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PubMed2005

Species-level heritability reaffirmed: a comment on "on the heritability of geographic range sizes".

For many current issues in macroevolution and macroecology, it is important to know to what degree the attributes of species are shared among closely related lineages, a concept sometimes referred to as species-level heritability. Recently, Webb and Gaston proposed a new method for analyzing the heritability of geographic range size and concluded that range size is not heritable in Cretaceous gastropods (data from Jablonski) and modern birds (their data). Here we show that Webb and Gaston's method is flawed in that it implicitly assumes that range sizes are uniformly distributed. When range size distributions show their characteristic strong right skew, Webb and Gaston's method spuriously tends to find that range sizes of closely related pairs of species are more dissimilar than the random expectation. A reanalysis of Jablonski's data finds range size to be robustly and strongly heritable in Cretaceous gastropods and less strongly but still significantly heritable in present-day birds.

Animals↗
PubMed1999

Risk assessment for surgical-site infections in orthopedic patients.

OBJECTIVE: To assess the relative importance of risk factors for surgical-site infections (SSIs) in orthopedic patients and thereby determine which risk factors to monitor in the national surveillance of SSI in The Netherlands. DESIGN: Reanalysis of data on SSI and associated risk factors from two surveillance projects on nosocomial infections, carried out in 1992 and 1993 in The Netherlands: Project Surveillance Nosocomial Infections in the region of Utrecht (PSZU) and the first Project Surveillance Surgical Wound Infections (SWIFT-1). Odds ratios (ORs) were calculated for age, gender, preoperative stay, and the number of operations. In addition, in PSZU, other nosocomial infections, and, in SWIFT-1, prophylactic antibiotics, acute surgery, and wound contamination were studied. PARTICIPANTS: The study was confined to hospitalized orthopedic patients (PSZU, 4,872; SWIFT-1, 6,437). RESULTS: In PSZU, the following ORs were significant in a multivariate model: age 0-44 years, 1.0; 45-64 years, 1.6; 65-74 years, 4.7; and 75-99 years, 6.0. For a preoperative stay over 4 days, the OR was 3.3 (95% confidence interval [CI95], 2.5-4.0), and for multiple surgery, 2.5 (CI95, 1.9-3.0). For females, the OR was 0.8 (not significant). The same model applied to SWIFT-1 gave similar ORs. Adjustment for additional nosocomial infections (PSZU) decreased the ORs for ages over 65 years remarkably. The OR for additional nosocomial infections in patients under 65 years of age was 15.6 (CI95, 4.3-57.4). Adjustment for prophylactic antibiotics, acute surgery, and wound-contamination class (SWIFT-1) did not influence the ORs of the original model, but showed that wound-contamination class was an important risk factor. CONCLUSIONS: Age, additional nosocomial infections, wound-contamination class, preoperative stay, and the number of operations were identified as important risk factors for SSI in Dutch orthopedic patients.

Adolescent↗
PubMed2002

Nonrandom selection and the attributable cost of surgical-site infections.

OBJECTIVE: To study the extent to which selection bias poses problems for estimating the attributable cost of deep chest surgical-site infection (SSI) following coronary artery bypass graft (CABG) surgery. DESIGN: Reanalysis of a prospective case-control study. SETTING: A large, Midwestern community medical center. PATIENTS: Cases were all patients who had an SSI (N = 41) following CABG and CABG and valve surgery between April 1996 and March 1998. Controls were every tenth uninfected patient (N = 160). METHODS: Estimates of the attributable cost of deep chest SSI were computed using unmatched comparison, matched comparison, linear regression, and Heckman's two-stage approach. RESULTS: The attributable cost of deep chest SSI was estimated to be $20,012 by unmatched comparison, $19,579 by matched comparison, $20,103 by linear regression, and $14,211 by Heckman's two-stage method. Controlling for selection bias substantially reduced the cost estimate, but the coefficient capturing selection bias was not statistically significant. CONCLUSIONS: Deep chest SSI significantly increases the cost of care for patients who undergo CABG surgery. Unmatched comparison, matched comparison, and linear regression estimated the attributable cost to be approximately $20,000. Although controlling for selection bias with Heckman's two-stage method resulted in a substantially smaller estimate, the coefficient for selection bias was not statistically significant, suggesting that the estimates derived from the other models should be acceptable. However, the magnitude of the difference between the models shows that the effect of selection bias can be substantial. Some exploration for selection bias is recommended when estimating the attributable cost of SSIs.

