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PubMed1999

Consistency achieved by 23 European pathologists from 12 countries in diagnosing breast disease and reporting prognostic features of carcinomas. European Commission Working Group on Breast Screening Pathology.

A detailed analysis of the consistency with which pathologists from 12 different European countries diagnose and classify breast disease was undertaken as part of the quality assurance programme of the European Breast Screening Pilot Network funded by the Europe against Cancer Programme. Altogether 107 cases were examined by 23 pathologists in 4 rounds. Kappa statistics for major diagnostic categories were: benign (not otherwise specified) 0.74, atypical ductal hyperplasia (ADH) 0.27, ductal carcinoma in situ (DCIS) 0.87 and invasive carcinoma 0.94. ADH was the majority diagnosis in only 2 cases but was diagnosed by at least 2 participants in another 14, in 9 of which the majority diagnosis was benign (explaining the relatively low kappa for this category). DCIS in 4 (all low nuclear grade) and invasive carcinoma (a solitary 1-mm focus) in 1. The histological features of these cases were extremely variable; although one feature that nearly all shared was the presence of cells with small, uniform, hyperchromatic nuclei and a high nucleo-cytoplasmic ratio. The majority diagnosis was DCIS in 33 cases; kappa for classifying by nuclear grade was 0.38 using three categories and 0.46 when only two (high and other) were used. When ADH was included with low nuclear grade DCIS there was only a slight improvement in kappa. Size measurement of DCIS was less consistent than that of invasive carcinoma. The majority diagnosis was invasive carcinoma in 57 cases, the size of the majority being 100% in 49. The remainder were either special subtypes (adenoid cystic, tubular, colloid, secretory, ductal/medullary) or possible microinvasive carcinomas. Subtyping was most consistent for mucinous (kappa, 0.92) and least consistent for medullary carcinomas (kappa, 0.56). Consistency of grading using the Nottingham method was moderate (kappa=0.53) and consistency of diagnosing vascular invasion, fair (kappa=0.38). There was no tendency for consistency to improve from one round to the next, suggesting that further improvements are unlikely without changes in guidelines or methodology.

Breast Diseases↗

PubMed2004

Presenting phenotype in 100 children with the 22q11 deletion syndrome.

UNLABELLED: The aim of this study was to investigate and describe the presenting phenotype of children with the 22q11 deletion syndrome and to describe common clinical features that could serve as guidelines in the clinical diagnostic process preceding genetic testing. A hospital-based study of 100 consecutive children and adolescents with 22q11 deletion was initiated. The patients were divided into two groups according to age at diagnosis: before or after 2 years of age. Clinical features were grouped into a core set of eight features: cardiac defects, non-visible/hypoplastic thymus or infection problems, hypocalcaemia, feeding difficulties, cleft palate/speech-language impairment, developmental delay/learning difficulties, characteristic dysmorphic features and other malformations and deformities. The median age at diagnosis was 6.7 years. Of all patients, 26% were diagnosed in infancy and 92% had a congenital cardiac defect, whereas 54% of those diagnosed later had a cardiac defect. A cleft palate was present in 25 cases and 44 had some other malformation or deformity. All presented with a combination of many of the core features. Of those diagnosed after 2 years of age, the majority presented with speech-language impairment, developmental delay or learning difficulties and recurrent infections. Characteristic mild dysmorphic features were noticed in all children. CONCLUSION: In spite of variable clinical expression, children with 22q11 deletion share a number of major features and have a characteristic phenotype. A high proportion have no cardiac defect and hence a risk of diagnostic delay. Increased awareness and knowledge among general paediatricians and other specialists who meet these children early in life is needed to reduce the diagnostic delay.

Abnormalities, Multiple↗

PubMed2005

Factors influencing aerosol characteristics over urban environment.

