Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “multiple clustering”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,081 records · Page 60Linked to original sources

The problem of multiple inference in identifying point-source environmental hazards.

Point-source environmental hazards are often identified by examination of unusual clusters of disease cases. The very large number of potential clusters give rise to the statistical problem of "multiple inference," i.e., the more clusters examined, the greater the risk of "false-positive" associations emerging by chance alone. This paper first distinguishes the situation of clusters identified by anecdotal observation from those that emerge from systematic searches. The latter may or may not include a systematic enumeration of potential causal factors associated with each potential disease cluster. If exposure information is not systematically available, empirical Bayes procedures are suggested as a basis for ranking the observed clusters in order of priority for further investigation. If exposure information is systematically available, empirical Bayes procedures can be used to select associations to report or to rank them in order of priority for confirmation. In addition, procedures are described for testing the global null hypothesis of no exposure-disease associations and for estimating the number of true-positive associations. These approaches are advocated in preference to classical frequentist approaches of multiplying p values by the number of tests performed.

Environmental Pollution↗

Now you see it, now you don't: statistical and methodological considerations in fMRI.

We illustrate the effects of statistical threshold, spatial clustering, voxel size, and two approaches to multiple comparison correction on fMRI results. We first analyzed fMRI images obtained from a single subject during a noun-verb matching task. Data were analyzed with Statistical Parametric Mapping (SPM) using two different voxel sizes, and results were displayed at three different levels of statistical significance. At each statistical threshold, results were first uncorrected for multiple comparisons and spatial extent and then presented using a spatial extent cluster of 20 voxels. We then statistically controlled the Type I error rate associated with multiple comparisons by using the false discovery rate and by the random field adjustment for false-positive rate used by SPM. We also examined group results from language and graphesthesia paradigms at three levels of statistical significance. In all circumstances, apparent random activations decreased as more conservative statistical approaches were employed, but activation in areas considered to be functionally significant was also reduced. These issues are important in the choice of analytic approach and interpretation of fMRI results, with clear implications for the surgical management of individual patients when fMRI results are used to delineate specific areas of eloquent cortex.

Journal Article↗

Improving large-scale proteomics by clustering of mass spectrometry data.

Tandem mass spectrometry (MS/MS), coupled with liquid chromatography (LC), is a powerful tool for the analysis and comparison of complex protein and peptide mixtures. However, the extremely large amounts of data that result from the process are very complex and difficult to analyze. We show how the clustering of similar spectra from multiple LC-MS/MS runs can help in data management and improve the analysis of complex peptide mixtures. The major effect of spectrum clustering is the reduction of the huge amounts of data to a manageable size. As a result, analysis time is shorter and more data can be stored for further analysis. Furthermore, spectrum quality improvement allows the identification of more peptides with greater confidence, the comparison of complex peptide mixtures is facilitated, and the entire proteomics project is presented in concise form. Pep-Miner is an advanced software tool that implements these clustering-based applications. It proved useful in several comparative proteomics projects involving lung cancer cells and various other cell types. In one of these projects, Pep-Miner reduced 517 000 spectra to 20 900 clusters and identified 2518 peptides derived from 830 proteins. Clustering and identification lasted less than two hours on an IBM Thinkpad T23 computer (laptop). Pep-Miner's unique properties make it a very useful tool for large-scale shotgun proteomics projects.

Algorithms↗

Prevalence and co-occurrence of psychiatric symptom clusters in the U.S. adolescent population using DISC predictive scales.

