bluuebunny/crossref_metadata_2025 huggingface dataset:
Amyloid Fibrils in Bionanotechnology
Authors: Waterhouse Sarah H. , Gerrard Juliet A.
Published: May 2004

An amyloid fibril is a highly ordered, insoluble form of protein that results when a normally soluble protein aggregates via a self-association process to form a structured nanotube. Such fibrils can now be routinely generated from purified proteins in the laboratory, and have attracted burgeoning interest due to their role in a variety of disease states. This article focusses on a new alternative direction in amyloid research, exploring the potential application of the amyloid fibril as a form of nanotubular scaffolding in bionanotechnology.
Gene expression alterations over large chromosomal regions in cancers include multiple genes unrelated to malignant progression
Authors: Masayesva Brett G. , Ha Patrick , Garrett-Mayer Elizabeth , Pilkington Thomas , Mao Rong , Pevsner Jonathan , Speed Traci , Benoit Nicole , Moon Chul-So , Sidransky David , Westra William H. , Califano Joseph
Published: May 2004

In solid tumors, the relationship between DNA copy number and global expression over large chromosomal regions has not been systematically explored. We used a 12,626-gene expression array analysis of head and neck squamous cell carcinoma and normal oral mucosa and annotated gene expression levels to specific chromosomal loci. Expression alterations correlated with reported data using comparative genomic hybridization. When genes with significant differences in expression between normal and malignant lesions, as defined by significance analysis of microarrays (SAM), were compared to nonsignificant genes, similar chromosomal patterns of alteration in expression were noted. Individual tumors underwent microsatellite analysis and χ
2
analysis of expression at 3p and 22q. Significant 3p underexpression and 22q overexpression were found in all primary tumors with 3p and 22q allelic imbalance, respectively, whereas no tumor without allelic imbalance on these chromosomal arms demonstrated expression differences. Loss and gain of chromosomal material in solid cancers can alter gene expression over large chromosomal regions, including multiple genes unrelated to malignant progression.
Two important exceptions to the relationship between energy density and fat content: foods with reduced-fat claims and high-fat vegetable-based dishes
Authors: Fontaine Helen A La , Crowe Timothy C , Swinburn Boyd A , Gibbons Carl J
Published: May 2004

Objective:

To test the hypothesis that many foods with reduced-fat (RF) claims are relatively energy-dense and that high-fat (HF) vegetable-based dishes are relatively energy-dilute.

Design:

Nutrient data were collected from available foods in Melbourne supermarkets that had an RF claim and a full-fat (FF) equivalent. Nutrient analyses were also conducted on recipes for HF vegetable-based dishes that had more than 30% energy from fat but less than 10% from saturated fat. The dietary intake data (beverages removed) from the 1995 National Nutrition Survey were used for the reference relationships between energy density (ED) and percentage energy as fat and carbohydrate and percentage of water by weight.

Statistics:

Linear regression modelled relationships of macronutrients and ED. Paired t-tests compared observed and predicted reductions in the ED of RF foods compared with FF equivalents.

Results:

Both FF and RF foods were more energy-dense than the Australian diet and the HF vegetable-based dishes were less energy-dense. The Australian diet showed significant relationships with ED, which were positive for percentage energy as fat and negative for percentage energy as carbohydrate. There were no such relationships for the products with RF claims or for the HF vegetable-based dishes.

Conclusion:

While, overall, a reduced-fat diet is relatively energy-dilute and is likely to protect against weight gain, there appear to be two important exceptions. A high intake of products with RF claims could lead to a relatively energy-dense diet and thus promote weight gain. Alternatively, a high intake of vegetable-based foods, even with substantial added fat, could reduce ED and protect against weight gain.
Application of 3D glycerol-compensated inclined-exposure technology to an integrated optical pick-up head*
Authors: Kuo-Yung Hung  , Heng-Tsang Hu  , Fan-Gang Tseng
Published: May 2004