Atmospheric aerosols are an important contributing factor to turbidity in urban areas besides having impact on health. Aerosol characteristics show a high degree of variability in space and time as nthropogenic share of total aerosol loading is quite substantial and is essential to monitor the aerosol features over long time scales. In the present study extensive observations of columnar aerosol optical depth (AOD), total columnar ozone (TCO) and precipitable water content (PWC) have been carried over a tropical urban city of Hyderabad, India. Significant variations of AOD have been observed during course of the day with low values of AOD during morning and evening hours and high values during afternoon hours. Spectral variation of AOD exhibits high AOD at smaller wavelengths and vice versa except a slight enhancement in AOD at 500 nm. Anomalies in AOD, particulate matter and black carbon concentrations have been observed during May, 2003. Back trajectory analysis of air mass during these episodes suggested variation in air mass trajectories. Analysis of the results suggests that air trajectories from land region north of study area cause high loading of atmospheric aerosols. The results are discussed in the paper.

Aerosols↗

PubMed1987

GTP binding proteins: a key role in cellular communication.

One of the major steps in the understanding of the hormonal and sensory transduction mechanisms in eukaryotic cells has been the discovery of a family of GTP binding proteins which couple receptors to specific cellular effectors. The absolute requirement of GTP for hormonal stimulation of adenylate cyclase was the initial observation which led to the purification of the protein involved: Gs. Gs couples stimulatory receptors to adenylate cyclase. It is a heterotrimer composed of an alpha chain (45 or 52 kDa), a beta chain (35-36 kDa) and a gamma chain (8 kDa). Several other G proteins of known functions have been purified: Gi, which couples inhibitory receptors to adenylate cyclase, and transducin which couples photoexcited rhodopsin to cyclic GMP phosphodiesterase. Some G proteins of uncertain function have also been purified: Go, a G protein mainly localized in nervous tissues and Gp, a G protein isolated from placenta and platelets. All these G proteins have a common design. Like Gs they all consist of 3 chains: alpha, beta and gamma. The beta chains are nearly identical, whereas the gamma chains are more variable. The alpha chains are different, but share common domains (especially at the level of the GTP binding site). These domains of homologies are also similar to those of other GTP binding proteins, such as the product of the ras gene (p21) and the initiation or elongation factors. alpha Chains are also ADP ribosylated by bacterial toxins. Gs and transducin are targets for cholera toxin, whereas Gi, Go and transducin are targets for pertussis toxin.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2004

A new high-throughput AFLP approach for identification of new genetic polymorphism in the genome of the clonal microorganism Mycobacterium tuberculosis.

We have here applied high-throughput amplified fragment length polymorphism (htAFLP) analysis to strains belonging to the five classical species of the Mycobacterium tuberculosis complex. Using 20 strains, three enzyme combinations and eight selective amplification primer pairs, 24 AFLP reactions were performed per strain. Overall, this resulted in 480 DNA fingerprints and more than 1200 htAFLP-amplified PCR fragments were visualised per strain. The cumulative dendrogram correctly clustered strains from the various species, albeit within a distance of 6.5% for most of them. The single isolate of Mycobacterium canettii presented separately at 19% distance. All over, 169 fragments (14%) appeared to be polymorphic. Sixty-eight were specific for M. canetti and forty-five for Mycobacterium bovis. For the 10 different M. tuberculosis strains included in the present analysis, 56 polymorphic markers were identified. Upon sequencing 20 of these marker regions and comparisons with the H37Rv genome sequence, 25% appeared to share homology to members of the antigenically variable PE/PPE surface protein encoding gene family confirming previous findings on the genetic heterogeneity within these genes. In addition, homologues for phage genes and insertion element-encoded genes were detected. Forty-five percent of the sequences derived from ORFs with a currently unknown function, which was corroborated by genome sequence comparison for the clinical M. tuberculosis CD 1551 isolate. Sequence variation in M. tuberculosis was assessed in more detail for a subset of these loci by newly designed PCR restriction fragment length polymorphism (RFLP) tests and direct sequencing. Fourteen novel PCR RFLP tests were developed and twelve novel single nucleotide polymorphisms (SNPs) were identified, all suited for epidemiological analysis of M. tuberculosis. The tests allowed for identification of the major Mycobacterium species and M. tuberculosis variants and clones.

