprotein lipase (LPL) gene was scored in three populations: African-Americans from Jackson, Mississippi (24 individuals), Finns from North Karelia, Finland (24), and non-Hispanic whites from Rochester, Minnesota (23). Earlier analyses had indicated that recombination was common but concentrated into a hotspot and that recurrent mutations at multiple sites may have occurred. We show that much evolutionary structure exists in the haplotype variation on either side of the recombinational hotspot. By peeling off significant recombination events from a tree estimated under the null hypothesis of no recombination, we also reveal some cladistic structure not disrupted by recombination during the time to coalescence of this variation. Additional cladistic structure is estimated to have emerged after recombination. Many apparent multiple mutational events at sites still remain after removing the effects of the detected recombination/gene conversion events. These apparent multiple events are found primarily at sites identified as highly mutable by previous studies, strengthening the conclusion that they are true multiple events. This analysis portrays the complexity of the interplay among many recombinational and mutational events that would be needed to explain the patterns of haplotype diversity in this gene. The cladistic structure in this region is used to identify four to six single-nucleotide polymorphisms (SNPs) that would provide disequilibrium coverage over much of this region. These sites may be useful in identifying phenotypic associations with variable sites in this gene. Evolutionary considerations also imply that the SNPs in the 3' region should have general utility in most human populations, but the 5' SNPs may be more population specific. Choosing SNPs at random would generally not provide adequate disequilibrium coverage of the sequenced region.

Black or African American↗
PubMed2002

Polymorphism and heteroplasmy of mitochondrial DNA in the D-loop region in Taiwanese.

BACKGROUND AND PURPOSE: Although the displacement loop (D-loop) of mitochondrial DNA (mtDNA) is known to have a large number of sequence variations, data on this variation are lacking. This study investigated D-loop sequence polymorphism in Taiwanese subjects. METHODS: The D-loop mtDNA region was amplified from whole blood samples of 63 unrelated Taiwanese individuals using the polymerase chain reaction (PCR). PCR products were sequenced and analyzed. Sequence electropherograms of nucleotides 303 to 315 that showed particularly high background after C-stretch were subcloned to the PGEM-TE vector for sequencing analysis. RESULTS: A total of 126 variable sites in 788 polymorphisms including 19 novel sites were found. The genetic diversity of the highly variable region (HVR)-I, HVR-II, HVR-III, and a region elsewhere were 0.999, 0.993, 0.850, and 0.707, respectively. The power of discrimination of these regions was 0.983, 0.977, 0.837, and 0.696, respectively. Both HVR-I and HVR-II contained segments of homopolymeric sequence. A high frequency (30%) of heteroplasmy made up of cytosine between nucleotides 303 and 315 appeared to be a unique feature of the Taiwanese population. Nucleotide substitutions at position 16,362 (T to C) in HVR-I have been found with high frequency in Taiwanese. CONCLUSION: In this study, 19 polymorphisms in the D-loop of mtDNA in Taiwanese were newly identified, and an unusually high frequency of heteroplasmy was found in the region between nucleotides 303 and 315 in this population.

DNA, Mitochondrial↗
PubMed1990

Substrate requirements of human rhinovirus 3C protease for peptide cleavage in vitro.

A series of synthetic peptides representing authentic proteolytic cleavage sites of human rhinovirus type 14 were assayed as substrates for purified 3C protease. Competition cleavage assays were employed to determine the relative specificity constants (Kcat/Km) for substrates with sequences related to the viral 2C-3A cleavage site. Variable length peptides representing the 2C-3A cleavage site were cleaved with comparable efficiency. These studies defined a minimum substrate of 6 amino acids (TLFQ/GP), although retention of the residue at position P5 (ETLFQ/GP) resulted in a better substrate by an order of magnitude. Amino acid substitutions at position P5, P4, P1', or P2' indicated that the identity of the residue at position P5 was not critical, whereas substitutions at position P4, P1' or P2' resulted in substrates with Kcat/Km values varying over 2 orders of magnitude. In contrast to the 2C-3A cleavage site, small peptide derivatives representative of the 3A-3B cleavage site were relatively poor substrates, which suggested that residues flanking the minimum core sequence may influence susceptibility to cleavage. The 3C protease of rhinovirus type 14 was also capable of cleaving peptides representing comparable cleavage sites predicted for coxsackie B virus and poliovirus.

3C Viral Proteases↗
PubMed2006

Complementary feeding in the WHO Multicentre Growth Reference Study.