This paper proposes a novel method for integrating inclined mirrors with precise angles and smooth surfaces in on-chip Fresnel lens optical pick-up-head applications. A glycerol-compensated inclined-exposure technology was adopted for 45° mirror pair fabrication. This technology can fabricate 19–90° inclined structures onto SU-8 negative tone resist with thickness from 100 to 1000 µm. Glycerol is employed as an index matching material during exposure to compensate for the refractive index difference between the air and SU8, thus extending the possible inclined angles from 54° (in air) down to 19° (in glycerol). To eliminate reflected induced patterns, CK-6020L resist is employed as an antireflection layer. The surface roughness, measured by AFM, is below 7 nm for various inclined angles. Device fabrication has been successfully completed and test results demonstrated a functional VCSEL (vertical cavity surface emitting laser) beam focusing on a 5 µm spot. Further beam size reduction into the sub-micrometer range requires an objective lens with high numerical aperture, which is not within the scope of this paper. The fabricated optical components are robust and accurately aligned. This new integrated approach provides an easy and low-cost fabrication method for optical pick-up heads eliminating the need for manual assembly.
Olfactory Response in the Temporal Cortex of the Elderly Measured with Near-Infrared Spectroscopy: A Preliminary Feasibility Study
Authors: Fladby Tormod , Bryhn Grete , Halvorsen Ola , Rosé Isabelle , Wahlund Martin , Wiig Pia , Wetterberg Lennart
Published: May 2004

The pathway for the olfactory response may be affected at an early stage of Alzheimer's disease. Measurement of the olfactory response in the elderly is therefore of particular interest. In this feasibility study, near-infrared spectroscopy was used to measure the olfactory response in 21 patients aged 56 to 79 years. Eight subjects had no memory complaints whereas 13 had subjective memory complaints, mild cognitive impairment, or very mild Alzheimer's disease. The optodes were placed over the temporal lobe, with the emitting optode over the pole and the receiving optode over the superior gyrus. The response to vanilla (1% in sterile H2O) in a test tube held immediately beneath the nostrils was compared to the response to sterile H2O only. Four control subjects had a clearly definable response with increased oxyhemoglobin and decreased deoxyhemoglobin bilaterally. The response was measured as the sum of the deviation of oxygenated and deoxygenated hemoglobin from baseline mean. With a cut-off determined after examination of responses to vanilla and sham stimulus, group difference was significant for response to vanilla (χ2 test, P = 0.03). Response amplitudes to vanilla in the patient group were within the range of those to sham stimuli.
Translation-State Analysis of Gene Expression in Mouse Brain after Focal Ischemia
Authors: MacManus John P. , Graber Tyson , Luebbert Christian , Preston Edward , Rasquinha Ingrid , Smith Brandon , Webster Jacqueline
Published: May 2004

Confounding any genome-scale analysis of gene expression after cerebral ischemia is massive suppression of protein synthesis. This inefficient translation questions the utility of examining profiles of total transcripts. Our approach to such postischemic gene profiling in the mouse by microarray analysis was to concentrate on those mRNAs bound to polyribosomes. In our proof-of-principle study, polysomally bound and unbound mRNAs were subjected to microarray analysis: of the 1,161 transcripts that we found to increase after ischemia, only 36% were bound to polyribosomes. In addition to the expected increases in heat-shock proteins and metallothioneins, increases in several other bound transcripts involved in the promotion of cell survival or antiinflammatory behavior were noted, such as CD63 (Lamp3), Lcn2 (lipocalin-2), Msn (moesin), and UCP2 (uncoupling protein 2), all of which showed increases in cognate protein by Western blotting. The list of heretofore nonfunctionally annotated transcripts (RIKEN clones/ESTs) that increased appeared to be novel. How some transcripts are selected in ischemic brain for translation into protein, while others are rejected, is not clear. The length of the 5′-UTR in the ischemically induced transcripts that occur in the NCBI RefSeq database did not indicate any general tendency to be more than 200 nt, nor to be longer than the 5′-UTRs of the unbound transcripts. Thus, the presence of a complex 5′-UTR region with internal ribosome entry sites (IRES) or polypyrimidine tracts (TOP) does not appear to be the basis of selection for translation in ischemic brain.
Addressing an Idiosyncrasy in Estimating Survival Curves Using Double Sampling in the Presence of Self‐Selected Right Censoring
Authors: Frangakis Constantine E. , Rubin Donald B.
Published: May 2004

