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PubMed2007

Combination of automated high throughput platforms, flow cytometry, and hierarchical clustering to detect cell state.

BACKGROUND: This study examined whether hierarchical clustering could be used to detect cell states induced by treatment combinations that were generated through automation and high-throughput (HT) technology. Data-mining techniques were used to analyze the large experimental data sets to determine whether nonlinear, non-obvious responses could be extracted from the data. METHODS: Unary, binary, and ternary combinations of pharmacological factors (examples of stimuli) were used to induce differentiation of HL-60 cells using a HT automated approach. Cell profiles were analyzed by incorporating hierarchical clustering methods on data collected by flow cytometry. Data-mining techniques were used to explore the combinatorial space for nonlinear, unexpected events. Additional small-scale, follow-up experiments were performed on cellular profiles of interest. RESULTS: Multiple, distinct cellular profiles were detected using hierarchical clustering of expressed cell-surface antigens. Data-mining of this large, complex data set retrieved cases of both factor dominance and cooperativity, as well as atypical cellular profiles. Follow-up experiments found that treatment combinations producing "atypical cell types" made those cells more susceptible to apoptosis. CONCLUSIONS Hierarchical clustering and other data-mining techniques were applied to analyze large data sets from HT flow cytometry. From each sample, the data set was filtered and used to define discrete, usable states that were then related back to their original formulations. Analysis of resultant cell populations induced by a multitude of treatments identified unexpected phenotypes and nonlinear response profiles.

Algorithms↗
PubMed1998

[Characteristics of attenders of low threshold syringe-exchange centers providing sterile syringes in Switzerland].

BACKGROUND: The objectives of the present study were to evaluate Aids prevention in drug users attending low threshold centres providing sterile injection equipment in Switzerland, to identify the characteristics of these users, and to monitor the progress of indicators of drug-related harm. METHODS: This paper presents results from a cross-sectional survey carried out in 1994. RESULTS: The mean age of attenders was 28 years, and women represented 27% of the sample. 75% of attenders used a combination of hard drugs (heroin and cocaine). Mean duration of heroin consumption was 8 years, and of cocaine 7 years; 76% of attenders had a fixed abode, but only 34% had stable employment; 45% were being treated with methadone; 9% had shared their injection material in the last 6 months; 24% always used condoms in the case of a stable relationship, and 71% in casual relationships. In a cluster analysis constructed on the basis of multiple correspondence analysis, two distinct profiles of users emerge: highly marginalised users with a high level of consumption (21%); irregular users, better integrated socially, of which the majority are under methadone treatment (79%). CONCLUSION: Theses centres play a major role in Aids prevention. Nevertheless, efforts to improve the hygiene conditions of drug injection in Switzerland should be pursued and extended. At the same time, prevention of HIV sexual transmissions should be reinforced.

Acquired Immunodeficiency Syndrome↗
PubMed1999

Genetic characterization of two Eragrostis species using AFLP and morphological traits.

Tef [Eragrostis tef (Zucc.) Trotter] is the most important cereal crop in Ethiopia. An experiment was conducted to investigate genetic diversity among four cultivars of tef and 14 accessions of Eragrostis pilosa using radiolabelled and silver stained amplified fragment length polymorphism. Morphological traits were also evaluated. A total of 897 markers were obtained out of which 395 were polymorphic using 11 primer combinations. Cluster analysis revealed accessions of E. pilosa which are distantly related and others closely related to tef. Our previous experience also indicates that E. pilosa is crossable with tef. Those accessions distantly related to tef could be used in a crossing program to generate a population for selection and/or genetic mapping. Such genetic mapping populations will form an important entry point towards the molecular genetic dissection of the plant genus, Eragrostis, especially in the context of comparative mapping. Knowledge gained from such study, apart from tef improvement, will also be useful for many forage and turf grass species where little molecular genetic information is available. Nine cultivars or accessions had one or more unique fragments using one or more AFLP primers indicating the potential of the technology in fingerprinting tef in a breeding or seed multiplication program. The results also showed that clusters obtained using silver staining and gamma 33P-ATP labeling were similar, suggesting that silver staining could be used as an alternative to radiolabeling at least in genetic diversity analysis. Significant genetic variation was obtained for morphological traits. Of particular interest to tef breeding was short plant stature in E. pilosa which could be transferred to tef to minimize the problem of lodging. Diversity revealed at the morphological trait level was not commensurate with that observed for AFLP. This was due to the small number of available morphological traits and their interaction with the environment.