AIM: To describe complementary feeding practices in the Multicentre Growth Reference Study (MGRS) sample. METHODS: Food frequency questionnaires and 24-h dietary recalls were administered to describe child feeding throughout the first 2 y of life. This information was used to determine complementary feeding initiation, meal frequency and use of fortified foods. Descriptions of foods consumed and dietary diversity were derived from the 24-h recalls. Compliance with the feeding recommendations of the MGRS was determined on the basis of the food frequency reports. Descriptive statistics provide a profile of the complementary feeding patterns among the compliant children. RESULTS: Complementary feeding in the compliant group began at a mean age of 5.4 mo (range: 4.8 (Oman)-5.8 mo (Ghana)). Complementary food intake rose from 2 meals/d at 6 mo to 4-5 meals in the second year, in a reverse trend to breastfeeding frequency. Total intake from the two sources was 11 meals/d at 6-12 mo, dropping to 7 meals/d at 24 mo. Inter-site differences in total meal frequency were mainly due to variations in breastfeeding frequency. Grains were the most commonly selected food group compared with other food groups that varied more by site due to cultural factors, for example, infrequent consumption of flesh foods in India. The use of fortified foods and nutrient supplements was also influenced by site-variable practices. Dietary diversity varied minimally between compliance groups and sites. CONCLUSION: Complementary diets in the MGRS met global recommendations and were adequate to support physiological growth.

Child Development↗
PubMed2002

Use of nasal potential difference and sweat chloride as outcome measures in multicenter clinical trials in subjects with cystic fibrosis.

One of the goals of current research in cystic fibrosis (CF) is to develop treatments that correct or compensate for defects in function of the cystic fibrosis transmembrane regulator (CFTR) gene. The use of outcome measures that assess CFTR function such as nasal potential difference (NPD) measurements and sweat chloride determinations will be required to evaluate the efficacy of such treatments in multicenter clinical trials. The purpose of this work was to identify the sources and magnitude of variability in NPD and sweat chloride measurements when performed at multiple centers. For the variance component analysis presented here, we used NPD and sweat chloride measurements from 37 subjects with CF participating in a phase I, four-center clinical trial of CPX (8-cyclopentyl-1,3-dipropylxanthine), a drug intended to enhance trafficking of Delta F508 CFTR to the cell membrane. The specific techniques used to measure these outcomes were not standardized, and varied between the four sites. Variability of both NPD measurements (baseline potential difference during infusion with Ringer's solution; change in response to addition of 0.1 mM amiloride; and subsequent change in response to perfusion with low chloride solution containing 0.1 mM amiloride and 0.01 mM isoproterenol) and sweat chloride measurements differed significantly between study sites. For change in NPD, one study site had significantly greater variability (lower reproducibility) of measurement than the other three sites. For sweat chloride measurements, reproducibility was lower at two of the sites relative to the other two sites. Sample size calculations showed that lower reproducibility at one or more sites can substantially reduce the power of studies using NPD or sweat chloride determinations as outcome measures. Standardization of measurement protocols, careful operator training and certification, and ongoing monitoring of individual operator performance may help to improve reliability in multicenter trials.

Adolescent↗
PubMed1997

Molecular phylogenetic characterization of Streptomyces protease inhibitor family.

We previously found that proteinaceous protease inhibitors homologous to Streptomyces subtilisin inhibitor (SSI) are widely produced by various Streptomyces species, and we designated them "SSI-like proteins" (Taguchi S, Kikuchi H, Suzuki M, Kojima S, Terabe M, Miura K, Nakase T, Momose H [1993] Appl Environ Microbiol 59:4338-4341). In this study, SSI-like proteins from five strains of the genus Streptoverticillium were purified and sequenced, and molecular phylogenetic trees were constructed on the basis of the determined amino acid sequences together with those determined previously for Streptomyces species. The phylogenetic trees showed that SSI-like proteins from Streptoverticillium species are phylogenetically included in Streptomyces SSI-like proteins but form a monophyletic group as a distinct lineage within the Streptomyces proteins. This provides an alternative phylogenetic framework to the previous one based on partial small ribosomal RNA sequences, and it may indicate that the phylogenetic affiliation of the genus Streptoverticillium should be revised. The phylogenetic trees also suggested that SSI-like proteins possessing arginine or methionine at the P1 site, the major reactive center site toward target proteases, arose multiple times on independent lineages from ancestral proteins possessing lysine at the P1 site. Most of the codon changes at the P1 site inferred to have occurred during the evolution of SSI-like proteins are consistent with those inferred from the extremely high G + C content of Streptomyces genomes. The inferred minimum number of amino acid replacements at the P1 site was nearly equal to the average number for all the variable sites. It thus appears that positive Darwinian selection, which has been postulated to account for accelerated rates of amino acid replacement at the major reaction center site of mammalian protease inhibitors, may not have dictated the evolution of the bacterial SSI-like proteins.

Amino Acid Sequence↗
PubMed1998

Sequence diversity in the 16S-23S intergenic spacer region (ISR) of the rRNA operons in representatives of the Escherichia coli ECOR collection.