OBJECTIVE: To estimate 12-month prevalence and co-occurrence of symptoms of specific mental problems among US adolescents (12-17 years) by age, sex and racial/ethnic subgroups. METHOD: Data from the 2000 National Household Survey of Drug Abuse (NHSDA) adolescent sample are used to estimate prevalence and co-occurrence rates using the DISC predictive scales. Multiple logistic regressions were used to derive significant correlates of each domain of DPS-derived symptom cluster indicators of psychiatric problems and of severe comorbidity, with control of demographics and environmental factors. SETTING: The National Household Survey on Drug Abuse (NHSDA), a national household probability sample, includes a nationally representative sample of 12-17 year-old adolescents (N = 19,430), through in-home surveys. RESULTS: Three out of five adolescents screened positive for at least one DPS symptom cluster with estimates for specific symptom cluster ranging over 9.7% (substance use disorder), 13.4% (affective), 36.3% (disruptive-behavior), and 40.1% (anxiety). Co-occurrence was high with almost one-third of any DPS symptom cluster reporting multiple positive screens of four or more clusters. Blacks and younger females were most likely to report mental health problems and co-occurrence. CONCLUSION: Mental health problems among U.S. youth may be far more common than previously believed, although these symptoms have not yet reached the point of clinical impairment. The data speak to important patterns of age, gender and racial/ethnic differences in mental health problems deserving of further study.

Journal Article↗

Stereotactic breast biopsy of clustered microcalcifications with a directional, vacuum-assisted device.

The success rate with the traditional 14-gauge, core-biopsy, multiple-pass technique was compared with that of a directional vacuum-assisted device in sampling calcification clusters in the breast. Of the 130 focal calcification clusters sampled with the multiple-pass technique, 12 clusters (9.2%) had no particles depicted on radiographs of the specimen. Specimens from all 106 (100%) clusters sampled with the directional, vacuum-assisted instrument contained calcifications at radiography. The directional, vacuum-assisted device improved the ability to percutaneously sample breast calcifications.

Biopsy, Needle↗

Multiple redundant sequence elements within the fission yeast ura4 replication origin enhancer.

BACKGROUND: Some origins in eukaryotic chromosomes fire more frequently than others. In the fission yeast, Schizosaccharomyces pombe, the relative firing frequencies of the three origins clustered 4-8 kbp upstream of the ura4 gene are controlled by a replication enhancer - an element that stimulates nearby origins in a relatively position-and orientation-independent fashion. The important sequence motifs within this enhancer were not previously localized. RESULTS: Systematic deletion of consecutive segments of approximately 50, approximately 100 or approximately 150 bp within the enhancer and its adjacent core origin (ars3002) revealed that several of the approximately 50-bp stretches within the enhancer contribute to its function in partially redundant fashion. Other stretches within the enhancer are inhibitory. Some of the stretches within the enhancer proved to be redundant with sequences within core ars3002. Consequently the collection of sequences important for core origin function was found to depend on whether the core origin is assayed in the presence or absence of the enhancer. Some of the important sequences in the core origin and enhancer co-localize with short runs of adenines or thymines, which may serve as binding sites for the fission yeast Origin Recognition Complex (ORC). Others co-localize with matches to consensus sequences commonly found in fission yeast replication origins. CONCLUSIONS: The enhancer within the ura4 origin cluster in fission yeast contains multiple sequence motifs. Many of these stimulate origin function in partially redundant fashion. Some of them resemble motifs also found in core origins. The next step is to identify the proteins that bind to these stimulatory sequences.

Journal Article↗

Determination of molecular geometry by high-order multiple-quantum evolution in solid-state NMR.

The principles of molecular geometry determination by high-quantum heteronuclear local field spectroscopy in solid-state NMR are discussed. The extreme multiple-quantum coherences in a cluster of nuclear spins are allowed to evolve in the presence of heteronuclear through-space couplings to two spins of a different type. The multiple-quantum dephasing curve is independent of the homonuclear spin-spin couplings and may be described in terms of geometric parameters. The triple-quantum version of the experiment is demonstrated by determining the psi torsion angle in a [(15)N(2), (13)C(3)]-labeled sample of the peptide ala-ala-gly. Two regions of torsion angle space fit the experimental data, one in the neighborhood of -152 degrees and one in the neighborhood of +161 degrees. The latter determination is in excellent agreement with the X-ray estimate of +160.5 degrees.