Base Sequence↗
PubMed2005

Terrestrial vertebrates have two keratin gene clusters; striking differences in teleost fish.

Keratins I and II form the largest subgroups of mammalian intermediate filament (IF) proteins and account as obligatory heteropolymers for the keratin filaments of epithelia. All human type I genes except for the K18 gene are clustered on chromosome 17q21, while all type II genes form a cluster on chromosome 12q13, that ends with the type I gene K18. Highly related keratin gene clusters are found in rat and mouse. Since fish seem to lack a keratin II cluster we screened the recently established draft genomes of a bird (chicken) and an amphibian (Xenopus). The results show that keratin I and II gene clusters are a feature of all terrestrial vertebrates. Because hair with its multiple hair keratins and inner root sheath keratins is a mammalian acquisition, the keratin gene clusters of chicken and Xenopus tropicalis have only about half the number of genes found in mammals. Within the type I clusters all genes have the same orientation. In type II clusters there is a rare gene of opposite orientation. Finally we show that the genes for keratins 8 and 18, which are the first expression pair in embryology, are not only adjacent in mammals, but also in Xenopus and three different fish. Thus neighboring K8 and K18 genes seem a feature shared by all vertebrates. In contrast to the two well defined keratin gene clusters of terrestrial vertebrates, three teleost fish show an excess of type I over type II genes, the lack of a keratin type II gene cluster and a striking dispersal of type I genes, that are probably the result of the teleost-specific whole genome duplication followed by a massive gene loss. This raises the question whether keratin gene clusters extend beyond the ancestral bony vertebrate to cartilage fish and lamprey. We also analyzed the complement of non-keratin IF genes of the chicken. Surprisingly, an additional nuclear lamin gene, previously overlooked by cDNA cloning, is documented on chromosome 10. The two splice variants closely resemble the lamin LIII a + b of amphibia and fish. This lamin gene is lost on the mammalian lineage.

Amphibians↗
PubMed2006

Microtopography of the dual corticothalamic projections originating from domains along the frequency axis of the cat primary auditory cortex.

Spatial relationships between clusters of corticothalamic (CT) large terminals originating from cortical domains tuned to different frequencies were examined by pair-injecting two different anterograde tracers. Large-terminal CT projection originating from layer 5 was highly divergent with each injection site producing, on average, 15 local clusters distributing throughout non-lemniscal thalamic nuclei following a single anterograde tracer injection in the cat primary auditory cortex. Paired injections in higher- and lower-frequency cortical domains, resulting in labeling of two independent sets of terminal clusters, showed five recognizable patterns of spatial interaction between them. (1) In the ventral division of the medial geniculate complex (vMGC), sheet-like plexuses of small terminals of different origins were situated in parallel, with minimal overlap. (2) Extensive overlap of two low-density plexuses of differently labeled small terminals was observed in the medial division of the medial geniculate complex (MGC). (3) At the transition zones between the vMGC and the superficial dorsal nucleus of the MGC dorsal division, and between the vMGC and the ventrolateral nucleus, there were relatively broad clusters of a high density of large-terminal structures from the two cortical domains, which overlapped extensively. (4) At multiple loci in the nonlemniscal nuclei, pairing of two small clusters of differently labeled large terminals was observed. (5) Small unpaired clusters of large terminals were also found in the nonlemniscal nuclei. For large terminals, approximately 14%, 59%, and 27% clusters per injection demonstrated patterns 3, 4, and 5, respectively. The results provide evidence for the precise topographical organization for the large-terminal CT system at the microscopic level despite its highly divergent projection. This microtopographical projection from the tonotopic cortical field to non-tonotopic thalamic nuclei may raise the possibility of presence of a map that has not been defined in auditory non-lemniscal thalamic nuclei yet.

Animals↗
PubMed1998

DR non-B1 mismatches influence allogeneic MLR-induced TH1- or TH2-like cytokine responses in rhesus monkeys.

