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PubMed2006

Psychosocial risk clustering in high school students.

BACKGROUND: This secondary analysis describes the frequency of self-reported psychosocial risk factors in a geographically defined population of adolescents and quantifies the extent of multiple risks. Cluster analysis is used to develop three empirically distinct psychosocial risk clusters. METHODS: High school students in grades 9-13 from all seven public and two catholic high schools in the study area completed a class-administered survey. The analysis is based on 3540 surveys reflecting approximately a 71% response. Cumulative risk was calculated by summing the number of times students exceeded a pre-defined threshold on a series of global rating scales. Risk clusters were created using a non-hierarchical cluster analysis technique for binary data. Clusters were partially validated by examining differences in socio-demographic and health utilization patterns. Reliability was assessed by examining two, three, and four-group solutions across gender and grade strata. RESULTS: Multiple symptoms of emotional distress were reported by 37% of the sample, multiple stressors by 62% of the sample, and poly-drug use by 33%. In addition, three empirically distinct clusters were derived. Normals, 21% of the sample, did not report excessive stress or distress, and did not use substances. The Stressed (45%) reported excessive stress and distress predominantly related to schoolwork, parents, and facing problems. Virtually none used drugs. Substance Users (34%) reported excessive stress, distress, and high levels of substance use: smoking, drinking, and use of illicit drugs. Clusters were significantly different with respect to most socio-demographic factors, self-reported general health, and most aspects of health service utilization suggesting that they have some validity for targeting programs. CONCLUSIONS: This study highlights the importance of focusing on multi-morbidities and illustrates the use of cluster analysis to identify risk profiles that may be amenable to school-based health promotion and prevention programs.

Adolescent↗
PubMed2000

Protein structure alignment using environmental profiles.

A new protein structure alignment procedure is described. An initial alignment is made by comparing a one-dimensional list of primary, secondary and tertiary structural features (profiles) of two proteins, without explicitly considering the three-dimensional geometry of the structures. The alignment is then iteratively refined in the second step, in which new alignments are found by three-dimensional superposition of the structures based on the current alignment. This new procedure is fast enough to do all-against-all structural comparisons routinely. The procedure sometimes finds an alignment that suggests an evolutionary relationship and which is not normally obtained if only geometry is considered. All pair-wise comparisons were made among 3539 protein structural domains that represent all known protein structures. The resulting 3539 z-scores were used to cluster the proteins. The number of main clusters increased continuously as the z-cutoff was raised, but the number of multiple-member clusters showed a maximum at z-cutoff values of 5.0 and 5.5. When a z-cutoff value of 5.0 was used, the total number of main clusters was 2043, of which only 336 clusters had more than one member.

Amino Acid Sequence↗
PubMed2004

Characterization of heavy metal particles embedded in tire dust.

Tire dust is a significant pollutant, especially as a source of zinc in the urban environment. This study characterizes the morphology and chemical composition of heavy metal particles embedded in tire dust and traffic-related materials (brake dust, yellow paint, and tire tread) as measured by a field emission scanning electron microscope equipped with an energy dispersive X-ray spectrometer (FESEM/EDX). In 60 samples of tire dust, we detected 2288 heavy metal particles, which we classified into four groups using cluster analysis according to the following typical elements: cluster 1: Fe, cluster 2: Cr/Pb, cluster 3: multiple elements (Ti, Cr, Fe, Cu, Zn, Sr, Y, Zr, Sn, Sb, Ba, La, Ce, Pb), cluster 4: ZnO. According to their morphologies and chemical compositions, the possible sources of each cluster were as follows: (1) brake dust (particles rich in Fe and with trace Cu, Sb, and Ba), (2) yellow paint (CrPbO(4) particles), (3) brake dust (particulate Ti, Fe, Cu, Sb, Zr, and Ba) and heavy minerals (Y, Zr, La, and Ce), (4) tire tread (zinc oxide). When the chemical composition of tire dust was compared to that of tire tread, the tire dust was found to have greater concentrations of heavy metal elements as well as mineral or asphalt pavement material characterized by Al, Si, and Ca. We conclude that tire dust consists not only of the debris from tire wear but also of assimilated heavy metal particles emitted from road traffic materials such as brake lining and road paint.

