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PubMed2006

Mosaic structure of human coronavirus NL63, one thousand years of evolution.

Before the SARS outbreak only two human coronaviruses (HCoV) were known: HCoV-OC43 and HCoV-229E. With the discovery of SARS-CoV in 2003, a third family member was identified. Soon thereafter, we described the fourth human coronavirus (HCoV-NL63), a virus that has spread worldwide and is associated with croup in children. We report here the complete genome sequence of two HCoV-NL63 clinical isolates, designated Amsterdam 57 and Amsterdam 496. The genomes are 27,538 and 27,550 nucleotides long, respectively, and share the same genome organization. We identified two variable regions, one within the 1a and one within the S gene, whereas the 1b and N genes were most conserved. Phylogenetic analysis revealed that HCoV-NL63 genomes have a mosaic structure with multiple recombination sites. Additionally, employing three different algorithms, we assessed the evolutionary rate for the S gene of group Ib coronaviruses to be approximately 3 x 10(-4) substitutions per site per year. Using this evolutionary rate we determined that HCoV-NL63 diverged in the 11th century from its closest relative HCoV-229E.

Algorithms↗

PubMed2005

Molecular evolution of the trnL(UAA) intron in bryophytes.

Structure, variability, and molecular evolution of the trnL(UAA) intron in bryophytes (mosses and liverworts) is analyzed based on more than 1000 sequences representing all classes, including comparisons of lengths and GC-contents, sequence similarities, evolutionary rates and ti/tv ratios of the major lineages and selected genera. Secondary structure analyses of the more variable stem-loop regions facilitated recognition of sequence repeats and minute inversions that often occurred independently in non-related lineages, thus supporting alignment construction and homology assessment. The most length-variable stem-loop region P8 does not share a common evolutionary history across all major bryophyte lineages. Independent nucleotide additions such as internally repeated sequence segments resulted in non-homologous P8 sequences that cannot be folded into a common P8 secondary structure, neither for all bryophytes nor for liverworts or mosses. To address evolutionary patterns, separate analyses of P6/P8 and the remaining intron (core) have to be performed, as overall values of the complete intron are misleading. It is argued that a transition bias observed above the genus level in the core structure is caused by structural constraints, not by its higher GC-content in comparison to the more AT-rich P6 and P8. Compensating base pair changes detected in highly conserved elements are often characteristic of the major bryophyte lineages (classes). Sequence divergence and evolutionary rates are generally higher in liverworts than in mosses, resulting in ambiguous alignments of P6 and P8 even within classes. In mosses, trends towards length reduction of P8 and lower evolutionary rates of the intron are observed. Average intraspecific variation is less than 1%, corresponding to 2-3 mutations in the complete intron.

Base Composition↗

PubMed2000

Chronic deciduitis in the placental basal plate: definition and interobserver reliability.

This study tested whether concordance could be achieved for abnormal inflammation in the basal decidua of placental specimens among 6 pathologists experienced in placental pathology. Thirty microscope slides were evaluated by the pathologists for chronic deciduitis. They also scored the severity and extent of inflammation and the presence of plasma cells. No definition of chronic deciduitis was provided. Concordance (5/6 or 6/6 agreement) was achieved in 23 cases (76%). Spearman's rank correlation showed that the diagnosis of chronic deciduitis was almost identical to the assessment of the severity of the inflammation. A regression analysis showed that the perception of severity (and hence chronic deciduitis) was influenced by the other 2 variables, extent and plasma cells. The results were shared with the pathologists, and 25 cases (excluding those with previous 6/6 consensus) were reevaluated. Concordance was now achieved in the 83% of those remaining cases. Using a threshold based on the severity and the extent of lymphocytes, and the presence of plasma cells, pathologists are able to diagnose chronic deciduitis with sufficient concordance to be of value in clinical correlation studies.

Adult↗

PubMed2003

Aortoiliac morphologic correlations in aneurysms undergoing endovascular repair.