Human and nonhuman primates have multiple DR B1 and non-B1 alleles. However, the role of mismatched DR non-B1 alleles in primary alloimmune responses is not well understood. Macaques, which share close DNA homologies with human MHC genes and have a high number of beta-chain genes in the DR subregion, are preeminent preclinical models for immunologic studies of transplant tolerance and immunosuppression. In this study, we examined the effect of allogeneic MHC Class II DRB mismatches in Th1- and Th2-like cytokine responses elicited in one-way MLR cultures in rhesus macaques. An ELISPOT method was used to estimate cytokine secretion at the single cell level. Molecular typing for DRB1 and DR non-B1 alleles was performed by a moderate-high resolution PCR-SSP method using a panel of 55 primer pairs covering 74 DRB alleles and clusters. Of 35 unrelated combinations, 66% had multiple (> or = 2) allelic MM at DRB1 and DR non-B1 with no significant correlation between numbers of DRB1 and DR non-B1 mismatches. Pairs with 1 or 0 MM were assigned to a mono/null MM group to obtain sufficient numbers for statistical analysis. The pairs differing by multiple vs. mono/null DRB1 MM showed no significant difference in cytokine prevalence (P = 0.69). In contrast, high IFN-gamma/ IL4 SFC ratios were noted in pairs with multiple vs. mono/null DR non-B1 MM (p = 0.0009). IFN-gamma/IL-10 spot forming cell (SFC) ratios were consistent with IFN-gamma/IL-4 SFC ratios (r = 0.98). Multiple DR non-B1 mismatches showed a trend towards higher MLR proliferative responses, although the stimulation index did not reflect the dominant cytokine response. These observations suggest a bias towards Th1-like cytokine production under allostimulation with multiple DR non-B1 gene products. Further study of the primary structure of DR non-B1 determinants may be helpful in understanding the fine molecular mechanisms governing the regulation of cytokine profiles during allostimulation in primates.

Animals↗
PubMed2004

A cluster of 21 keratin-associated protein genes within introns of another gene on human chromosome 21q22.3.

Recently, we identified multiple unique sequences in the 21q22.3 region and predicted them to be a cluster of genes encoding hair-specific keratin-associated proteins (KAPs). Detailed computer-aided analysis of these clustered genes revealed that the cluster spans over 165 kb and consists of 21 KAP-related sequences including 16 putative genes and 5 pseudogenes. These were further divided into two subfamilies, KRTAP12 (KRTAP12.1-12.4 and KRTAP12.5P) and KRTAP18 (KRTAP18.1-18.12 and KRTAP18.13P-18.16P). All 16 putative genes possess several intragenic repeat sequences and apparently belong to the high-sulfur KAP gene family (16-30% cysteine content) known for nonhuman mammalian species. Transcripts were detected by RT-PCR analysis for all 16 putative KAP genes and their expression was restricted to hair root cells (radix pili cells) and not found in 28 other tissues, including skin. All 16 KAP genes produced unspliced transcripts, indicating their nature to be that of active intronless genes. Interestingly, all these KAP-related genes are located within introns of the recently identified gene TSPEAR (approved gene symbol C21orf29), 214 kb in size. Surprisingly, the transcriptional direction of 8 of the 16 active genes is the same as that of C21orf29/TSPEAR. This finding suggests a novel transcription mechanism in which C21orf29/TSPEAR gene transcription passes over the multiple transcriptional termination sites of the KAP genes.

Amino Acid Sequence↗
PubMed2004

Association of Fcgamma receptor IIb polymorphism with susceptibility to systemic lupus erythematosus in Chinese: a common susceptibility gene in the Asian populations.

The association of Fcgamma receptor (FcgammaR) polymorphisms with systemic lupus erythematosus (SLE) has been demonstrated in various populations; however, the results have been inconsistent. We recently identified a single-nucleotide polymorphism encoding a non-synonymous substitution, Ile232Thr (I232T), of FCGR2B and its association with SLE in Japanese and in Thais. Multiple functional FcgammaR genes with polymorphisms (FCGR2A, FCGR2B, FCGR3A, and FCGR3B) cluster in 1q23, and some of them are in linkage disequilibrium (LD). To differentiate contributions from multiple-linked loci, comparison of different populations may provide useful information. In this study, we analyzed the above four FCGR polymorphisms of the Chinese patients and controls for the association with SLE. FCGR2A-H131R, FCGR2B-I232T, FCGR3A-F176V, and FCGR3B genotypes were determined in 167 Chinese patients with SLE and 129 healthy controls. Association was examined using case-control analysis. Allele frequencies of FCGR2B-232T and FCGR3A-176F were significantly increased in SLE [odds ratio (OR) = 1.67 and OR = 1.41, respectively]. Interestingly, while these alleles had a tendency of positive LD in the controls, FCGR2B-232T was in positive association with FCGR3A-176V in SLE, suggesting that these two alleles were associated with SLE in an independent manner. Comparison between SLE with and without nephritis indicated significant association of FCGR2B-232T with nephritis (OR = 2.65). When the present results were combined with our previous data on the Japanese and the Thais using meta-analytic methods, highly significant and independent association was observed for FCGR2B and FCGR3A genotypes. These results strongly suggested that FCGR2B is a common susceptibility factor to SLE in the Asians.