Automobiles↗
PubMed2004

Sequencing and comparative analysis of flagellin genes fliC, fljB, and flpA from Salmonella.

Salmonella isolates have traditionally been classified by serotyping, the serologic identification of two surface antigens, O-polysaccharide and flagellin protein. Serotyping has been of great value in understanding the epidemiology of Salmonella and investigating disease outbreaks; however, production and quality control of the hundreds of antisera required for serotyping is difficult and time-consuming. To circumvent the problems associated with antiserum production, we began the development of a system for determination of serotype in Salmonella based on DNA markers. To identify flagellar antigen-specific sequences, we sequenced 280 alleles of the three genes that are known to encode flagellin in Salmonella, fliC, fljB, and flpA, representing 67 flagellar antigen types. Analysis of the data indicated that the sequences from fliC, fljB, and flpA clustered by the antigen(s) they encode not by locus. The sequences grouped into four clusters based on their conserved regions. Three of the four clusters included multiple flagellar antigen types and were designated the G complex, the Z4 complex, and the alpha cluster. The fourth cluster contained a single antigen type, H:z(29). The amino acid sequences of the conserved regions within each cluster have greater than 95% amino acid identity, whereas the conserved regions differ substantially between clusters (75 to 85% identity). Substantial sequence heterogeneity existed between alleles encoding different flagellar antigens while alleles encoding the same flagellar antigen were homologous, suggesting that flagellin genes may be useful targets for the molecular determination of flagellar antigen type.

Alleles↗
PubMed2004

Chronic barium intoxication disrupts sulphated proteoglycan synthesis: a hypothesis for the origins of multiple sclerosis.

High level contamination by natural and industrial sources of the alkali earth metal, barium (Ba) has been identified in the ecosystems/workplaces that are associated with high incidence clustering of multiple sclerosis (MS) and other neurodegenerative diseases such as the transmissible spongiform encephalopathies (TSEs) and amyotrophic lateral sclerosis (ALS). Analyses of ecosystems supporting the most renowned MS clusters in Saskatchewan, Sardinia, Massachusetts, Colorado, Guam, NE Scotland demonstrated consistently elevated levels of Ba in soils (mean: 1428 ppm) and vegetation (mean: 74 ppm) in relation to mean levels of 345 and 19 ppm recorded in MS-free regions adjoining. The high levels of Ba stemmed from local quarrying for Ba ores and/or use of Ba in paper/foundry/welding/textile/oil and gas well related industries, as well as from the use of Ba as an atmospheric aerosol spray for enhancing/refracting the signalling of radio/radar waves along military jet flight paths, missile test ranges, etc. It is proposed that chronic contamination of the biosystem with the reactive types of Ba salts can initiate the pathogenesis of MS; due to the conjugation of Ba with free sulphate, which subsequently deprives the endogenous sulphated proteoglycan molecules (heparan sulfates) of their sulphate co partner, thereby disrupting synthesis of S-proteoglycans and their crucial role in the fibroblast growth factor (FGF) signalling which induces oligodendrocyte progenitors to maintain the growth and structural integrity of the myelin sheath. Loss of S-proteoglycan activity explains other key facets of MS pathogenesis; such as the aggregation of platelets and the proliferation of superoxide generated oxidative stress. Ba intoxications disturb the sodium-potassium ion pump--another key feature of the MS profile. The co-clustering of various neurodegenerative diseases in these Ba-contaminated ecosystems suggests that the pathogenesis of all of these diseases could pivot upon a common disruption of the sulphated proteoglycan-growth factor mediated signalling systems. Individual genetics dictates which specific disease emerges at the end of the day.

Barium↗
PubMed2006

Hepatocellular carcinoma: microwave ablation with multiple straight and loop antenna clusters--pilot comparison with pathologic findings.