Magnetic Resonance Spectroscopy↗

Distinct iron-sulfur cluster assembly complexes exist in the cytosol and mitochondria of human cells.

Iron-sulfur (Fe-S) clusters are cofactors found in many proteins that have important redox, catalytic or regulatory functions. In mammalian cells, almost all known Fe-S proteins are found in the mitochondria, but at least one is found in the cytosol. Here we report cloning of the human homologs to IscU and NifU, iron-binding proteins that play a critical role in Fe-S cluster assembly in bacteria. In human cells, alternative splicing of a common pre-mRNA results in synthesis of two proteins that differ at the N-terminus and localize either to the cytosol (IscU1) or to the mitochondria (IscU2). Biochemical analyses demonstrate that IscU proteins specifically associate with IscS, a cysteine desulfurase that is proposed to sequester inorganic sulfur for Fe-S cluster assembly. Protein complexes containing IscU and IscS can be found in the mitochondria as well as in the cytosol, implying that Fe-S cluster assembly takes place in multiple subcellular compartments in mammalian cells. The possible roles of the IscU proteins in mammalian cells and the potential implications of compartmentalization of Fe-S cluster assembly are discussed.

Alternative Splicing↗

Characterization of a Bordetella pertussis fimbrial gene cluster which is located directly downstream of the filamentous haemagglutinin gene.

The biosynthesis of fimbriae is a complex process requiring multiple genes which are generally found clustered on the chromosome. In Bordetella pertussis, only major fimbrial subunit genes have been identified, and no evidence has yet been found that they are located in a fimbrial gene cluster. To locate additional genes involved in the biosynthesis of B. pertussis fimbriae, we used TnphoA mutagenesis. A PhoA+ mutant (designated B176) was isolated which was affected in the production of both serotype 2 and 3 fimbriae. Cloning and sequencing of the DNA region harbouring the transposon insertion revealed the presence of at least three additional fimbrial genes, designated fimB, fimC and fimD. The transposon was found to be located in fimD. Analysis of PhoA activity indicated that the fimbrial gene cluster was positively regulated by the bvg locus. A potential binding site for BvgA was observed upstream of fimB. FimB showed homology with the so-called chaperone-like fimbrial proteins, while FimC was homologous with a class of fimbrial proteins located in the outer membrane and presumed to be involved in transport and anchorage of fimbrial subunits. An insertion mutation in fimB abolished the expression of fimbrial subunits, implicating this gene in the biosynthesis of both serotype 2 and 3 fimbriae. Upstream of fimB a pseudogene (fimA) was observed which showed homology with the three major fimbrial subunit genes, fim2, fim3 and fimX. The construction of a phylogenetic tree suggested that fimA may be the primordial major fimbrial subunit gene from which the other three were derived by gene duplication. Interestingly, the fimbrial gene cluster was found to be located directly downstream from the gene coding for the filamentous haemagglutinin, an important B. pertussis adhesin, possibly suggesting co-operation between the two loci in the pathogenesis of pertussis.

Adhesins, Bacterial↗

A microswitch cluster to enhance arm-lifting responses without dystonic head tilting by a child with multiple disabilities.

This study assessed whether a microswitch duster with favorite stimulation could help a 9.1-yr.-old child with multiple disabilities increase arm-lifting responses without dystonic, sideways head tilting. The microswitch cluster involved two microswitches, one at the child's arm to monitor the lifting response, and the other at the child's head to monitor whether it was tilted during arm lifting. Analysis showed that the percentage of arm-lifting responses occurring without head tilting increased most visibly when favorite stimulation focused on those (appropriate) responses.

Arm↗

Comparison of international dairy sire evaluations from meta-analysis of national estimated breeding values and direct analysis of individual animal performance records.