Adult↗
PubMed2004

Dietary patterns and the adenomacarcinoma sequence of colorectal cancer.

BACKGROUND: Food components of a diet are highly related, so that building up dietary patterns may help understand the relationship between chronic diseases and diet, and identify high risk groups that need preventive advice. AIM: The aim of this study was to determine dietary patterns associated with the colorectal adenoma-carcinoma pathway. METHODS: We performed a two-step analysis using first principal component analysis to select the most appropriate food groups, then a hierarchical agglomerative clustering method, in order to determine dietary patterns in 1372 subjects included in a case-control study. Patients with hyperplastic polyps (n = 103), adenomas < 10 mm, (n = 154) or larger adenomas (n = 208) were then compared with polyp-free controls (n = 426), and colorectal cancer cases (n = 171) compared with population controls (n = 309) using unconditional logistic regression adjusted on age and gender. RESULTS: Cluster analysis determined five food patterns. Cluster 1 identified a low-energy diet; cluster 2 a high-starch, highfat, and low-fruit diet; cluster 3 a high-processed meat, -energy, -alcohol, and -starchy foods diet; cluster 4 a high-fish, -cereals, -honey, -olive oil, -fruit and -vegetables diet; and cluster 5 a high-flour, -sugar, -chocolate, -animal fats, and -eggs diet. Logistic regression identified cluster 2 [corrected] as significantly associated with risk of small adenomas (OR = 1.7; 95% confidence interval 1.0-2.7), large adenomas (OR = 1.9; 1.2-3.0) and cancers (OR = 1.7; 1.1-2.8) compared with cluster 1 [corrected] Cluster 4 diet was inversely associated with risk of small adenomas (OR = 0.4; 0.2-1.0). There was no relationship between patterns and risk of hyperplastic polyps. Multiple adjustment decreased the strength of the relationships with cluster 2 [corrected] which remained significantly associated with adenomas, but not cancer. CONCLUSION: A lowenergy diet appeared as protective all along the adenoma-carcinoma sequence, contrary to a high-energy, high-processed meat and -animal fat diet.

Adenocarcinoma↗
PubMed2003

Symmetry and clustering of symptomatic hand osteoarthritis in elderly men and women: the Framingham Study.

OBJECTIVE: While symmetry and clustering of radiographic hand osteoarthritis (OA) have been described in middle-aged women, these have not been studied in elderly individuals and similar investigations are lacking for symptomatic hand OA. The goal of this study was to study patterns of joint involvement in symptomatic hand OA among elderly Caucasian men and women. METHODS: Using data from the Framingham Osteoarthritis Study, we defined a joint as having symptomatic OA if it had symptoms and radiographic OA (Kellgren and Lawrence grade > or =2). We assessed clustering of symptomatic OA using a chi(2)-test and evaluated the interrelationship of occurrence of symptomatic OA among different joints with generalized estimating equations. RESULTS: Of 976 subjects (age 71-99 yr, 36% men) examined, symptomatic OA more often affected multiple hand joints in an individual than would be expected by chance (P<0.001). The presence of symptomatic OA at a particular joint was strongly associated with symptomatic OA in the same joint of the opposite hand, followed by other joints in the same row of the same hand, and then other joints in the same ray of the same hand. The symmetrical pattern of symptomatic OA was more apparent in women than in men. CONCLUSION: Our study demonstrates that symptomatic OA often affects multiple hand joints, and is more likely to cluster by row than by ray. The disease also occurs in a remarkably symmetrical pattern, especially in women.