PURPOSE: The feasibility of endovascular aneurysm repair depends on morphologic characteristics of the aortoiliac segment. Knowledge of such characteristics is relevant to safe deployment of a particular device in a single patient and to development of new devices for use in patients with a broader spectrum of anatomic variations. METHODS: We evaluated findings on computed tomography scans for 277 patients being considered for endovascular aneurysm repair. Aortic neck length and angulation estimates were generated with three-dimensional trigonometry. Specific centerline points were recorded, corresponding to the aorta at the celiac axis, lowest renal artery, cranial aspect of the aneurysm sac, aortic terminus, right hypogastric artery origin, and left hypogastric origin. Aortic neck thrombus and calcium content were recorded, and neck conicity was calculated in degrees. Statistical analysis was performed with the Spearman rank correlation. Data are expressed as median and interquartile range. RESULTS: Median diameter of the aneurysms was 52 mm (interquartile range, 48-59 mm) in minor axis and 56 mm (interquartile range, 51-64 mm) in major axis, and median length was 88 mm (interquartile range, 74-103 mm). Median proximal aortic neck diameter was 26 mm (interquartile range, 22-29 mm), and median neck length was 30 mm (interquartile range, 18-45 mm). The common iliac arteries were similar in diameter (right artery, 16 mm [interquartile range, 13-20 mm]; left artery, 15 mm [interquartile range, 11-18 mm]) and length (right, 59 mm [interquartile range, 50-69 mm]; left, 60 mm [interquartile range, 49-70 mm]). Median angulation of the infrarenal aortic neck was 40 degrees (interquartile range, 29-51 degrees), and median angulation of the suprarenal segment was 45 degrees (interquartile range, 36-57 degrees). By gender, sac diameter, proximal neck diameter, and iliac artery diameter were significantly larger in men. Significant linear associations were identified between sac diameter and sac length, neck angulation, and iliac artery diameter. As the length of the aneurysm sac increased the proximal aortic neck length decreased. Conversely, as the sac length decreased sac eccentricity increased. Mural thrombus content within the neck increased with increasing neck diameter. CONCLUSIONS: There is considerable variability in aortoiliac morphologic parameters. Significant associations were found between various morphologic variables, links that are presumably related to a shared pathogenesis for aberration in aortoiliac diameter, length, and angulation. Ultimately this information can be used to develop new endovascular devices with broader applicability and improved long-term results.

Angioplasty↗

PubMed2000

A multilevel analysis of the demands--control model: is stress at work determined by factors at the group level or the individual level?

This study explored the extent to which negative health-related outcomes are associated with differences between work groups and with differences between individuals within work groups using R.A. Karasek's (1979) demands-control model. The sample consisted of 260 employees in 31 working groups of a national bank in the Netherlands. Results suggest that job demands and job control should be conceptualized as having both group- and individual-level foundations. Support for Karasek's demands-control model was found only when these variables were split into the 2 parts, reflecting shared perceptions and employees' subjective assessment, respectively. One of the most appealing practical implications is that absence rates among homogeneous work groups can be reduced by enhancing actual control on the job.

Adult↗

PubMed2005

Bullying and victimization in elementary schools: a comparison of bullies, victims, bully/victims, and uninvolved preadolescents.

Research on bullying and victimization largely rests on univariate analyses and on reports from a single informant. Researchers may thus know too little about the simultaneous effects of various independent and dependent variables, and their research may be biased by shared method variance. The database for this Dutch study was large (N = 1,065) and rich enough to allow multivariate analysis and multi-source information. In addition, the effect of familial vulnerability for internalizing and externalizing disorders was studied. Gender, aggressiveness, isolation, and dislikability were most strongly related to bullying and victimization. Among the many findings that deviated from or enhanced the univariate knowledge base were that not only victims and bully/victims but bullies as well were disliked and that parenting was unrelated to bullying and victimization once other factors were controlled.

Aggression↗

PubMed1997

Structure of the proteasome activator REGalpha (PA28alpha).

The specificity of the 20S proteasome, which degrades many intracellular proteins, is regulated by protein complexes that bind to one or both ends of the cylindrical proteasome structure. One of these regulatory complexes, the 11S regulator (known as REG or PA28), stimulates proteasome peptidase activity and enhances the production of antigenic peptides for presentation by class I molecules of the major histocompatibility complex (MHC). The three REG subunits that have been identified, REGalpha, REGbeta and REGgamma (also known as the Ki antigen), share extensive sequence similarity, apart from a highly variable internal segment of 17-34 residues which may confer subunit-specific properties. REGalpha and REGbeta preferentially form a heteromeric complex, although purified REGalpha forms a heptamer in solution and has biochemical properties similar to the heteromeric REGalpha/REGbeta complex. We have now determined the crystal structure of human recombinant REGalpha at 2.8 A resolution. The heptameric barrel-shaped assembly contains a central channel that has an opening of 20 A diameter at one end and another of 30 A diameter at the presumed proteasome-binding surface. The binding of REG probably causes conformational changes that open a pore in the proteasome alpha-subunits through which substrates and products can pass.

Amino Acid Sequence↗

PubMed2002

Making and sharing decisions about management with patients: the views and experiences of pre-registration house officers in general practice and hospital.