Our objective was to assess the predictive ability of different methodologies for international genetic evaluation of milk yield and to determine the magnitude of differences in the resulting sire estimated breeding values (EBV). Data included first lactation records of 16,057,335 Holstein-sired cows from 237,049 herds in 14 countries. Meta-analysis of national sire EBV using the multiple-trait across country evaluation (MACE) procedure, single-trait analysis of individual animal performance records, multiple-trait analysis of individual animal performance records, and borderless herd cluster model were compared by assessing predictive ability. Comparisons were based on root mean square error of sire EBV from a subset of records from cows calving between 1990 and 1995 and corresponding pedigree indices for sires that received their first genetic evaluations in 1996 or 1997. The number of bulls first evaluated in 1996 or 1997 that were in common between the top 25, 100, and 250 for pedigree index and the top 25, 100, and 250 for EBV were also determined for each method. Average root mean square error of prediction was 10.3 kg2 for the borderless single-trait model, 6.6 kg2 for the borderless herd cluster model, and 6.7 kg2 for both the borderless multiple-trait model and meta-analysis of national sire EBV using MACE. The mean numbers of common bulls among the top 25, 100, and 250, respectively, when selected on pedigree index and subsequent EBV were 11, 48, and 154 for the borderless single-trait model; 16, 66, and 176 for the borderless multiple-trait model; 16, 66, and 178 for the borderless herd cluster model; and 15, 66, and 178 for meta-analysis of national sire EBV using MACE. Rank correlations between sire EBV from different models ranged from 0.77 for the single-trait borderless model and the meta-analysis using MACE to 0.92 for the borderless multiple-trait and the borderless herd cluster models.

Animals↗

Natural history and prognostic factors for survival in patients with acquired immune deficiency syndrome (AIDS)-related primary central nervous system lymphoma (PCNSL).

The incidence of primary central nervous system lymphoma (PCNSL) is increasing rapidly. It will be the most common primary malignant neoplasm of the brain by the year 2000. PCNSL is an important lethal complication in acquired immunodeficiency syndrome (AIDS) patients. Our objective was to study the natural history and prognostic factors for survival in patients with AIDS-related PCNSL. This is a retrospective cohort study of 75 patients with the diagnosis of AIDS-related PCNSL followed at Jackson Memorial Hospital/University of Miami. Medical records were abstracted for information about age, gender, race, and ethnicity. The method of diagnosis, treatment, and outcome of AIDS and PCNSL in this group were examined. Univariate and multivariate analyses were performed to identify prognostic factors for survival. The median age was 37 years. Males comprised 84% of the patients and 55% of the patients were Hispanic. The most common human immunodeficiency virus (HIV) risk factors were homosexuality and multiple sexual partners. The median cluster designation (CD) 4 count was 15/microl and the median lactic dehydrogensase (LDH) was 1.5x normal. Computed-assisted tomographic (CT) scans of the brain showed multiple lesions in 44% of the patients. Single-photon emission CT scan (SPECT) Thallium-201 of the brain was performed in two-thirds of patients. The most common histologies were immunoblastic and large cell lymphoma. Cranial radiation was given to 72% of the patients, and 55% of them did not complete treatment. The median survival of the group was 1.3 months. Univariate and multivariate analysis showed that longer survival was associated with good performance status (ECOG = 1 to 2 vs. 3 to 4). The presence of prior opportunistic infections, risk factors for AIDS, CD4 counts, level of LDH, ethnicity, gender, duration of symptoms before diagnosis, and race did not influence survival. PCNSL is a neoplasm with a very poor prognosis and short survival even with CNS radiation therapy. Performance status appears to be the main prognostic factor for survival. No significant differences in presentation or outcome were detected between the Hispanic and non-Hispanic patients.

Adult↗

Privacy protection versus cluster detection in spatial epidemiology.