Cluster Analysis↗

PubMed2004

Discrimination of oriented visual textures by poultry chicks.

We investigated how poultry chicks discriminate textures of lines sharing a common orientation from textures of variably oriented lines. Stimulus colours along with illumination were adjusted to selectively stimulate different receptor mechanisms. Chicks could discriminate achromatic textures, but not textures isoluminant to the double cones that gave a long vs. medium wavelength chromatic signal, nor an intensity signal for the short and very-short wavelength cones. These results suggest that detection of line orientation and texture discrimination uses an achromatic signal derived either from the double cones, or summed outputs of long and medium wavelength sensitive single cones.

Animals↗

PubMed2000

Men with prostate cancer: influence of psychological factors on informational needs and decision making.

OBJECTIVES: Studies indicate that men with prostate cancer (MPC) adopt passive roles in cancer management; however, increasing public awareness of prostate cancer and advocacy by MPC and their allies suggest otherwise. This study looks at the information that is important to MPC; their preferred participation in decision making; and the influence of sociodemographic, disease, and psychological factors on information needs and decision preferences. METHOD: Consecutive men diagnosed with prostate cancer and attending two tertiary care cancer clinics completed questionnaires on information needs and decision preferences. Questions included demographic information, health and disease status, psychosocial functioning, optimism, and decisional preferences and information preferences for content, type, focus, format, and amount. RESULTS: Questionnaires were completed by 101 MPC. Their mean age was 70 years and most were married and well-educated. Over 70% wanted detailed information at all illness stages focusing on their disease, treatment, survival, self-care, and empowerment. Over 60% of MPC wanted shared decision making with their physician. Psychological variables were found to influence information needs but not involvement in decision making. CONCLUSION: These results represent a challenge to health-care providers for accomodating the informational needs and decision preferences of individual MPC.

Adaptation, Psychological↗

PubMed2001

A well-differentiated liposarcoma with a new type of chromosome 12-derived markers.

Well-differentiated liposarcomas (WDLPS) are cytogenetically characterized by the presence of supernumerary ring or giant rod marker chromosomes. These supernumerary chromosomes are composed of amplified sequences from chromosome 12 (12q14 approximately 15) in association with amplified segments from various other chromosomes, and contain alterations of the alpha satellite sequences. We report a case of WDLPS of the lipoma-like and sclerosing subtype that contains a novel type of supernumerary marker chromosome. Instead of rings or giant rods, these cells had three apparently identical copies of a subtelocentric supernumerary marker with a size and shape similar to C-group chromosomes. Fluorescence in situ hybridization analysis revealed that the markers were composed of amplified material from 12q14 approximately 15, including the genes MDM2 and CDK4. Similar to the rings and giant rods observed in other WDLPS cases, these unusual markers had no alpha satellite repeats at the primary constriction site, but centromeric activity could be demonstrated by using anti-centromere protein C antibodies. These findings show that the supernumerary markers of WDLPS may be variable in size and shape, but consistently share the same genomic structure, specifically 12q amplified sequences together with centromere alterations, and underline the importance of molecular methods in the diagnosis of adipose tissue tumors.

Aged↗

PubMed2002

Unfolding of pyridoxal 5'-phosphate-dependent O-acetylserine sulfhydrylase probed by time-resolved tryptophan fluorescence.