OBJECTIVES: To explore the views and experiences of pre-registration house officers (PRHOs) in general practice and hospital settings regarding the concept of patient partnership and their experience of involving patients in management decisions. DESIGN: The 12 PRHOs who had graduated from British universities and who were working within the Yorkshire Deanery were interviewed towards the end of their four-month general practice attachments. The interviews were semi-structured and analysed qualitatively. RESULTS: Three major themes emerged. The PRHOs perceived differences in approach between consultations carried out in hospital and primary care settings, with general practitioners being more likely to share information and decisions with patients. As medical students, the PRHOs had little opportunity to practise sharing information and management decisions with patients, and variable experience of this after graduation. On the whole they were favourable to the concept of patient partnership. CONCLUSIONS: Medical students and PRHOs lack training and opportunities to decide on management and discuss this with patients and yet, particularly in general practice settings, they have to practise these skills. The PRHOs had begun to develop strategies to decide how much information to give to patients and to what extent to involve patients in management decisions. This is an area that needs further consideration when planning both undergraduate and postgraduate medical education.

Attitude of Health Personnel↗

PubMed1997

Intrinsic specificity of the reactive site loop of alpha1-antitrypsin, alpha1-antichymotrypsin, antithrombin III, and protease nexin I.

Members of the serpin (serine protease inhibitor) family share a similar backbone structure but expose a variable reactive-site loop, which binds to the catalytic groove of the target protease. Specificity originates in part from the sequence of this loop and also from secondary binding sites that contribute to the inhibitor function. To clarify the intrinsic contribution of the reactive-site loop, alpha1-antichymotrypsin has been utilized as a scaffold to construct chimeras carrying the loop of antithrombin III, protease nexin 1, or alpha1-antitrypsin. Reactive-site loops not only vary in sequence but also in length; therefore, the length of the reactive-site loop was also varied in the chimeras. The efficacy of the specificity transfer was evaluated by measuring the stoichiometry of the reaction, the ability to form an SDS-stable complex, and the association rate constant with a number of potential targets (chymotrypsin, neutrophil elastase, trypsin, thrombin, factor Xa, activated protein C, and urokinase). Overall, substitution of a reactive-site loop was not sufficient to transfer the specificity of a given serpin to alpha1-antichymotrypsin. Specificity of the chimera partly matched that of the loop donor and partly that of the acceptor, whereas the behavior as an inhibitor or a substrate depended upon the targeted protease. Results suggest that, aside from the contributions of the loop sequence and the framework-specific secondary binding sites, an intramolecular control may be essential for productive interaction.

Amino Acid Sequence↗

PubMed2004

Characterization and localization of drug resistance determinants in multidrug-resistant, integron-carrying Salmonella enterica serotype Typhimurium strains.

The genetic background of the antimicrobial resistance of 10 selected multiresistant Salmonella serotype Typhimurium (S. Typhimurium) strains (including the emerging monophasic variant [4,5,12:i:- ]) was investigated. All strains shared class 1 integrons (with seven types of variable regions) and belonged to different lineages (L1-L6) according to their phage types, DNA polymorphisms by XbaI-pulsed-field gel electrophoresis (PFGE), integrons, and/or resistance patterns. The strains were screened for the presence and localization (chromosomal or plasmid) of 32 DNA sequences representing integron-, Tn21-like transposon-, resistance-, and virulence-plasmid genes. Strains belonging to lineage L1 (definitive phage type DT104) carried the 90-kb Salmonella virulence plasmid together with the complete or partial chromosomally located Salmonella Genomic Island 1 (SGI1). All strains belonging to the other five lineages carried their resistance determinants on various resistance plasmids. Two of these strains showed complex plasmid profiles, which included a 95 kb virulence plasmid together with two or four resistance plasmids. Two strains carried a resistance plasmid that lacked the virulence-plasmid-encoding sequences. The remaining two strains carried two different hybrid virulence-resistance plasmids. Twenty-three of the DNA sequences could be assigned to distinct XbaI genomic restriction patterns (PFGE profiles). In this way, the influence of the resistance and virulence plasmids on the PFGE profiles was determined, and several groups of resistance genes could be identified. The data obtained represent a useful epidemiological tool for tracing the emergence and distribution of multiresistant S. Typhimurium worldwide.

Base Sequence↗

PubMed1998

Phosphoglycosylation: a new structural class of glycosylation?