Summary. We investigate the use of follow‐up samples of individuals to estimate survival curves from studies that are subject to right censoring from two sources: (i) early termination of the study, namely, administrative censoring, or (ii) censoring due to lost data prior to administrative censoring, so‐called dropout. We assume that, for the full cohort of individuals, administrative censoring times are independent of the subjects' inherent characteristics, including survival time. To address the loss to censoring due to dropout, which we allow to be possibly selective, we consider an intensive second phase of the study where a representative sample of the originally lost subjects is subsequently followed and their data recorded. As with double‐sampling designs in survey methodology, the objective is to provide data on a representative subset of the dropouts. Despite assumed full response from the follow‐up sample, we show that, in general in our setting, administrative censoring times are not independent of survival times within the two subgroups, nondropouts and sampled dropouts. As a result, the stratified Kaplan–Meier estimator is not appropriate for the cohort survival curve. Moreover, using the concept of potential outcomes, as opposed to observed outcomes, and thereby explicitly formulating the problem as a missing data problem, reveals and addresses these complications. We present an estimation method based on the likelihood of an easily observed subset of the data and study its properties analytically for large samples. We evaluate our method in a realistic situation by simulating data that match published margins on survival and dropout from an actual hip‐replacement study. Limitations and extensions of our design and analytic method are discussed.
Joint Regression Analysis of Survival and Quality‐Adjusted Survival
Authors: Fine Jason P. , Gelber Richard D.
Published: May 2004

Summary. In this paper, a semiparametric bivariate linear regression model for survival and quality‐adjusted survival is investigated. Even with a parametric specification for the joint distribution, maximum likelihood is not applicable because of induced informative censoring. We propose inference procedures based on estimating functions. The estimators are consistent and asymptotically normal. Hypothesis tests and confidence intervals may be constructed with easy‐to‐implement resampling techniques. Simultaneous regression modeling of survival and quality‐adjusted survival has not been studied formally. Our methodology gives parameter estimates that are highly interpretable in the context of a cost‐effectiveness analysis. The usefulness of the proposal is illustrated with a breast cancer dataset.
Inference in Randomized Studies with Informative Censoring and Discrete Time‐to‐Event Endpoints
Authors: Scharfstein Daniel , Robins James M. , Eddings Wesley , Rotnitzky Andrea
Published: May 2004

Summary. In this article, we present a method for estimating and comparing the treatment‐specific distributions of a discrete time‐to‐event variable from right‐censored data. Our method allows for (1) adjustment for informative censoring due to measured prognostic factors for time to event and censoring and (2) quantification of the sensitivity of the inference to residual dependence between time to event and censoring due to unmeasured factors. We develop our approach in the context of a randomized trial for the treatment of chronic schizophrenia. We perform a simulation study to assess the practical performance of our methodology.
Estimating the Frequency Distribution of Crossovers during Meiosis from Recombination Data
Authors: Yu Kai , Feingold Eleanor
Published: May 2004

Summary.Estimation of tetrad crossover frequency distributions from genetic recombination data is a classic problem dating back to Weinstein (1936,Genetics21, 155–199). But a number of important issues, such as how to specify the maximum number of crossovers, how to construct confidence intervals for crossover probabilities, and how to obtain correctp‐values for hypothesis tests, have never been adequately addressed. In this article, we obtain some properties of the maximum likelihood estimate (MLE) for crossover probabilities that imply guidelines for choosing the maximum number of crossovers. We give these results for both normal meiosis and meiosis with nondisjunction. We also develop an accelerated EM algorithm to find the MLE more efficiently. We propose bootstrap‐based methods to find confidence intervals andp‐values and conduct simulation studies to check the validity of the bootstrap approach.
Statistical Measures of DNA Sequence Dissimilarity under Markov Chain Models of Base Composition
Authors: Wu Tiee‐Jian , Hsieh Ya‐Ching , Li Lung‐An
Published: May 2004