Aged↗
PubMed2006

Larval ecology, geographic range, and species survivorship in Cretaceous mollusks: organismic versus species-level explanations.

The observation that geographic range size in Cretaceous mollusks is correlated with species survivorship and is heritable at the species level has figured repeatedly in discussions of species selection over the past two decades. However, some authors have suggested that the relationship between mode of larval development and geographic range supports the reduction of this example to selection on organismic properties. Our reanalysis of Jablonski's work on heritability at the species level finds that geographic range is significantly heritable (using a randomization test) in both bivalves and gastropods, even within a single larval mode. Further, generalized linear models show that geographic range size is more important than larval mode in predicting extinction probability in both gastropods and bivalves. These results reaffirm the role and heritability of geographic range as a species-level property that can promote species selection; the model-based approach applied here may help to operationalize "screening off " and related approaches to evaluating hierarchical explanations in evolution.

Animals↗
PubMed1998

Are the Duke criteria superior to the Beth Israel criteria for the diagnosis of infective endocarditis in children?

Accurate diagnosis of infective endocarditis may be difficult. The Beth Israel criteria and the newer Duke criteria assign probability to the diagnosis of infective endocarditis on the basis of the presence of common features and manifestations. We reviewed 111 cases of pediatric infective endocarditis diagnosed and treated over 19 years. Each case was classified by the two criteria, and the results were compared. Of 111 cases, 73 (66%) and 18 (16%) were classified as definite by the Duke criteria and the Beth Israel criteria, respectively. No cases were rejected by the Duke criteria, while 21 (19%) of 111 were rejected by the Beth Israel criteria. In 18 pathologically proven cases, reanalysis without pathological data showed that the Duke criteria had significantly greater sensitivity (83%) than the Beth Israel criteria (67%) (P < .03). Echocardiographic evidence was required in 22 cases for definite classification by the Duke criteria; none were rejected, however, when echocardiographic findings were ignored. Our results suggest that the Duke criteria are superior to the Beth Israel criteria for the diagnosis of pediatric infective endocarditis.

Adolescent↗
PubMed2003

A method for assessing occupational exposure to power-frequency magnetic fields for electricity generation and transmission workers.

A new method for assessing both current and historical occupational exposures to magnetic fields has been developed and used in health studies involving a cohort of electricity generation and transmission workers in England and Wales. The exposure values are derived by calculation from engineering and operational data about the power stations rather than from measurements. They are provided for each of 11 job categories for each year of operation of each power station represented in the cohort. The engineering data are used to determine the average magnetic fields in specified areas of work within the power station and then applied to information about the time spent in these areas by each of the job categories. The operational data are used to adjust the exposures for each year according to the power station output for the year. Earlier methods used measurements or the advice of panels of experts to provide exposure scores for a number of job categories across all power stations and years. Such methods were not able to distinguish exposures from different power facilities or during the different years of their operation. Measurement surveys at 10 power stations of the magnetic fields in the work areas gave confidence that the calculations were realistic. Exposure measurements on 215 workers at three power stations were compared in job groups with the exposures predicted by the method. The Pearson correlation coefficient was 0.86 and the slope and intercept of the line of best fit were 0.87 and 0.07 microT respectively. The method gives a good prediction of measured exposure and is being used for studies of occupational exposure to magnetic fields and leukaemia, and of cardiovascular disease, and a reanalysis of brain cancer.

Electric Wiring↗
PubMed2004

From a phylogenetic tree to a reticulated network.

In many phylogenetic problems, assuming that species have evolved from a common ancestor by a simple branching process is unrealistic. Reticulate phylogenetic models, however, have been largely neglected because the concept of reticulate evolution have not been supported by using appropriate analytical tools and software. The reticulate model can adequately describe such complicated mechanisms as hybridization between species or lateral gene transfer in bacteria. In this paper, we describe a new algorithm for inferring reticulate phylogenies from evolutionary distances among species. The algorithm is capable of detecting contradictory signals encompassed in a phylogenetic tree and identifying possible reticulate events that may have occurred during evolution. The algorithm produces a reticulate phylogeny by gradually improving upon the initial solution provided by a phylogenetic tree model. The new algorithm is compared to the popular SplitsGraph method in a reanalysis of the evolution of photosynthetic organisms. A computer program to construct and visualize reticulate phylogenies, called T-Rex (Tree and Reticulogram Reconstruction), is available to researchers at the following URL: www.fas.umontreal.ca/biol/casgrain/en/labo/t-rex.