There are a number of different glycoproteins that have been identified relatively recently which contain oligosaccharides linked to serine or threonine in a peptide backbone via phosphodiesters. It is possible that these glycoproteins may form an alternative structural class of glycosylation. This modification has been referred to as phosphoglycosylation (Mehta et al., 1996; J. Biol. Chem., 271, 10897-10903), and has been reported in slime molds and several unicellular parasites. In this review, examples of phosphoglycosylation from different biological sources are discussed. Those which are well characterized have been found to be highly variable with respect to the glycan moiety, while sharing some common features. An experimental approach detailing how to determine whether a protein is phosphoglycosylated is also presented.

Animals↗

PubMed2003

Gender differences in sexual and injection risk behavior among active young injection drug users in San Francisco (the UFO Study).

Female injection drug users (IDUs) represent a large proportion of persons infected with HIV in the United States, and women who inject drugs have a high incidence of hepatitis B virus (HBV) and hepatitis C virus (HCV) infection. Therefore, it is important to understand the role of gender in injection risk behavior and the transmission of blood-borne virus. In 2000-2002, 844 young (<30 years old) IDUs were surveyed in San Francisco. We compared self-reported risk behavior between 584 males and 260 female participants from cross-sectional baseline data. We used logistic regression to determine whether demographic, structural, and relationship variables explained increased needle borrowing, drug preparation equipment sharing, and being injected by another IDU among females compared to males. Females were significantly younger than males and were more likely to engage in needle borrowing, ancillary equipment sharing, and being injected by someone else. Females were more likely than males to report recent sexual intercourse and to have IDU sex partners. Females and males were not different with respect to education, race/ethnicity, or housing status. In logistic regression models for borrowing a used needle and sharing drug preparation equipment, increased risk in females was explained by having an injection partner who was also a sexual partner. Injecting risk was greater in the young female compared to male IDUs despite equivalent frequency of injecting. Overlapping sexual and injection partnerships were a key factor in explaining increased injection risk in females. Females were more likely to be injected by another IDU even after adjusting for years injecting, being in a relationship with another IDU, and other potential confounders. Interventions to reduce sexual and injection practices that put women at risk of contracting hepatitis and HIV are needed.

Adolescent↗

PubMed1986

Blood pressure concordance between spouses.

In 1982, 4,474 noninstitutionalized residents of Connecticut who were 18 years or older were interviewed as part of the Connecticut High Blood Pressure Program. This cross-sectional study was undertaken to determine the prevalence of hypertension among the 2.1 million adults in the state. Spouse correlations for systolic and diastolic blood pressures were examined in 1,260 white spouse pairs. Upon demonstrating a significant correlation in blood pressure between spouses (r = 0.262 for systolic and 0.248 for diastolic, p less than 0.001), subsequent stepwise multiple regressions were used to determine which aspects of the shared marital environment might influence the spouse concordance. Variables related to each spouse as well as variables reflecting similarity between spouses were analyzed. When spouse concordance in blood pressure was examined controlling for age, obesity, dietary salt intake, socioeconomic status, income, education, occupation, smoking, and exercise of both spouses and similarities in these variables, the correlations between spouses' blood pressures remained significant.

Adolescent↗

PubMed2004

Functional convergence in hydraulic architecture and water relations of tropical savanna trees: from leaf to whole plant.

Functional convergence in hydraulic architecture and water relations, and potential trade-offs in resource allocation were investigated in six dominant neotropical savanna tree species from central Brazil during the peak of the dry season. Common relationships between wood density and several aspects of plant water relations and hydraulic architecture were observed. All species and individuals shared the same negative exponential relationship between sapwood saturated water content and wood density. Wood density was a good predictor of minimum (midday) leaf water potential and total daily transpiration, both of which decreased linearly with increasing wood density for all individuals and species. With respect to hydraulic architecture, specific and leaf-specific hydraulic conductivity decreased and the leaf:sapwood area ratio increased more than 5-fold as wood density increased from 0.37 to 0.71 g cm(-3) for all individuals and species. Wood density was also a good predictor of the temporal dynamics of water flow in stems, with the time of onset of sap flow in the morning and the maximum sap flow tending to occur progressively earlier in the day as wood density increased. Leaf properties associated with wood density included stomatal conductance, specific leaf area, and osmotic potential at the turgor loss point, which decreased linearly with increasing wood density. Wood density increased linearly with decreasing bulk soil water potential experienced by individual plants during the dry season, suggesting that wood density was greatest in individuals with mostly shallow roots, and therefore limited access to more abundant soil water at greater depths. Despite their taxonomic diversity and large intrapopulation differences in architectural traits, the six co-occurring species and their individuals shared similar functional relationships between all pairs of variables studied. Thus, rather than differing intrinsically in physiological responsiveness, the species and the individuals appeared to have distinct operating ranges along common physiological response curves dictated by plant architectural and structural features. The patterns of water uptake and access to soil water during the dry season appeared to be the main determinant of wood density, which constrained evolutionary options related to plant water economy and hydraulic architecture, leading to functional convergence in the neotropical savanna trees studied.