Summary. In molecular biology, the issue of quantifying the similarity between two biological sequences is very important. Past research has shown that word‐based search tools are computationally efficient and can find some new functional similarities or dissimilarities invisible to other algorithms like FASTA. Recently, under the independent model of base composition, Wu, Burke, and Davison (1997, Biometrics53, 1431–1439) characterized a family of word‐based dissimilarity measures that denned distance between two sequences by simultaneously comparing the frequencies of all subsequences of n adjacent letters (i.e., n‐words) in the two sequences. Specifically, they introduced the use of Mahalanobis distance and standardized Euclidean distance into the study of DNA sequence dissimilarity. They showed that both distances had better sensitivity and selectivity than the commonly used Euclidean distance. The purpose of this article is to extend Mahalanobis and standardized Euclidean distances to Markov chain models of base composition. In addition, a new dissimilarity measure based on Kullback–Leibler discrepancy between frequencies of all n‐words in the two sequences is introduced. Applications to real data demonstrate that Kullback–Leibler discrepancy gives a better performance than Euclidean distance. Moreover, under a Markov chain model of order k̂Q for base composition, where k̂Q is the estimated order based on the query sequence, standardized Euclidean distance performs very well. Under such a model, it performs as well as Mahalanobis distance and better than Kullback–Leibler discrepancy and Euclidean distance. Since standardized Euclidean distance is drastically faster to compute than Mahalanobis distance, in a usual workstation/PC computing environment, the use of standardized Euclidean distance under the Markov chain model of order k̂Q of base composition is generally recommended. However, if the user is very concerned with computational efficiency, then the use of Kullback–Leibler discrepancy, which can be computed as fast as Euclidean distance, is recommended. This can significantly enhance the current technology in comparing large datasets of DNA sequences.
Bayesian Nonparametric Modeling Using Mixtures of Triangular Distributions
Authors: Perron F. , Mengersen K.
Published: May 2004

Summary. Nonparametric modeling is an indispensable tool in many applications and its formulation in an hierarchical Bayesian context, using the entire posterior distribution rather than particular expectations, increases its flexibility. In this article, the focus is on nonparametric estimation through a mixture of triangular distributions. The optimality of this methodology is addressed and bounds on the accuracy of this approximation are derived. Although our approach is more widely applicable, we focus for simplicity on estimation of a monotone nondecreasing regression on [0, 1] with additive error, effectively approximating the function of interest by a function having a piecewise linear derivative. Computationally accessible methods of estimation are described through an amalgamation of existing Markov chain Monte Carlo algorithms. Simulations and examples illustrate the approach.
Bayesian Spatiotemporal Inference in Functional Magnetic Resonance Imaging
Authors: Gössl C. , Auer D. P. , Fahrmeir L.
Published: May 2004

Summary. Mapping of the human brain by means of functional magnetic resonance imaging (fMRI) is an emerging field in cognitive and clinical neuroscience. Current techniques to detect activated areas of the brain mostly proceed in two steps. First, conventional methods of correlation, regression, and time series analysis are used to assess activation by a separate, pixelwise comparison of the fMRI signal time courses to the reference function of a presented stimulus. Spatial aspects caused by correlations between neighboring pixels are considered in a separate second step, if at all. The aim of this article is to present hierarchical Bayesian approaches that allow one to simultaneously incorporate temporal and spatial dependencies between pixels directly in the model formulation. For reasons of computational feasibility, models have to be comparatively parsimonious, without oversimplifying. We introduce parametric and semiparametric spatial and spatiotemporal models that proved appropriate and illustrate their performance applied to visual fMRI data.
Semiparametric Regression Modeling with Mixtures of Berkson and Classical Error, with Application to Fallout from the Nevada Test Site
Authors: Mallick Bani , Hoffman F. Owen , Carroll Raymond J.
Published: May 2004