The purpose of this study was to evaluate the clinical implementation of triangular and spherical designs for simultaneous multiple-antenna ablation of human hepatocellular carcinoma (HCC) with a recently engineered microwave coagulation system. Institutional review board approval and informed consent were obtained, and the study was compliant with HIPAA requirements. Nine patients (five men, four women; age range, 53-79 years; mean age, 66.2 years) with resectable HCC (diameter, 2.9-6.0 cm; mean, 4.2 cm) underwent intraoperative ultrasonography-guided tumor ablation followed by resection and pathologic examination. Standard single-straight (n = 2), triangular triple-straight (n = 4), and spherical triple-loop (n = 3) antenna configurations produced mean estimated coagulation volumes of 16.7, 51.7, and 54.3 cm(3), respectively, during a single concurrent 5-10-minute ablation cycle. The triple-loop configuration yielded the most uniformly round ablation shape. Simultaneous activation of multiple straight or loop antennae is a potentially promising technique for rapid and effective treatment of large HCCs.

Aged↗
PubMed1999

Segmentation of confocal microscope images of cell nuclei in thick tissue sections.

Segmentation of intact cell nuclei from three-dimensional (3D) images of thick tissue sections is an important basic capability necessary for many biological research studies. However, segmentation is often difficult because of the tight clustering of nuclei in many specimen types. We present a 3D segmentation approach that combines the recognition capabilities of the human visual system with the efficiency of automatic image analysis algorithms. The approach first uses automatic algorithms to separate the 3D image into regions of fluorescence-stained nuclei and unstained background. This includes a novel step, based on the Hough transform and an automatic focusing algorithm to estimate the size of nuclei. Then, using an interactive display, each nuclear region is shown to the analyst, who classifies it as either an individual nucleus, a cluster of multiple nuclei, partial nucleus or debris. Next, automatic image analysis based on morphological reconstruction and the watershed algorithm divides clusters into smaller objects, which are reclassified by the analyst. Once no more clusters remain, the analyst indicates which partial nuclei should be joined to form complete nuclei. The approach was assessed by calculating the fraction of correctly segmented nuclei for a variety of tissue types: Caenorhabditis elegans embryos (839 correct out of a total of 848), normal human skin (343/362), benign human breast tissue (492/525), a human breast cancer cell line grown as a xenograft in mice (425/479) and invasive human breast carcinoma (260/335). Furthermore, due to the analyst's involvement in the segmentation process, it is always known which nuclei in a population are correctly segmented and which not, assuming that the analyst's visual judgement is correct.

Animals↗
PubMed2005

Application of sliding-window discretization and minimization of stochastic complexity for the analysis of fAFLP genotyping fingerprint patterns of Vibrionaceae.

Minimization of stochastic complexity (SC) was used as a method for classification of genotypic fingerprints. The method was applied to fluorescent amplified fragment length polymorphism (fAFLP) fingerprint patterns of 507 Vibrionaceae representatives. As the current BinClass implementation of the optimization algorithm for classification only works on binary vectors, the original fingerprints were discretized in a preliminary step using the sliding-window band-matching method, in order to maximally preserve the information content of the original band patterns. The novel classification generated using the BinClass software package was subjected to an in-depth comparison with a hierarchical classification of the same dataset, in order to acknowledge the applicability of the new classification method as a more objective algorithm for the classification of genotyping fingerprint patterns. Recent DNA-DNA hybridization and 16S rRNA gene sequence experiments proved that the classification based on SC-minimization forms separate clusters that contain the fAFLP patterns for all representatives of the species Enterovibrio norvegicus, Vibrio fortis, Vibrio diazotrophicus or Vibrio campbellii, while previous hierarchical cluster analysis had suggested more heterogeneity within the fAFLP patterns by splitting the representatives of the above-mentioned species into multiple distant clusters. As a result, the new classification methodology has highlighted some previously unseen relationships within the biodiversity of the family Vibrionaceae.