Proteins utilizing pyridoxal 5'-phosphate as a coenzyme constitute a large superfamily and are currently classified into three functional groups and five structural fold types. Despite the variability of sequences and catalyzed reactions, they share relevant structural, dynamic and functional properties. Therefore, they constitute an optimal system to investigate the relative influence of primary sequence and coenzyme interactions on folding pathways, structural stability and enzymatic function. O-Acetylserine sulfhydrylase is a dimeric pyridoxal 5'-phosphate dependent enzyme that catalyzes the synthesis of L-cysteine from O-acetylserine and sulfide. The time-resolved fluorescence study of O-acetylserine sulfhydrylase unfolding, here reported, indicates that the coenzyme stabilizes the protein structure. The dependence on denaturant concentration of tryptophan lifetimes in the holo- and apo-enzyme demonstrates that the interactions with the coenzyme stabilize the C-terminal domain to a higher extent with respect to the N-terminal domain. This result is discussed in terms of a linkage between the differential stabilization brought about by the coenzyme and the different degrees of conformational flexibility required by the specialized functional role of distinct protein regions.

Circular Dichroism↗

PubMedDate not supplied

Mentoring through predoctoral fellowships to enhance research productivity.

This article reports a study of the mentoring relationships that developed during predoctoral fellowships awarded to five nursing students who worked with faculty mentors at the University of Kansas, School of Nursing. Data were gathered through interviews and a written questionnaire from each of eight study participants (four of the five pairs). The analysis of interview and questionnaire data supported the existence of a mentoring relationship according to Yoder's (1990) model of mentoring, with the addition of two variables, socialization as a researcher and mutual sharing, that are unique to doctoral education. Themes that represented the experience of the mentor-protégé pairs were identified: (1) productivity, (2) work organization, (3) mutual learning, (4) problems encountered, (5) beneficial research application skills, and (6) innovative communication. All participants were enthusiastic about the experience, and students indicated increased confidence in application of the research process.

Communication↗

PubMedDate not supplied

A new member of the immunoglobulin superfamily--CTLA-4.

The immunoglobulin superfamily is a group of proteins, each made of one or several domains sharing key structural features with either the variable (V) or the constant (C) immunoglobulin domains. It includes such functionally important members as the immunoglobulins themselves, major histocompatibility complex (MHC) class I and class II and T-cell receptor (TCR) molecules. Several members of this superfamily are expressed on lymphocytes where they are membrane-bound and capable of interactions with other members of the family, thus taking part in cell-cell recognition. In screening mouse cytolytic-T-cell-derived cDNA libraries, we came across cDNA clones defining a sequence, CTLA-4, which could encode a 223-amino-acid protein clearly belonging to the immunoglobulin superfamily. It consists of one V-like domain flanked by two hydrophobic regions, one of which has a structure suggestive of membrane anchoring. CTLA-4 is mainly expressed in activated lymphocytes and is coinduced with T-cell-mediated cytotoxicity in inducible models of this process. The mouse ctla-4 gene maps to band C of chromosome 1.

Amino Acid Sequence↗

PubMed2000

Six novel mutations of the fibrillin-1 gene in Korean patients with Marfan syndrome.

BACKGROUND: Mutations in the FBN1 gene, encoding fibrillin-1, result in Marfan syndrome (MFS). According to previous reports, the mutations in FBN1 share certain characteristics in each family with variable penetrance and overlapping symptoms, even in the same genotype. In the present study, we report six novel mutations and evaluate the clinical significance of these nucleotide changes. METHODS: To screen for nucleotide changes in all 65 exons of the FBN1 gene in 38 unrelated Korean patients, we performed polymerase chain reaction, single-strand conformational polymorphism (SSCP) and sequencing for the shift of the band in SSCP. RESULTS: We identified six mutations: a 2253 del 7 b.p., N1043S, C1254S, L1421F, C1895R and S2662P. CONCLUSIONS: These results suggest that many different mutations are responsible for MFS in the Korean population.

Adolescent↗

PubMed2005

Overview of the domains of variables relevant to end-of-life care.