Summary. We construct Bayesian methods for semiparametric modeling of a monotonic regression function when the predictors are measured with classical error, Berkson error, or a mixture of the two. Such methods require a distribution for the unobserved (latent) predictor, a distribution we also model semi‐parametrically. Such combinations of semiparametric methods for the dose‐response as well as the latent variable distribution have not been considered in the measurement error literature for any form of measurement error. In addition, our methods represent a new approach to those problems where the measurement error combines Berkson and classical components. While the methods are general, we develop them around a specific application, namely, the study of thyroid disease in relation to radiation fallout from the Nevada test site. We use this data to illustrate our methods, which suggest a point estimate (posterior mean) of relative risk at high doses nearly double that of previous analyses but that also suggest much greater uncertainty in the relative risk.
Testing for Dependence Between Failure Time and Visit Compliance with Interval‐Censored Data
Authors: Betensky Rebecca A. , Finkelstein Dianne M.
Published: May 2004

Summary.Interval‐censored failure‐time data arise when subjects miss prescheduled visits at which the failure is to be assessed. The resulting intervals in which the failure is known to have occurred are overlapping. Most approaches to the analysis of these data assume that the visit‐compliance process is ignorable with respect to likelihood analysis of the failure‐time distribution. While this assumption offers considerable simplification, it is not always plausible. Here we test for dependence between the failure‐ and visit‐compliance processes, applicable to studies in which data collection continues after the occurrence of the failure. We do not make any of the assumptions made by previous authors about the joint distribution of the visit‐compliance process, a covariate process, and the failure time. Instead, we consider conditional models of the true failure history given the current visit compliance at each visit time, allowing for correlation across visit times. Because failure status is not known at some visit times due to missed visits, only models of the observed failure history given current visit compliance are estimable. We describe how the parameters from these models can be used to test for a negative association and how bounds on unestimable parameters provided by the observed data are needed additionally to infer a positive association. We illustrate the method with data from an AIDS study and we investigate the power of the test through a simulation study.
Locomotion in bonobos (Pan paniscus): differences and similarities between bipedal and quadrupedal terrestrial walking, and a comparison with other locomotor modes
Authors: D’Août K. , Vereecke E. , Schoonaert K. , De Clercq D. , Van Elsacker L. , Aerts P.
Published: May 2004

One of the great ongoing debates in palaeo‐anthropology is when, and how, hominids acquired habitual bipedal locomotion. The newly adopted bipedal gait and the ancestral quadrupedal gait are most often considered as very distinct, with each habitual locomotor mode showing corresponding anatomical adaptations. Bonobos (Pan paniscus), along with common chimpanzees (P. troglodytes), are the closest living relatives to humans and their locomotion is valuable for comparison with other primates, and to gain an insight in the acquisition of human bipedalism. Bonobos are habitual quadrupeds, but they also engage in bipedal locomotion, both on terrestrial and in arboreal substrates. In terms of kinematics and dynamics, the contrast between bipedal and quadrupedal walking seems to be more subtle than one might expect. Apart from the trunk being approximately 37° more erect during bipedal locomotion, the leg movements are rather similar. Apart from the heel, plantar pressure distributions show subtle differences between bipedal and quadrupedal locomotion. Regardless, variability is high, and various intermediate forms of locomotion (e.g. tripedal walking) exist both in captivity and in the wild. Moreover, there is overlap between the characteristics of walking and other locomotor modes, as we show with new data of walking on an inclined pole and of vertical squat jumps. We suggest that there is great overlap between the many locomotor modes in bonobos, and that the required polyvalence is reflected in their anatomy. This may hamper the development of one highly specialized gait (i.e. bipedalism), which would constrain performance of the other types of locomotion.
Biomimetic robotics should be based on functional morphology
Authors: Witte Hartmut , Hoffmann Helge , Hackert Rémi , Schilling Cornelius , Fischer Martin S. , Preuschoft Holger
Published: May 2004