Algorithms↗
PubMed2002

Generation and characterization of human hematopoietic cell lines expressing factor VIII.

Considering the plasticity of hematopoietic stem cells (HSC), they would be ideal targets for gene therapy of hemophilia A by virtue of their progeny providing immediate access to the bloodstream. However, several attempts to show expression of recombinant factor VIII (rFVIII) by primary hematopoietic cells and cell lines have failed; this failure was attributed to the inability of HSC to secrete rFVIII. Here we describe the generation of stable, FVIII-secreting hematopoietic cell lines representing different blood-cell types using a bicistronic lentiviral vector encoding for a B-domain-deleted FVIII (FVIII Delta B) and enhanced green fluorescence protein (EGFP). Transduced cell lines with erythroid and/or megakaryocytic background, (K562-F8 and TF-1-F8) secrete high levels of FVIII in the order of 76.4 and 41.6 ng FVIII:C/ml, whereas moderate and low levels are observed in B lymphoblastoid Raji-F8 cells and the T leukemia line Jurkat-F8 which secrete 6.73 and 1.83 ng FVIII:C/ml, respectively. The capacity to secrete rFVIII appeared to depend on factors related to the cell lineage rather than on the transduction efficacy. Stimulation of transduced cells with the protein kinase C (PKC)-activator phorbol myristate acetate (PMA) resulted in a marked augmentation of rFVIII secretion and enhanced green fluorescent protein (EGFP). Incubation with 0.1 and 1 ng/ml PMA resulted in up to 2.7-fold (K562-F8, Raji-F8) and 1.8-fold (293T-F8) increased rFVIII secretion. The established cell lines should be helpful in further elucidating mechanisms that are able to improve FVIII secretion in hematopoietic cells on a post-translational level and suggest reanalysis of hematopoietic cells as target for gene therapy of hemophilia.

Base Sequence↗
PubMed2005

Presence of CRF09_cpx and complex CRF02_AG/CRF09_cpx recombinant HIV type 1 strains in Côte d'Ivoire, West Africa.

Based on partial env and pol (protease and RT) subtyping, we recently documented that the majority (>80%) of the HIV-1 strains that circulate in Côte d'Ivoire were CRF02_AG and about 11% were recombinants or could not be clearly assigned to a known subtype or CRF. In order to determine in more detail the precise structure of these viruses we sequenced the full-length genomes for six such strains. Bootscan and phylogenetic tree analysis showed that four strains were complex and unique CRF02_AG/CRF09_cpx recombinants, one was a CRF02_AG/CRF06_cpx recombinant, and one was a pure CRF09_cpx. Reanalysis of the remaining recombinants asserted the predominance of CRF09_cpx within intersubtype recombinants and circulation of CRF09_cpx in Côte d'Ivoire. More detailed analysis of the CRF09_cpx strains revealed also that part of the pol gene belonged to subtype K. This is the first time that such recombinants are described.

Cote d'Ivoire↗
PubMedDate not supplied

Selective serotonin reuptake inhibitors in pediatric depression: is the balance between benefits and risks favorable?

Recent controversies surrounding the use of selective serotonin reuptake inhibitors (SSRIs) have highlighted the need to reassess potential benefits, as well as potential risks of this class of medications in the treatment of pediatric depression. The recent availability of data from meta-analyses of published and unpublished antidepressant trials, epidemiological studies, and the Treatment for Adolescents with Depression Study (TADS) has facilitated a reanalysis of this risk/benefit relationship. Despite reviewing similar data, various regulatory agencies have arrived at rather disparate conclusions regarding the data, resulting in continued controversy. Although all groups appear to agree that careful assessment, education regarding risks, and closer monitoring are essential for SSRIs, only the U.S. Food and Drug Administration (FDA) and the U.K. Medicine and Health Care Products Regulatory Agency maintain that an acceptable risk/benefit relationship exists for fluoxetine. The European Medicines Agency concluded that the SSRIs should not be used in the treatment of depression in children and adolescents. The authors of this review have taken into consideration many of these same data and offer a critical discussion of the pros and cons of SSRIs in pediatric depression. The authors have concluded that SSRIs -- in particular, fluoxetine -- do have a role in the treatment of pediatric depression.

Adolescent↗
PubMed1999

On the structure of the scaffolding core of bacteriophage T4.