Algorithms↗
PubMed1995

Promoter region of the transcriptional unit for human alpha 1-chimaerin, a neuron-specific GTPase-activating protein for p21rac.

alpha 1-chimaerin is a neuron-specific GTPase-activating protein for p21rac, a protein involved in morphological events. The mRNA is highly expressed in certain brain regions. It is also detected in cultured neuronal, but not in non-neuronal cells. As a first step towards understanding the mechanisms underlying this regulation, genomic clones containing the 5'-flanking region of the human alpha 1-chimaerin transcriptional unit were isolated and characterised. A cluster of multiple transcription start sites of alpha 1-chimaerin mRNAs was detected by primer-extension and S1-mapping analyses. The cluster was mapped to nucleotides -464 to -434 (relative to nucleotide A in the initiation codon) in genomic DNA. The 5'-proximal region contained no TATA box, initiator motif and Sp1-binding site. A 210-bp fragment with approximately 110 bp 5'-flanking sequence could function as a minimal promoter upon analysis using hybrid chloramphenicol acetyltransferase reporter constructs and transient transfection. Internal deletion and point-mutation experiments revealed that a GGCCAATC sequence located at nucleotides -519 to -512 was essential for alpha 1-chimaerin promoter activity. Mobility-shift assay showed the specific binding of nuclear factor(s) to this region, which was competed by the oligonucleotides corresponding to wild-type but not mutant forms. The data also suggest the existence of possible novel CCAAT-binding factor(s) interacting with the alpha 1-chimaerin CCAAT box binding site. A cell-type-preferred suppressor located in the 5'-distal region was found which may play a role in controlling neuron-specific expression of alpha 1-chimaerin mRNA. These findings of a specific promoter for alpha 1-chimaerin transcription will facilitate further studies on its neuronal-specific expression and function.

Amino Acid Sequence↗
PubMed2004

Synchronization and entrainment of cytoplasmic Ca2+ oscillations in cell clusters prepared from single or multiple mouse pancreatic islets.

In contrast to pancreatic islets, isolated beta-cells stimulated by glucose display irregular and asynchronous increases in cytoplasmic Ca(2+) concentration ([Ca(2+)](i)). Here, clusters of 5-30 cells were prepared from a single mouse islet or from pools of islets, loaded with fura-2, and studied with a camera-based system. [Ca(2+)](i) oscillations were compared in pairs of clusters by computing the difference in period and a synchronization index lambda. During perifusion with 12 mM glucose, the clusters exhibited regular [Ca(2+)](i) oscillations that were quasi-perfectly synchronized (Delta period of 1.4% and index lambda close to 1.0) between cells of each cluster. In contrast, separate clusters were not synchronized, even when prepared from one single islet. Pairs of clusters neighboring on the same coverslip were not better synchronized than pairs of clusters examined separately (distinct coverslips). We next attempted to synchronize clusters perifused with 12 mM glucose by applying external signals. A single pulse of 20 mM glucose, 10 mM amino acids, or 10 microM tolbutamide transiently altered [Ca(2+)](i) oscillations but did not reset the clusters to oscillate synchronously. On a background of 12 mM glucose, repetitive applications (1 min/5 min) of 10 microM tolbutamide, but not of 20 mM glucose, synchronized separate clusters. Our results identify a level of beta-cell heterogeneity intermediate between single beta-cells and the whole islet. They do not support the idea that substances released by islet cells serve as paracrine synchronizers. However, synchronization can be achieved by an external signal, if this signal has a sufficient strength to overwhelm the intrinsic rhythm of glucose-induced oscillations and is repetitively applied.

Animals↗
PubMed2003

The structures of vanadium oxide cluster-ethene complexes. A combined IR multiple photon dissociation spectroscopy and DFT calculation study.

Infrared spectra of complexes of small vanadium oxide clusters with ethene are determined using infrared multiple photon dissociation (IR-MPD) spectroscopy in the range of 550-1850 cm-1. The structures of the complexes have been identified by comparison of the experimental spectra with the harmonic vibrational frequencies and corresponding IR intensities of possible isomers calculated with DFT methods. We find that the ethene molecule binds directly to a vanadium atom in the cluster, although this it is not in all cases the most stable arrangement.

Journal Article↗
PubMed2002

Is multiple sclerosis a sexually transmitted infection?