The ribosomal RNA multigene family in Escherichia coli comprises seven rrn operons of similar, but not identical, sequence. Four operons (rrnC, B, G, and E) contain genes in the 16S-23S intergenic spacer region (ISR) for tRNA(Glu-2) and three (rrnA, D, and H) contain genes for tRNA(Ile-1) and tRNA(Ala-1B). To increase our understanding of their molecular evolution, we have determined the ISR sequence of the seven operons in a set of 12 strains from the ECOR collection. Each operon was specifically amplified using polymerase chain reaction primers designed from genes or open reading frames located upstream of the 16S rRNA genes in E. coli K12. With a single exception (ECOR 40), ISRs containing one or two tRNA genes were found at the same respective loci as those of strain K12. Intercistronic heterogeneity already found in K12 was representative of most variation among the strains studied and the location of polymorphic sites was the same. Dispersed nucleotide substitutions were very few but 21 variable sites were found grouped in a stem-loop, although the secondary structure was conserved. Some regions were found in which a stretch of nucleotides was substituted in block by one alternative, apparently unrelated, sequence (as illustrated by the known putative insertion of rsl in K12). Except for substitutions of different sizes and insertions/deletions found in the ISR, the pattern of nucleotide variation is very similar to that found for the 16S rRNA gene in E. coli. Strains K12 and ECOR 40 showed the highest intercistronic heterogeneity. Most strains showed a strong tendency to homogenization. Concerted evolution could explain the notorious conservation of this region that is supposed to have low functional restrictions.

Base Sequence↗
PubMed2006

Strategies to reduce site differences in multisite studies: a case study of Alzheimer disease progression.

OBJECTIVES: The objectives of this study were to evaluate the magnitude and sources of site differences in a multisite study of rates of cognitive decline among patients with Alzheimer disease and to seek strategies to reduce the magnitude of site differences in this and future such studies. METHODS: A total of 3,280 participants from 15 different sites was analyzed. For each participant, the average rate of change in the Mini-Mental State Examination (MMSE) was calculated. Participants who declined at least three MMSE points per year were classified "rapid decliners." Site differences in sociodemographic distributions and the percentage of rapid decliners were examined, and a signal detection approach was used to identify the main correlates of rapid decline. RESULTS: The percentage of rapid decliners for the 15 sites initially varied from 8%-40%. Two of the correlates of rapid decline were largely the result of different sampling protocols, namely baseline MMSE and elapsed time between the first and last MMSE. By selecting only those participants at each site with a baseline MMSE between 15 and 23, and limiting the follow-up time to a period of 11-24 months, the authors created greater homogeneity in the protocols across sites and reduced site variability of rapid decliners from 27%-50%. CONCLUSION: Results of single-site studies are often nonreproducible, and multisite studies that follow different protocols and do not take site differences into account may be misleading. This study indicates the importance of site differences and how relatively simple efforts to impose common sampling, measurement, and design criteria can reduce, if not totally remove, site differences.

Aged↗
PubMedDate not supplied

Completeness and validity of cancer registration in a major public referral hospital in Saudi Arabia.

BACKGROUND: The 1994 Saudi National Cancer Registry (NCR), a population-based registry, showed a crude incidence rate (CIR) of 39/100,000 for all cancers in the Saudi population. The low CIR suggested possible under-reporting, especially during the early years of operation. This study as aimed at estimating the number of missed cases due to under-reporting, and to assess the validity of reported data from a major public referral hospital in Riyadh city. MATERIALS AND METHODS: We compared cancer cases from the three data sources: medical records (MR), which were the original source of NCR cases; pathology reports (PR); and death certificates (DC). We estimated the missing cancer cases using the capture-recapture method with log-linear models of Fienberg to correct for interdependency between the three data sources. To assess the validity of the data, we reabstracted records of about 8% (39/4760 of previously reported cases from the same hospital. RESULTS: A total of 811 cancer cases were reported through the three sources, i.e., MR 611 (75.3%), PR 639 (78.8%) and DC 204 (25.2%). After fitting a series of log-linear models to the three sources of data, the three sources were found to be statistically dependent. Capture-repcapture method indicated that 384 cases were missed, giving an estimation of 1195 cancer cases to be reported. Using these 1195 estimated cases; the estimated ascertainment rates were 51% for medical records, 53% for pathology reports, 17% for death certificates, and 68% for the aggregated registry. In the validity assessment, major disagreement between the abstracted and reabstracted data was found to be highest for stage of disease (44%), followed by histology code and behavior (25.6%). Minor disagreements were most common for date of diagnosis (36%) and grade (36%). Overall, agreements were highest for laterality (95%), followed by primary site codes (90%) and basis of diagnosis (85%). Agreement of tumor description variables (site, histology, behavior, and stage) was 57%. CONCLUSION: Cancer registration will require substantial improvements in both completeness of reporting and data quality at the hospital level. Use of multiple data sources and estimation of missed cases will help ensure completeness of case registration.

Journal Article↗