Age Distribution↗
PubMed2006

[Applying matching matrix, factor analysis and clustering analysis to investigation of characteristics of syndromes of phlegm and blood stasis in patients with coronary heart disease].

OBJECTIVE: To investigate the characteristics of syndromes of phlegm and blood stasis in patients with coronary heart disease by multiple statistical methods of matching matrix, factor analysis and clustering analysis, and to provide some references for classification and normalization of diagnosis of syndromes of phlegm and blood stasis of coronary heart disease. METHODS: The correlations among 46 kinds of symptoms in syndrome of non-phlegm and non-blood stasis, syndrome of blood stasis, syndrome of phlegm and syndrome of phlegm-blood stasis blocking in 200 patients with coronary heart disease were analyzed by matching matrix, factor analysis and clustering analysis. RESULTS: The manifestations of tongue and pulse in syndromes of phlegm and blood stasis were significantly different from those in syndrome of non-phlegm and non-blood stasis. The pathogenesis of viscera in syndromes of phlegm and blood stasis lied in the heart and kidney, and the syndrome of deficiency of heart qi was the most common one while the syndrome of deficiency of kidney qi took the secondary place. The syndrome of phlegm was often accompanied by syndrome of deficiency of spleen qi. Only 15 ones of 46 clinical symptoms showed high frequency in concomitant appearance in syndrome of blood stasis, syndrome of phlegm and syndrome of phlegm-blood stasis blocking. Apart from having the common symptoms in syndrome of deficiency in origin, the syndrome of phlegm especially showed white and greasy fur and slippery pulse as well as distention and fullness of chest and abdominal distension; the syndrome of blood stasis showed purplish tongue and ecchymosis on tongue as well as fixed pain; and the syndrome of phlegm-blood stasis blocking showed the main symptoms of both syndrome of phlegm and syndrome of blood stasis. CONCLUSION: The statistical methods of matching matrix, factor analysis and clustering analysis are convenient, and can definitely indicate the clinical characteristics and syndrome differentiation of viscera of different syndromes of phlegm and blood stasis, which are beneficial to further research of diagnosis and differentiation of such syndromes of coronary heart disease.

Cluster Analysis↗
PubMed2005

[Polymorphisms screening of PON gene cluster].

To identify all putative functional polymorphisms of PON gene cluster in Chinese Han population. Common polymorphisms of PON1, PON2 and PON3 gene were identified by directly sequencing of genomic DNAs derived from 48 randomly selected patients with coronary heart disease. We designed PCR arrays to amplify regions up to about 1kb upstream from transcription-initiation sites, i.e., putative promoter regions, all exons and adjacent non-coding regions. In a total length of 13.9 kb explored, we identified thirty-one SNPs, of which, 17 were first reported. A new coding polymorphism was detected in PON1 gene, which gives rise to amino acid substitutions of arginine (R) for glycine (G) at codon 160, whereas L54M polymorphism, which is common in white population, was not detected in our Han population. Among the five polymorphisms identified in PON3 gene, one in the promoter regions at position -133 (C/A) was located in a potential binding site for transcription factor LF-A1. Allele frequencies of some polymorphisms are significantly different from those reported in Caucasian populations. Complete or nearly complete association between polymorphisms was frequently observed. The identified multiple putative functional polymorphisms in PON gene cluster and their linkage disequilibrium patterns in combination with the population specific frequencies are of values for futher association studies of PON gene cluster with cardiovascular disease.

Aryldialkylphosphatase↗
PubMed2000

A comparison of frailty and other models for bivariate survival data.

Multivariate survival data arise when each study subject may experience multiple events or when study subjects are clustered into groups. Statistical analyses of such data need to account for the intra-cluster dependence through appropriate modeling. Frailty models are the most popular for such failure time data. However, there are other approaches which model the dependence structure directly. In this article, we compare the frailty models for bivariate data with the models based on bivariate exponential and Weibull distributions. Bayesian methods provide a convenient paradigm for comparing the two sets of models we consider. Our techniques are illustrated using two examples. One simulated example demonstrates model choice methods developed in this paper and the other example, based on a practical data set of onset of blindness among patients with diabetic Retinopathy, considers Bayesian inference using different models.

Bayes Theorem↗
PubMed2004

Imaging diagnosis of 12 patients with hepatic tuberculosis.