It is proposed that multiple sclerosis may be transmitted chiefly by sexual contact. Arguments favouring this include: migration studies that suggest a transmissible agent in adolescence; clusters of multiple sclerosis which have occurred in low prevalence areas following entry of young males; the similarity of multiple sclerosis to tropical spastic paraplegia, a known sexually transmitted infection with resemblance to primary progressive multiple sclerosis; an increased rate in drug misusers; a similar age of onset and sex pattern to that found in sexually transmitted disease; increased incidence of multiple sclerosis in those using oral contraceptives; low multiple sclerosis rates in societies with a strict moral code; longitudinal shifts in sex prevalence that show an increase in women after the sexual revolution of the 1960s; and important exceptions to the worldwide distribution corresponding to countries with permissive attitudes to sex. Family, conjugal pair, twin, and adoption studies are compatible with an infectious cause of multiple sclerosis if this is sexually transmitted. It is not proposed that sexual transmission is the only cause but that inherited factors create a susceptibility to a sexually transmitted neurotropic agent. It is hoped this hypothesis might encourage a new direction of neurological research.

Adult↗
PubMed2006

Marginal modeling of nonnested multilevel data using standard software.

Epidemiologic data are often clustered within multiple levels that may not be nested within each other. Generalized estimating equations are commonly used to adjust for correlation among observations within clusters when fitting regression models; however, standard software does not currently accommodate nonnested clusters. This paper introduces a simple generalized estimating equation strategy that uses available commercial or public software for the regression analysis of nonnested multilevel data. The authors describe how to obtain empirical standard error estimates for constructing valid confidence intervals and conducting statistical hypothesis tests. The method is evaluated using simulations and illustrated with an analysis of data from the Breast Cancer Surveillance Consortium that estimates the influence of woman, radiologist, and facility characteristics on the positive predictive value of screening mammography. Performance with a small number of clusters is discussed. Both the simulations and the example demonstrate the importance of accounting for the correlation within all levels of clustering for proper inference.

Adult↗
PubMed2026

Single-cell transcriptional profiling identifies the swimming crab Portunus trituberculatus in response to bacterial infection.

Crustaceans rely entirely on innate immunity, yet the cellular composition, functional specialization, and pathogen-induced remodeling of their immune system remain poorly resolved. Here, we generated a high-resolution single-cell transcriptomic atlas of hemocytes from the swimming crab Portunus trituberculatus following Vibrio parahaemolyticus infection using 10× Genomics scRNA-seq. Seven putatively distinct hemocyte clusters were identified, including granulocytes, semigranular hemocytes, prohemocytes, unresolved hemocytes, hyalinocyte-like hemocytes, biosynthetically active secretory hemocytes, and regulatory hemocytes. Although the overall cellular composition remained relatively stable after infection, hemocytes exhibited pronounced cluster-specific transcriptional reprogramming involving Toll/NF-κB signaling, antimicrobial peptide synthesis and metabolic rewiring. By integrating single-cell and bulk transcriptomes, we identified multiple anti-lipopolysaccharide factors (ALFs) as key secretory effectors and experimentally validated their antibacterial activities. FITC-based bacterial engulfment assays and RNA-seq of sorted phagocytes demonstrated that phagocytic capability was shared across multiple hemocyte clusters. Notably, the immunoglobulin superfamily receptor DSCAM displayed extensive alternative splicing and strong infection-induced activation in unresolved hemocytes. Immune-training experiments showed that prior bacterial exposure was associated with altered DSCAM expression and reduced early cumulative mortality upon secondary challenge, suggesting a memory-like immune phenotype. These findings provide a foundational framework for understanding crustacean immunity and advancing disease-resistant breeding in aquaculture.

Antimicrobial peptides↗
PubMed2002

Specification and visualization of anisotropic interaction tensors in polypeptides and numerical simulations in biological solid-state NMR.