Advancing the science of end-of-life care requires a foundation of clear domains and variables to guide research and clinical practice. Palliative care and hospice programs have grown rapidly in recent years in response to an increasing proportion of the population living with chronic, debilitating, and life-threatening illness. Numerous studies and key publications have proposed frameworks that identify key concepts or domains of end-of-life care. A major advance in defining the essential domains of palliative care has been the release in 2004 of national guidelines published by the National Consensus Project for Quality Palliative Care (NCP). This paper reviews and compares several models that have proposed domains of end-of-life care and then applies the domains of the NCP Clinical Practice Guidelines as a framework to identify potential outcome variables for research. Having definitions and concepts shared by scientists in end-of-life care can advance the science and provide an evidence base for practice to improve quality care.

Consensus↗

PubMed2005

Habitual physical activity in children: the role of genes and the environment.

BACKGROUND: Understanding the factors that contribute to physical inactivity in children is important because sedentary behavior strongly relates to metabolic disorders such as obesity and diabetes. OBJECTIVE: We aimed to quantify the genetic and environmental influences on physical activity energy expenditure (PAEE) in 100 sex-concordant dizygotic (n = 38) and monozygotic (n = 62) twin pairs aged 4-10 y. DESIGN: Resting metabolic rate (RMR) was assessed by using respiratory gas exchange, total energy expenditure (TEE) by using doubly labeled water, and body composition by using dual-energy X-ray absorptiometry. Structural equation modeling was used to partition the phenotypic variance into additive genetic (a2) and common (c2) and unshared (e2) environmental components. RESULTS: Because PAEE [TEE - (RMR + 0.1 x TEE)] depends on body weight, which is highly heritable, we tested several models: 1) after adjustment for age, sex, ethnicity, study date, season, and weight, a2 explained none of the phenotypic variance in PAEE (95% CI: 0%, 38%), whereas c2 and e2 accounted for 69% (33%, 77%; P = 0.001) and 31% (23%, 39%; P < 0.001) of the variance, respectively; 2) after adjustment for the cofactors in model 1, a2 explained 19% of the phenotypic variance in TEE (0%, 60%; P = 0.13), whereas c2 and e2 accounted for 59% (16%, 79%; P = 0.007) and 23% (17%, 31%; P < 0.0001) of the variance, respectively; 3) in models adjusted as above (excluding weight), a2 explained no variance in physical activity level (TEE/RMR) (0%, 32%; P = 0.50), whereas c2 and e2 explained 65% (34%, 60%; P = 0.001) and 35% (28%, 45%; P < 0.0001) of the variance, respectively. CONCLUSIONS: Our data suggest that the familial resemblance in physical activity in these children is explained predominantly by shared environmental factors and not by genetic variability.

Absorptiometry, Photon↗

PubMed2006

Optimizing occupational exposure measurement strategies when estimating the log-scale arithmetic mean value--an example from the reinforced plastics industry.

When assessing occupational exposures, repeated measurements are in most cases required. Repeated measurements are more resource intensive than a single measurement, so careful planning of the measurement strategy is necessary to assure that resources are spent wisely. The optimal strategy depends on the objectives of the measurements. Here, two different models of random effects analysis of variance (ANOVA) are proposed for the optimization of measurement strategies by the minimization of the variance of the estimated log-transformed arithmetic mean value of a worker group, i.e. the strategies are optimized for precise estimation of that value. The first model is a one-way random effects ANOVA model. For that model it is shown that the best precision in the estimated mean value is always obtained by including as many workers as possible in the sample while restricting the number of replicates to two or at most three regardless of the size of the variance components. The second model introduces the 'shared temporal variation' which accounts for those random temporal fluctuations of the exposure that the workers have in common. It is shown for that model that the optimal sample allocation depends on the relative sizes of the between-worker component and the shared temporal component, so that if the between-worker component is larger than the shared temporal component more workers should be included in the sample and vice versa. The results are illustrated graphically with an example from the reinforced plastics industry. If there exists a shared temporal variation at a workplace, that variability needs to be accounted for in the sampling design and the more complex model is recommended.