OBJECTIVES: Patient data that includes precise locations can reveal patients' identities, whereas data aggregated into administrative regions may preserve privacy and confidentiality. We investigated the effect of varying degrees of address precision (exact latitude and longitude vs the center points of zip code or census tracts) on detection of spatial clusters of cases. METHODS: We simulated disease outbreaks by adding supplementary spatially clustered emergency department visits to authentic hospital emergency department syndromic surveillance data. We identified clusters with a spatial scan statistic and evaluated detection rate and accuracy. RESULTS: More clusters were identified, and clusters were more accurately detected, when exact locations were used. That is, these clusters contained at least half of the simulated points and involved few additional emergency department visits. These results were especially apparent when the synthetic clustered points crossed administrative boundaries and fell into multiple zip code or census tracts. CONCLUSIONS: The spatial cluster detection algorithm performed better when addresses were analyzed as exact locations than when they were analyzed as center points of zip code or census tracts, particularly when the clustered points crossed administrative boundaries. Use of precise addresses offers improved performance, but this practice must be weighed against privacy concerns in the establishment of public health data exchange policies.

Algorithms↗

Hemodialysis patients' symptom experiences: effects on physical and mental functioning.

Dialysis patients experience numerous symptoms, some serious in terms of medical outcomes and all serious in terms of potential reductions in functioning and well-being. This cross-sectional study used self-reports of hemodialysis patients to catalogue symptoms; hypothesizing that frequently experienced symptoms, regardless of acuity, negatively affect functioning and well-being. Data were collected from 307 randomly selected hemodialysis patients from 14 dialysis facilities. Twenty-two of the 47 symptoms queried had mean experience scores of > or = 1 on a scale of 0-4, that is, were experienced by patients at least "a little of the time." Seventeen of these 22 symptoms were significantly correlated (< or = .01) with the SF-36 Physical Component Summary (PCS) scale, Mental Component Summary (MCS) scale, or both. All but four of these 17 symptoms (dry mouth, itchy skin, lack of appetite, and restless legs) clustered around fatigue/sleep, sexual concerns, or mobility. Linear multiple regression showed age, diabetes, the fatigue/sleep and mobility clusters, and itchy skin to be negatively associated with the PCS (p < or = .01). The fatigue/sleep cluster was also negatively associated with the MCS. Because previous research has shown the PCS and MCS to be associated with morbidity and mortality, management of common, non-acute symptoms may have long-term benefits for hemodialysis patients.

Activities of Daily Living↗

Single channels activated by high concentrations of GABA in superior cervical ganglion neurones of the rat.

1. Single-channel currents evoked by high concentrations of GABA (10-2000 microM) have been analysed to investigate the characteristics of GABAA receptor channels in outside-out patches from rat sympathetic neurones. When high concentrations of GABA were applied to a patch, channel openings occurred in prolonged clusters (3.8 +/- 3.7 s (mean +/- S.D.) at 50 microM-GABA) consisting, on average, of 350 apparent openings per cluster. Individual clusters were separated by long silent intervals. 2. Channel openings were to many (often ill-defined) conductance states (range 7-36 pS), but the most frequently observed conductance level was approximately 30 pS, (29.6 +/- 0.34 pS). Only these clusters during which the channel was open to this main state conductance for at least 95% of the cluster open time were used in the analysis of probability of being open. Other less frequently observed conductance levels were 15-18 and 22-23 pS, while levels of 33-36 and 7-9 pS were occasionally, but reliably, observed. 3. Bursts within clusters were defined as a series of openings separated by closed intervals shorter than some critical value, tc. At 50 microM-GABA the mean burst length was 439 +/- 434 ms (+/- S.D., tc = 50 ms). 4. The probability of being open, po, during bursts within clusters has been analysed as a function of GABA concentration. As expected, increasing the concentration of GABA resulted in an overall increase in po. However, for a given agonist concentration there was a wide spread in po, far greater than that predicted for a population of identical and independent receptor channels (demonstrated by comparison with stimulated channel activity). 5. The wide range of po values at a particular concentration of GABA was not due to inappropriate selection of tc. At 50 microM-GABA the range of po values was similar for tc of 20-1000 ms, although the overall mean po became lower (0.64 rather than 0.81). 6. On the basis of simulated channel activity, it appears that most clusters which do not contain multiple openings, arise from the activity of one individual channel. Furthermore, there was no detectable tendency for gaps between bursts to be shorter in the middle of a cluster than at its ends. Therefore it is unlikely that variability in po arose from overlapping activity of two or more channels. 7. The values for po, mean open time, and mean shut time for bursts within the same cluster, and between different clusters, were compared by a randomization test.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

Milk fluoridation: a comparison of dental health in two school communities in England.