Brazil↗

PubMed1993

Trans-sialidase: a unique enzyme activity discovered in the protozoan Trypanosoma cruzi.

Trypanosoma cruzi, the agent of Chagas' disease, an ailment characterized by a progressive chronic fibrotic myocarditis and degeneration of tissues that are innervated by the autonomic nervous system, is a voracious sialic acid eater from glycoconjugates of the surrounding medium. This is accomplished through an active trans-sialidase residing on the surface membrane of the trypomastigote stage, which is the parasite form that invades vertebrate cells. The existence of the enzyme was proposed and established only 7 years ago and yet a flood of information on the subject is already available. Trans-sialidase is able to reversibly transfer sialic acid alpha(2-->3)-linked to an external Gal beta from the host cell surface sialoglycoconjugates to a terminal Gal beta of an appropriate acceptor on the parasite surface. In the absence of an acceptor, the enzyme acts as a hydrolase transferring sialic acid to water. Trans-sialidase belongs to a highly heterogeneous gene family of surface molecules sharing with each other and with bacterial neuraminidases variable degrees of nucleotide sequence homology and common motifs. It has been proposed that sialylation of the parasite surface catalyzed by trans-sialidase is necessary for successful invasion of the host cell, but the evidence available is still indirect. Another function could be a protection from lysis by the alternative pathway of complement while the parasite is circulating in the acute phase of the disease.

Amino Acid Sequence↗

PubMed1994

Endocrine tumors of the gastrointestinal tract.

Endocrine tumors of the gastrointestinal tract are among the most interesting and heterogeneous of human malignancies. Presenting in highly variable fashions, carcinoid tumors and pancreatic endocrine tumors share natural histories that may range from the serendipitously found, easily cured appendiceal carcinoid to the highly malignant pancreatic islet cell tumors associated with unique endocrine syndromes. The heterogeneity and the relative rarity of these tumors hinder both basic and clinical research. However, new concepts of tumor biology, diagnosis, and treatment are emerging, which will lead to better understanding of the behavior of these tumors and, ultimately, to better treatment of the individual patient.

Gastrointestinal Neoplasms↗

PubMed2001

Contrast-Enhanced magnetic resonance angiography of the carotid bifurcation using the time-resolved imaging of contrast kinetics (TRICKS) technique.

The time-resolved contrast-enhanced magnetic resonance (MR) angiographic technique TRICKS (time-resolved imaging of contrast kinetics) reconstructs a temporal series of three-dimensional (3D) images. The temporal resolution is increased by using a short TR (<8 ms) and TE (<2 ms), zero filling, partial echo sampling, view sharing, and temporally sampling k-space at variable rates. TRICKS allows reconstruction of multiple sequential 3D volumes following bolus injection of a gadolinium chelate (0.2 mmol/kg body weight up to 40 ml, injection rate -2 ml/s). The resulting temporally defined datasets are conceptually similar to a catheter-based intra-arterial digital subtraction angiographic series, except that they are 3D volumes and not projection images. Similar to other contrast-enhanced MR angiographic methods, TRICKS improves delineation of carotid artery stenosis by minimizing saturation effects. TRICKS and other contrast-enhanced MR angiographic techniques use short echo times and small voxels, thus reducing intravoxel dephasing. Surface morphology of atherosclerotic plaque and slow flow in nearly occluded vessels ("string sign") are well delineated. The major advantage of the TRICKS technique is that the timing of the acquisition in relation to the passage of the contrast bolus occurs automatically, allowing for consistent capture of the arterial phase. and eliminating the need for sophisticated synchronization methods.

Carotid Arteries↗

PubMedDate not supplied

Communication patterns and conflict in marital dyads.

Responses--pauses, laughter, and interruptions (postulated to be communication techniques of couples with more equal power in decision making) and questions, silence time, and longer decision time (hypothesized to be communication techniques of couples in a dominant-submissive power structure)--of 68 middle-class suburban couples who volunteered to take the Inventory of Marital Conflicts were analyzed. Although study hypotheses were not supported, a high intercorrelation was revealed among communication variables hypothesized to be characteristic of power-sharing couples.

Adult↗