AIM: To assess CT, MR manifestations and their diagnostic value in hepatic tuberculosis. METHODS: CT findings in 12 cases and MR findings in 4 cases of hepatic tuberculosis proved by surgery or biopsy were retrospectively analyzed. RESULTS: (1) CT findings: One case of serohepatic type of hepatic tuberculosis had multiple-nodular lesions in the subcapsule of liver. Parenchymal type was found in 10 cases, including multiple, miliary, micronodular and low-density lesions with miliary calcifications in 2 cases; singular, low-density mass with multiple flecked calcifications in 3 cases; multiple cystic lesions in 1 case; multiple micronodular and low-density lesions fusing into multiloculated cystic mass or "cluster" sign in 3 cases; and singular, macronodular and low-density lesion with multiple miliary calcifications in 1 case. One case of tuberculous cholangitis showed marked dilated intrahepatic ducts with multiple flecked calcifications in the porta hepatis. (2) MR findings in 4 cases were hypointense on both T1-weighted imagings and T2-weighted imagings in one case, hypointense on T1-weighted imagings and hyperintense on T2-weighted imagings in 3 cases. Enhanced MR in 3 cases was slightly shown peripheral enhancement or with multilocular enhancement. CONCLUSION: Various types of hepatic tuberculosis have different imaging findings, and typical CT and MR findings can suggest the diagnosis.

Adolescent↗
PubMed2001

The centromere composition of multiple repetitive sequences on rice chromosome 5.

The large-scale primary structure of the centromeric region of rice chromosome 5 was analyzed, the first example in a cereal species. The yeast artificial chromosome (YAC) and bacterial artificial chromosome (BAC) contigs aligned on the centromere of rice chromosome 5 (CEN5) covered a distance of more than 670 kb. Strong suppression of genetic recombination, one of the features of a functional centromere, occurred along the contig region. The most remarkable feature of CEN5 is the composition of the multiple repetitive elements. Oryza-specific RCS2 short tandem repeats were clustered along less than 100 kb at one end of the contig. At least 15 copies of the conserved domain of the 1.9 kb RCE1 centromeric repeats, which are similar to the long terminal repeats (LTRs) of gypsy-type retrotransposon RIRE7, were dispersed mainly in 320 kb stretches next to RCS2 tandem clusters. Many copies of the LTR-like sequences of RIRE3 and RIRE8, another gypsy-type retrotransposon, were also found throughout the contig. On the other hand, the gagpol region was less conserved in the contig. These results indicate that the rice centromere is composed of multiple repetitive sequences with the RCS2 tandem cluster probably being situated as the core of a functional centromere of some hundreds of kilobases to megabases in length.

Base Sequence↗
PubMed1998

Patterns of recurrence of intussusception in children: a 17-year review.

PURPOSE: Patterns of recurrence of intussusception (INT) were reviewed to determine whether changes in management have affected the rate and patterns of recurrence as well as long-term outcome in children with multiple (i. e., 2 or more) recurrences. MATERIALS AND METHODS: Review was done of 763 children with 876 intussusceptions, including (1) recurrence rate, (2) patterns of recurrence (number of and interval between recurrences), (3) reducibility, (4) pathologic lead points (PLP), (5) operative findings and (6) long-term follow-up in those with multiple recurrences. RESULTS: Above features (1)-(6) were the same in those managed with barium enema (1979-1985) and those managed with air enema (1985-1996). Overall recurrence rate was 9 %; 11 % with barium enema and 8 % with air enema. Sixty-nine patients had 113 recurrences: 47/69 (68 %) and 1 recurrence and 22/69 (32 %) had multiple recurrences. Multiple recurrences presented as isolated episodes or in clusters up to 8 years. Reducibility was 100 % for initial INT and 95 % for recurrent episodes; there were no perforations. Surgery, in 4 with irreducible recurrence, revealed no PLP. PLP were present in 5 (8 %): 2 (4 %) with 1 recurrence and 3 (14 %) with multiple recurrences. No pattern of recurrence was predictive for PLP. Long-term follow-up (up to 15 years) available in 11 with multiple recurrences revealed a favourable outcome. CONCLUSIONS: Rates and patterns of recurrence did not change with altered management. Because of the high reduction rate of recurrences, lack of perforation and favourable long-term follow-up, we recommend radiological reduction for recurrent INT. Multiple recurrences are not a contraindication. A careful search for PLP is mandatory. Surgery should be reserved for irreducible recurrences or for demonstrated PLP.