Due to technological improvements made during the last decade, bipedal robots today present a surprisingly high level of humanoid skill. Autonomy, with respect to the processing of information, is realized to a relatively high degree. What is mainly lacking in robotics, moving from purely anthropomorphic robots to ‘anthropofunctional’ machines, is energetic autonomy. In a previously published analysis, we showed that closer attention to the functional morphology of human walking could give robotic engineers the experiences of an at least 6 Myr beta test period on minimization of power requirements for biped locomotion. From our point of view, there are two main features that facilitate sustained walking in modern humans. The first main feature is the existence of ‘energetically optimal velocities’ provided by the systematic use of various resonance mechanisms: (a) suspended pendula (involving arms as well as legs in the swing phase of the gait cycle) and matching of the pendular length of the upper and lower limbs; (b) inverted pendula (involving the legs in the stance phase), driven by torsional springs around the ankle joints; and (c) torsional springs in the trunk. The second main feature is compensation for undesirable torques induced by the inertial properties of the swinging extremities: (a) mass distribution in the trunk characterized by maximized mass moments of inertia; (b) lever arms of joint forces at the hip and shoulder, which are inversely proportional to their amplitude; and (c) twisting of the trunk, especially torsion. Our qualitative conclusions are three‐fold. (1) Human walking is an interplay between masses, gravity and elasticity, which is modulated by musculature. Rigid body mechanics is insufficient to describe human walking. Thus anthropomorphic robots completely following the rules of rigid body mechanics cannot be functionally humanoid. (2) Humans are vertebrates. Thus, anthropomorphic robots that do not use the trunk for purposes of motion are not truly humanoid. (3) The occurrence of a waist, especially characteristic of humans, implies the existence of rotations between the upper trunk (head, neck, pectoral girdle and thorax) and the lower trunk (pelvic girdle) via an elastic joint (spine, paravertebral and abdominal musculature). A torsional twist around longitudinal axes seems to be the most important.
Application of the dual‐beam FIB/SEM to metals research
Authors: SIVEL V. G. M. , VAN DEN BRAND J. , WANG W. R. , MOHDADI H. , TICHELAAR F. D. , ALKEMADE P. F. A. , ZANDBERGEN H. W.
Published: May 2004

The dual‐beam microscope is a combination of a focused ion beam with an electron beam. The instrument used in this work is also equipped with an energy‐dispersive X‐ray system for local elemental analysis. This powerful tool gives access to specific features inside a material. Two different applications are presented in this paper: (1) cross‐sections and transmission electron microscope specimens cut in order to investigate the interface between an aluminium substrate and its epoxy coating; and (2) a grain boundary in a Cu3Au alloy. In both cases, the dual beam succeeded where other methods failed.
Length of Stay after Vaginal Birth: Sociodemographic and Readiness‐for‐Discharge Factors
Authors: Weiss Marianne , Ryan Polly , Lokken Lisa , Nelson Magdalen
Published: May 2004

Abstract:  Background: The impact of reductions in postpartum length of stay have been widely reported, but factors influencing length of hospital stay after vaginal birth have received less attention. The study purpose was to compare the sociodemographic characteristics and readiness for discharge of new mothers and their newborns at 3 discharge time intervals, and to determine which variables were associated with postpartum length of stay. Methods: The study sample comprised 1,192 mothers who were discharged within 2 postpartum days after uncomplicated vaginal birth at a tertiary perinatal center in the midwestern United States. The sample was divided into 3 postpartum length‐of‐stay groups: group 1 (18–30 hr), group 2 (31–42 hr), and group 3 (43–54 hr). Sociodemographic and readiness‐for‐discharge data were collected by self‐report and from a computerized hospital information system. Measures of readiness for discharge included perceived readiness (single item and Readiness for Discharge After Birth Scale), documented maternal and neonatal clinical problems, and feeding method. Results: Compared with other groups, the longest length‐of‐stay group was older; of higher socioeconomic status and education; and with more primiparous, breastfeeding, white, married mothers who were living with the baby's father, had adequate home help, and had a private payor source. This group also reported greater readiness for discharge, but their newborns had more documented clinical problems during the postbirth hospitalization. In logistic regression modeling, earlier discharge was associated with young age, multiparity, public payor source, low socioeconomic status, lack of readiness for discharge, bottle‐feeding, and absence of a neonatal clinical problem. Conclusions: Sociodemographic chracteristics and readiness for discharge (clinical and perceived) were associated with length of postpartum hospital stay. Length of stay is an outcome of a complex interface between patient, provider, and payor influences on discharge timing that requires additional study. Including perceived readiness for discharge in clinical discharge criteria will add an important dimension to assessment of readiness for discharge after birth.
Increasing Cesarean Section Rates: Exploring the Role of Culture in an Australian Community
Authors: Walker Ruth , Turnbull Deborah , Wilkinson Chris
Published: May 2004