The scaffolding core in bacteriophages is a temporary structure that plays a major role in determining the shape of the protein shell that encapsulates the viral DNA. In the currently accepted structure for the scaffolding core in bacteriophage T4, there is a symmetry mismatch between the protein shell, which has fivefold symmetry, and the scaffolding core, which is believed to consist of six helical chains. The analysis of T4 giant prohead data that was used to determine this structure made an implicit assumption about the manner in which giant proheads flatten during preparation for electron microscopy. Namely, it was assumed that techniques for analysis of Fourier transforms of flattened single-layer cylinders could be applied independently to the shell and the core. This analysis makes the implicit assumption that connections between the core and the shell do not affect the flattening process, and thus are stretched or broken during the flattening process. Reexamination of the experimental data shows that this assumption is likely to be incorrect. A reanalysis shows that the data could be consistent with six, eight, or 10 helical chains, and is a better match for eight or 10 helical chains. Ten helical chains would match the fivefold symmetry of the shell. The 10-helix core model is particularly attractive because it suggests a Vernier mechanism, which is able to explain the process of length determination in giant head mutants of T4. It is possible that the same assumption has been made for structural analysis of other biological systems. If this is the case, any results obtained should also be reexamined.

Bacteriophage T4↗
PubMed1986

Carbohydrate epitope defined by an antitumor monoclonal antibody detected on glycoproteins and a glycolipid by immunoblotting.

The murine monoclonal antibody (MAb) MOv2 was found to be directed against the carbohydrate moieties of different kinds of molecules expressed on a human ovarian cystoadenocarcinoma. To define further the glycoconjugates carrying the MOv2-defined epitope, different procedures were used to analyze materials from surgical specimens and carcinoma cell lines. SDS-PAGE and immunoblotting showed glycoprotein molecules migrating in the gel as high and intermediate molecular weight components. A low-molecular-weight band, migrating approximately with the dye front, was also immunostained by MOv2. On the other hand, the immunostaining of high-performance thin-layer chromatography (HPTLC) of the total glycolipid extract and its neutral and acid fractions, after DEAE chromatography, showed selective reactivity with a neutral glycolipid. Reanalysis by immunoblotting of this glycolipid band scraped off the HPTLC plate indicated that it corresponds to the low-molecular-weight component. Periodate oxidation and Pronase digestion further demonstrate the saccharide nature of the determinant on both types of glycoconjugates. In conclusion, we report evidence that with a single analytical procedure, i.e., immunoblotting, it is possible to recognize the same carbohydrate determinant carried on both protein and lipid molecules.

Antibodies, Monoclonal↗
PubMed1978

Dietary fibers: their definition and nutritional properties.

Fiber is a variable material with respect to its nutritional qualities depending upon its composition and physical properties. Biological properties possessed by one type of fiber might not be shared by another type. Separate methods are required to describe quantity, composition, and quality of fiber in foods. Fibers can be generally classified into three groups: vegetable fibers, which are highly fermentable with low indigestible residue; brans, which are less fermentable; and chemically purified fibers such as wood cellulose, which are relatively unfermentable. A class of soluble substances including pectins and gums may not be true fibers, but are considered part of the dietary fiber complex because of the similar effects they can elicit in the diet. A major need is the replacement of the crude fiber method, the present official method, which is seriously defective. Since crude fiber values are erratic and poorly related to the true fiber value of food, a second major need is the reanalysis of all foodstuffs by appropriate methods and the replacement of standard tables of food composition. Accomplishment of these purposes will require more support and promotion than is presently being received.

Cellulose↗
PubMed1999

Evaluation of a new reagent for preserving fresh blood samples and its potential usefulness for internal quality controls of multichannel hematology analyzers.

We describe a new, easy-to-use reagent, Cyto-Chex (Streck Laboratories, Omaha, Neb), that preserves fresh whole blood in a non-cross-linking, nonformalin manner. Target values assigned to fresh blood were essentially met after preservation and storage of up to 31 days. Respective mean analytic inaccuracies and short-term intra-assay coefficients of variation (n = 30) were as follows: WBCs, 6.7% and 1.99%; RBCs, 0.7% and 0.76%; hemoglobin, -1.8% and 0.79%; hematocrit, -0.3% and 0.75%; mean corpuscular volume, -1.0% and 0.78%; and platelets, 6.9% and 3.12%. Linearity of dilution-sensitive analytes was satisfactory over a wide range of dilutions after preservation of blood samples. Ten independent laboratories using 10 different instruments determined day-to-day interassay imprecision during four 7-day periods after blood preservation. Mean interassay coefficients of variation for participating laboratories were WBC, 1.92%; RBC, 1.00%; hemoglobin, 1.29%; hematocrit, 2.00%; and platelets 3.29%. Cyto-Chex enables long-term monitoring of instrument accuracy and precision with retained blood specimens of healthy persons. Blood from patient cohorts with various hematologic disorders and with a wide range of numeric abnormalities and/or parameter aberrations can be preserved satisfactorily with this reagent. The reanalysis of preserved patient blood samples is an important adjunct to the use of commercial control material in quality control programs of multichannel hematology analyzers.