Adolescent↗
PubMed1995

Molecular characterization and identification of Saprolegnia by restriction analysis of genes coding for ribosomal RNA.

Restriction fragment length polymorphisms (RFLPs) in two regions of the ribosomal DNA (rDNA) repeat unit were examined in 33 strains representing 18 species of Saprolegnia. The Polymerase Chain Reaction (PCR) was used to separately amplify the 18S rDNA and the region spanning the two internal transcribed spacers (ITS) and the 5.8S ribosomal RNA gene. Amplified products were subjected to a battery of restriction endonucleases to generate various fingerprints. The internal transcribed spacer region exhibited more variability than the 18S rDNA and yielded distinctive profiles for most of the species examined. Most of the species showing 100% similarity for the 18S rDNA could be distinguished by 5.8S + ITS restriction polymorphisms except for S. hypogyna, S. delica, S. lapponica, and S. mixta. The rDNA data indicate that S. lapponica and S. lapponica and S. mixta are conspecific with S. ferax, whereas there is no support for the proposed synonymies of S. diclina with S. delica and of S. mixta with S. monoica. Results from cluster analysis of the two data sets were very consistent and tree topologies were the same, regardless of the clustering method used. A further examination of multiple strains in the S. diclina-S. parasitica complex showed that restriction profiles are conserved across different strains of S. parasitica originating from the U.K. and Japan. HhaI and BsaI restriction polymorphisms were observed in isolates from the U.S. and India. The endonuclease BstUI was diagnostic for S. parasitica, generating identical fingerprints for all stains regardless of host and geographic origin. Except for the atypical strain ATCC 36144, restriction patterns were also largely conserved in S. diclina. Correlation of the rDNA data with morphological and ultrastructural features showed that S. diclina and S. parasitica are not conspecific. Restriction polymorphisms in PCR-amplified rDNA provide a molecular basis for the classification of Saprolegnia and will be useful for the identification of strains that fail to produce antheridia and oogonia.

Base Sequence↗
PubMed2006

Geostatistical analysis of disease data: visualization and propagation of spatial uncertainty in cancer mortality risk using Poisson kriging and p-field simulation.

BACKGROUND: Smoothing methods have been developed to improve the reliability of risk cancer estimates from sparsely populated geographical entities. Filtering local details of the spatial variation of the risk leads however to the detection of larger clusters of low or high cancer risk while most spatial outliers are filtered out. Static maps of risk estimates and the associated prediction variance also fail to depict the uncertainty attached to the spatial distribution of risk values and does not allow its propagation through local cluster analysis. This paper presents a geostatistical methodology to generate multiple realizations of the spatial distribution of risk values. These maps are then fed into spatial operators, such as in local cluster analysis, allowing one to assess how risk spatial uncertainty translates into uncertainty about the location of spatial clusters and outliers. This novel approach is applied to age-adjusted breast and pancreatic cancer mortality rates recorded for white females in 295 US counties of the Northeast (1970-1994). A public-domain executable with example datasets is provided. RESULTS: Geostatistical simulation generates risk maps that are more variable than the smooth risk map estimated by Poisson kriging and reproduce better the spatial pattern captured by the risk semivariogram model. Local cluster analysis of the set of simulated risk maps leads to a clear visualization of the lower reliability of the classification obtained for pancreatic cancer versus breast cancer: only a few counties in the large cluster of low risk detected in West Virginia and Southern Pennsylvania are significant over 90% of all simulations. On the other hand, the cluster of high breast cancer mortality in Niagara county, detected after application of Poisson kriging, appears on 60% of simulated risk maps. Sensitivity analysis shows that 500 realizations are needed to achieve a stable classification for pancreatic cancer, while convergence is reached for less than 300 realizations for breast cancer. CONCLUSION: The approach presented in this paper enables researchers to generate a set of simulated risk maps that are more realistic than a single map of smoothed mortality rates and allow the propagation of cancer risk uncertainty through local cluster analysis. Coupled with visualization and querying capabilities of geographical information systems, animated display of realizations can highlight areas that depart consistently from the general behavior observed across the region, guiding further investigation and control activities.

Cluster Analysis↗