Abstract:  Background: The proportion of births by cesarean section in Australia has recently increased by 35 percent, rising from 17 percent in 1990 to 23 percent in 2000. Unlike previous research, which has focused on women's role in increasing rates of cesarean section, this study aimed to explore the existence of wider cultural norms of acceptance of cesarean section in the Australian community, and the implications these might have for rising rates. Methods: A postal self‐completion questionnaire was sent to a consecutive sample of 148 women who delivered 7 weeks earlier at the Women's and Children's Hospital, a tertiary‐referral public maternity hospital in metropolitan Adelaide, South Australia. These women were recruited at 18 weeks’ gestation, and had been involved in a wider study. The questionnaire included three sections, one section on agreement with statements pertaining to cultural acceptance of cesarean section, a second on personal consideration of cesarean section in early pregnancy, and a third including sociodemographic questions. Results: Of the total sample, 92 women responded to the questionnaire (response rate 62%). Of 6 items relating to community acceptance of cesarean section, responses ranged from 71.4 percent agreement (“common for people to think that cesarean section offers an easier way of giving birth”) to 23.1 percent agreement (“the media seems to portray cesarean section as a better option than vaginal delivery”). The option of having a cesarean section was considered by almost 15 percent (10/68) of women early in their pregnancy. For the vast majority (8/10) this consideration was clinically based. Conclusions: This investigation demonstrated that these Australian women, independent of sociodemographic variables such as age and education level, agreed that cesarean section was perceived as an easy, convenient way of giving birth.
Secondary metabolites and plant/environment interactions: a view through Arabidopsis thaliana tinged glasses
Authors: KLIEBENSTEIN D. J.
Published: May 2004

Arabidopsis thaliana is a successful model plant for studying wide‐ranging topics including plant development, genetics and pathogen resistance. In addition, significant research has been conducted in the area of secondary metabolite biochemical genetics. The secondary metabolites in Arabidopsis include glucosinolates, terpenoids, phenylpropanoids, the alkaloid‐like camalexin, and other uncharacterized compounds. The genetic tools developed in studying secondary metabolite biochemistry are now being used to study how secondary metabolites control various biological processes. This includes compounds involved in plant/insect and plant/pathogen interactions, compounds preventing UV‐B damage, and compounds involved in hormone homeostasis. This review will describe what light Arabidopsis is shedding on the biological and ecological importance of specific secondary metabolites.
On the mystery of the golden angle in phyllotaxis
Authors: KING S. , BECK F. , LÜTTGE U.
Published: May 2004

Phyllotaxis, the arrangement of leaves around a stem, shows in the vast majority of cases a regularity in the divergence angle of subsequent leaves which divide the whole circle into regular fractions. These are in most cases rational fractions of two Fibonacci numbers in an alternating series, converging towards the irrational limit of the golden section, corresponding to the golden divergence angle of 137.5  . . . degrees. This peculiarity was a long‐standing mystery. Here, it is related to the evolutionary pressure of optimal light capture for maximal photosynthetic activity. A model is established which relates minimal shadowing for the lower leaves to the divergence angle. Numerical results of this model agree well with semi‐empirical data on the dependence of light capture from the divergence angle. The basic shadow function of the model is also related with the demand of minimal shadowing for the angular separation of leaves and obtain, using elementary number theory, as solution the golden section. Further numerical studies show that the rational approach to the golden section (Schimper–Braun series) is related to the leaf width and the number of leaves of the plant.
Reef‐capping laminites in the Upper Silurian carbonate‐ to‐evaporite transition, Michigan Basin, south‐western Ontario
Authors: Coniglio Mario , Frizzell ROB , Pratt Brian R.
Published: May 2004