OBJECTIVE: To compare levels of caries experience in children attending schools in Wirral that have a fluoridated milk programme with children in a similar community which does not have a fluoridated milk programme. STUDY DESIGN: A cross sectional study measuring caries experience in first permanent molars. Children were examined on an 'intention to treat' basis and the effect of clustering of children within schools was taken into account. PARTICIPANTS: 690 children in Wirral (test group) and 1,835 children in Sefton (comparison group) were examined for caries experience (DMFT/DT/DFS) in 2003. The mean ages of the children examined in the test and comparison groups were 10.79 and 10.83 years respectively. RESULTS: Mean DMFT/DT/DFS values were 1.01/0.59/1.20 respectively in the test group and 1.46/1.02/1.89 respectively in the comparison group. Multiple linear regression analysis taking clustering of children within schools into account and with the Index of Multiple Deprivation 2000 as an explanatory variable gave the coefficients and p-values for DMFT/DT/DFS of 0.49 (p < 0.001)/0.43 (p < 0.001)/0.74 (p < 0.001) respectively. CONCLUSION: A difference in children with caries experience of 13% and a difference in children with active decay of 16% was found when a district with a community fluoridated milk programme was compared with a district without a fluoridated milk programme.

Animals↗

Patterns of childhood sexual abuse characteristics and their relationships to other childhood abuse and adult health.

The purpose of this study was twofold: (a) to cluster women who experienced childhood sexual abuse (CSA) according to their shared patterns of CSA characteristics and (b) to examine differences across clusters on measures of other childhood abuse and adult health. Seven CSA characteristic variables were used for cluster analysis. The seven-cluster solution that emerged ranged from a noncontact extrafamilial CSA cluster that occurred without force only once to the most severe clusters in which penetration by an intrafamilial or extrafamilial abuser occurred multiple times with force. Significant differences among clusters were found for childhood emotional abuse and physical abuse, adult physical and psychosocial symptomatology, and depression. There were no significant differences for health care utilization. The results promote further understanding of which victims of CSA are more likely to have experienced other forms of childhood abuse and which victims are more at risk for poor health in adulthood.

Adolescent↗

Novel and recurrent mutations clustered in the von Willebrand factor A domain of MATN3 in multiple epiphyseal dysplasia.

Multiple epiphyseal dysplasia (MED) is a common skeletal dysplasia characterized by joint pain and stiffness, delayed and irregular ossification of epiphyses, and early-onset osteoarthritis. Six genes responsible for MED have been identified, including COMP, COL9A1, COL9A2, COL9A3, DSTDT and MATN3. MATN3 encodes matrilin-3, a cartilage-specific extracellular matrix protein. To date, seven different MATN3 mutations have been identified; all are located within the beta-sheet regions of the von Willebrand factor type A (vWFA) domain, which is encoded by exon 2. We examined MATN3 mutations in27 Japanese MED patients who were possibly autosomal dominant inheritance and had been excluded for COMP mutations. Ten of them had a positive family history. We examined all eight exons of MATN3 by PCR and direct sequencing from genomic DNA. We have identified four missense mutations in eight unrelated families; two are novel, and two have been characterized previously. Like previously characterized MATN3 mutations, those identified in this study are clustered within exon 2, specifically in and around the 2nd beta-sheet region of the vWFA domain (aa. 120-127). Contrary to the previous assumption that the MATN3 mutation in MED is confined to the beta-sheet regions, one novel mutation (p.F105S) is located outside the beta-sheet region, within an alpha-helix region.

Adolescent↗