Air Pollutants, Occupational↗

PubMed1985

Failure of monoclonal antibodies to core glycolipid to bind intact smooth strains of Escherichia coli.

To study the ability of antibody to the core glycolipid (CGL) region of lipopolysaccharide (LPS) to bind intact gram-negative bacterial cells, we produced monoclonal antibodies that bind LPS from the Escherichia coli rough mutant J5. Four representative monoclonal antibodies that bound four distinct epitopes on the CGL region of LPS were studied. All four antibodies bound both isolated J5 LPS and intact J5 bacterial cells, but none of the antibodies bound to intact cells of E. coli O111:B4 or K1:O7. Binding of the monoclonal antibodies to isolated LPS from these latter two smooth strains was variable. These results confirm the presence of shared antigenic sites in the CGL region of heterologous LPS molecules but indicate that these sites are not necessarily available on smooth gram-negative bacteria for binding by antibody to CGL.

Antibodies, Bacterial↗

PubMed2002

Genetic diversity and relationships of Campylobacter species and subspecies.

The existence of tremendous genetic diversity within Campylobacter species has been well documented. To analyse the population structure of Campylobacter and determine whether or not a clonal population structure could be detected, genetic diversity was assessed within the genus Campylobacter by multilocus enzyme electrophoresis of 156 isolates representing 11 species and subspecies from disparate sources. Analyses of electrophoretic mobility of 11 enzymes revealed 109 electrophoretic types (ETs) and 118 ETs when nulls were counted as an allele. Cluster analysis placed most ETs into groups that correlated with species. With nulls counted as alleles, 19 ETs were identified among 33 isolates of Campylobacter lari, 31 ETs among 34 isolates of Campylobacter coli and 43 ETs among 59 isolates of Campylobacter jejuni subsp. jejuni. Nine C. jejuni subsp. jejuni isolates, confirmed as this species by DNA-DNA hybridization, were hippuricase-negative. Reported linkage analyses were done with nulls ignored. Scores for mean genetic diversity (H) were high for the total population (mean H = 0.802). Allelic mismatch-frequency distributions and allelic tracing pointed to possible genetic exchange between subpopulations. C. lari appears to be a panmictic species. Some pairs of species shared multiple alleles of certain loci, possibly indicating genetic exchange between species. Of the species tested, C. jejuni appeared to be the most active in sharing alleles. However, there was evidence of variable involvement in recombination by the different loci. Linkage analysis of loci in C. jejuni and C. coli revealed a clonal framework, with some loci tightly linked to each other. The loci appeared to occur in linkage groups or islands. Campylobacter may have a clonal framework with other portions of the genome involved in frequent recombination. Population genetic structure among Campylobacter is inconclusive and it remains to be seen if pathogenic types can be identified.

Alleles↗

PubMed1991

Characterization of the opa (class 5) gene family of Neisseria meningitidis.

Class 5 outer membrane proteins of Neisseria meningitidis show both phase- and antigenic variation of expression. The proteins are encoded by a family of opa genes that share a conserved framework interspersed with three variable regions, designated the semivariable (SV) region and hypervariable regions 1 (HV1) and 2 (HV2). In this study, we determined the number and DNA sequence of all of the opa genes of meningococcal strain FAM18, to assess the structural and antigenic variability in the family of proteins made by one strain. Pulsed field electrophoresis and Southern blotting showed that there are four opa genes in the FAM18 chromosome, and that they are not tightly clustered. DNA sequence analysis of the four cloned genes showed a modest degree of diversity in the SV region and more extensive differences in the HV1 and HV2 regions. There were four versions of HV1 and three versions of HV2 among the four genes. Each of the FAM18 opa loci contained a gene with a unique combination of SV, HV1, and HV2 sequences. We used lambda gt11 cloning and synthetic peptides to demonstrate that HV2 sequences completely encode the epitopes for two monoclonal antibodies specific for different class 5 proteins of FAM18.

Amino Acid Sequence↗