Software facilitating numerical simulation of solid-state NMR experiments on polypeptides is presented. The Tcl-controlled SIMMOL program reads in atomic coordinates in the PDB format from which it generates typical or user-defined parameters for the chemical shift, J coupling, quadrupolar coupling, and dipolar coupling tensors. The output is a spin system file for numerical simulations, e.g., using SIMPSON (Bak, Rasmussen, and Nielsen, J. Magn. Reson. 147, 296 (2000)), as well as a 3D visualization of the molecular structure, or selected parts of this, with user-controlled representation of relevant tensors, bonds, atoms, peptide planes, and coordinate systems. The combination of SIMPSON and SIMMOL allows straightforward simulation of the response of advanced solid-state NMR experiments on typical nuclear spin interactions present in polypeptides. Thus, SIMMOL may be considered a "sample changer" to the SIMPSON "computer spectrometer" and proves to be very useful for the design and optimization of pulse sequences for application on uniformly or extensively isotope-labeled peptides where multiple-spin interactions need to be considered. These aspects are demonstrated by optimization and simulation of novel DCP and C7 based 2D N(CO)CA, N(CA)CB, and N(CA)CX MAS correlation experiments for multiple-spin clusters in ubiquitin and by simulation of PISA wheels from PISEMA spectra of uniaxially oriented bacteriorhodopsin and rhodopsin under conditions of finite RF pulses and multiple spin interactions.

Anisotropy↗
PubMed2003

Cluster headaches and sleep disorders.

Cluster headaches are characterized by unilateral paroxysmal attacks of severe pain with associated symptoms. The headaches occur during particular sleep stages and are associated with other chronobiologic factors. Several sleep disorders have been associated with the occurrence of cluster headache; multiple hormonal influences affect the relationship between sleep and headache. Melatonin and other treatments that affect circadian rhythm have been suggested for the treatment of cluster headache. Obstructive sleep apnea can occur in patients with cluster headache; attempts to treat one disorder may influence the other. Sleep disorders such as insomnia and narcolepsy also may be associated with and influence cluster headaches. This article examines the relationship between the various sleep disorders and cluster headache, and reviews current research. Normal and abnormal sleep and details of treatments for specific sleep disorders that may decrease the frequency and severity of cluster headaches also are discussed. The relationship between obstructive sleep apnea, which is the most common sleep disorder, and cluster headache is discussed in detail.

Cluster Headache↗
PubMed1976

[Glomus cell clusters of the lymph node].

Nine lymph nodes with so-called benign nevus cell nevi were studied by light microscopy. In three cases the lymph nodes were also examined by electron microscopy. The solitary or multiple cell clusters were 35-645 mu in diameter and were usually found in the lymph node capsule or cortex. They were more frequent in the older patients. There was no predisposition for either sex. Specific morphologic features allowing clear cytologic identification of the cells were not evidient. In particular, there was no indication that they represented nevus cells. However, they showed a great morphologic similarity to glomus cells. In addition, they were usually found near blood vessels. We assume that the cell clusters were hamartias related to glomangiomas. We call them glomus cell clusters.

Adult↗
PubMed2006

Tic symptom profiles in subjects with Tourette Syndrome from two genetically isolated populations.

BACKGROUND: Tourette Syndrome (TS) has a complex etiology and wide variability in phenotypic expression. Identifying underlying symptom patterns may be useful for etiological and outcome studies of TS. METHODS: Lifetime tic and related symptom data were collected between 1996 and 2001 in 121 TS subjects from the Central Valley of Costa Rica and 133 TS subjects from the Ashkenazi Jewish (AS) population in the US. Subjects were grouped by tic symptoms using an agglomerative hierarchical cluster analysis. Cluster membership was tested for association with available ancillary information (age of onset, tic severity, comorbid disorders, medication treatment and family history). RESULTS: Cluster analysis identified two distinct groups in each sample, those with predominantly simple tics (cluster 1), and those with multiple complex tics (cluster 2). Membership in cluster 2 was correlated with increased tic severity, global impairment, medication treatment, and presence of comorbid obsessive-compulsive symptoms in both samples, and with family history of tics, lower verbal IQ, earlier age of onset, and comorbid obsessive-compulsive disorder and attention-deficit/hyperactivity disorder in the AS sample. CONCLUSIONS: This study provides evidence for consistent and reproducible symptom profiles in two independent TS study samples. These findings have implications for etiological studies of TS.

Adolescent↗