Blood Preservation↗
PubMed1976

Assessment of the serum separator tube as an intermediate storage device within the laboratory.

An integral blood-drawing-serum separator tube, (SST) is evaluated for use as an in-laboratory serum storage device. Sera stored in the SST were compared with paired controls that were specimens from the same subjects stored in closed culture tubes. Eighty-six serum chemistry determinations showed no clinically significant change as a result of 48 hours of storage in the original blood-drawing tubes. Storage of serum in this manner provides the laboratory with specimens for reanalysis or additional analyses while eliminating manipulative steps, including serum removal, tube relabeling, and intertube transfers, and reducing errors due to misidentification and/or contamination.

Blood Chemical Analysis↗
PubMed1984

Sterile Corvac silicone gel tubes: efficacy and storage capabilities.

The storage capability of the sterile Corvac silicone gel tube as a specimen collection device is evaluated. Sera collected and stored in sterile Corvac silicone gel tubes were compared with control specimens collected in regular Monoject tubes and transferred to new Monoject tubes for storage. Sera for the efficacy tests were transferred from both the gel tube and the control tube without concern for storage. Sixty-seven analytes were compared, 20 of which were included in the storage portion. Only glucose, potassium, carbon dioxide, phosphorus, alkaline phosphatase, and lactic acid dehydrogenase (LDH) were statistically different in the storage experiment and amylase, T-3 uptake, folates, HDL, and again LDH by another method, were statistically different in the efficacy experiment. These evaluations determine the validity of storing specimens in this manner for reanalysis or additional analyses.

Blood Glucose↗
PubMed1984

Effects of abstinence on the ability of clinical laboratory tests to identify male alcoholics.

Quadratic discriminant analysis of 25 commonly ordered clinical laboratory tests resulted in correct classification of 100% of nonalcoholic inpatients (n = 41), 100% of medical ward alcoholics as alcoholic (n = 63), and 95% of alcoholism treatment program participants as alcoholic (n = 274). Admission laboratory values for a random sample of 138 additional alcoholism treatment program participants were used to correctly classify 96% of them as alcoholics. Repeat analysis of these same laboratory tests after some 27 days of hospitalization resulted in 94% of the 138 patients still being classified as alcoholic, even though significant improvements in individual hepatic and hematologic laboratory values were noted. Classification was not changed with reanalysis after long-term abstinence (7 or 24 months), suggesting widespread and persistent alcohol-related alterations in organ system functioning with chronic alcohol abuse. Quadratic discriminant analysis of laboratory tests is an effective means of identifying people with present or past alcohol abuse but is not yet of value in detecting compliance with a treatment goal of abstinence.

Adult↗
PubMed1985

Lactation and breast cancer. Evidence for a negative association in premenopausal women.

The authors report a case-control study of breast cancer based on an analysis of data collected by interview between the years 1957-1965 from women residing in the communities of Buffalo and Kenmore, New York. Prior reproductive factors, including a detailed lactation history, were examined for 453 white females with breast cancer and 1,365 white females without breast cancer who were selected randomly from the population of Buffalo and Kenmore. There is evidence of a negative association between length of nursing and breast cancer risk in premenopausal women which is not seen in the postmenopausal women. This apparent "protective" effect of lactation persists after statistical control for the potential confounding factors of age, parity, age at first pregnancy, age at menarche, and education. Cases are more likely than controls to have reported unsuccessful lactations due to "insufficient milk." The findings of this study, in conjunction with the authors' review of previously published studies that have examined prior lactation as related to breast cancer risk, suggest that there may be an independent negative association between nursing and subsequent breast cancer risk in premenopausal women. Whether this means that breast feeding is protective or that some women who are unsuccessful at lactation are at increased risk for subsequent breast cancer is not clear. A detailed reanalysis of existing data and more careful attention to detailed prior breast function/dysfunction in future studies are recommended.

Adolescent↗