Silurian pinnacle reefs in the subsurface of the south‐western Ontario portion of the Michigan Basin display a variety of laminated carbonates (laminites) within predominantly muddy reef‐capping facies in the upper part of the Guelph Formation and the overlying A‐1 Carbonate of the Salina Group. Laminites, which are limestone, dolomite or partially dolomitized limestones, have a range of morphologies, from simple planar to a variety of wavy and serrated forms. Individual laminae are composed mainly of micrite, microspar or replacive dolomite, and vary internally from isopachous and continuous over the diameter of the core to non‐isopachous and often discontinuous. Clotted and peloidal micrite, sometimes defining small knobs and chambers, is interpreted as being microbial in origin and occurs within all types of laminites. Fibrous cement locally comprises laminite clasts in breccias or coats clasts in breccias, and also occurs as spherulites in the interparticle spaces in breccias. Although similar laminites have been described from elsewhere in the Michigan Basin and interpreted as caliche, travertine and abiotic subtidal stromatolites, the laminites in south‐western Ontario are most realistically regarded as microbial. The causes for the variations in morphology and characteristics of the constituent laminae are uncertain, although fluctuations in local microenvironmental conditions would have been important, set against a backdrop of an increasingly restricted overall setting. Caliche or travertine origins for these laminites are unlikely in general, except perhaps locally at the subaerial exposure surface at the tops of pinnacle reefs.
Formation of decollement upwarps during thrusting
Authors: Dubey Ashok Kumar
Published: May 2004

Geometric and kinematic models reveal that rotation of layers during thrusting or development of drag folds produced by movement along listric thrust faults results in the formation of dilation space at the junction of the thrust ramp with the basal decollement. This is accompanied by upwarping of the basement to occupy the available space thereby producing an antiformal structure, which restricts the thrust displacement. The structure is termed a decollement upwarp and examples are cited from the foothill belt of the Himalaya.
Evidence, Research, Knowledge: A Call for Conceptual Clarity
Authors: Scott‐Findlay Shannon , Pollock Carolee
Published: May 2004

Objective:To dispel some of the conceptual confusion in the field of evidence‐based practice that has resulted from the overlapping use of the termsresearch,evidence, andknowledge.

Approach:Theoretical discussion.

Findings:Often the termsresearchandknowledgeare used as synonyms forevidence, but the overlap is never complete. The termevidencehas long been understood to mean the findings of research.

Discussion:Recent attempts to broaden the definition of evidence to include clinical experience and experiential knowledge have been misguided. Broadening our understanding of the basis for clinical decision making and conceptualizing evidence are quite different tasks. Other factors (not other forms of evidence) do shape the clinical decision‐making process, but they are not evidence. We might better term them knowledge. Confusing evidence with these other factors has hindered research and the improvement of clinical decision making in health care. We argue that this confusion results from the use of the termevidencewhen we really mean either research findings or knowledge.

Conclusions:In this article, we have argued for specificity in the use of the termevidence. We urge the restriction of the termevidenceto research findings, and while we acknowledge the importance of other influences on the clinical decision‐making process, we insist that they are not evidence. The time has come to value personal experience and experiential knowledge for what they are—we should not have to disguise them as types of evidence for them to be deemed of any value. Being specific to language, the goal is to improve clinical decision making by increasing practitioners' reliance on research findings (evidence) while acknowledging (and valuing) the important part played by other forms of knowledge in the decision‐making process. The distinctions are important.
A Qualitative Study to Identify Barriers and Facilitators to Implementation of Pilot Interventions in the Veterans Health Administration (VHA) Northwest Network
Authors: Sharp Nancy D. , Pineros Sandra L. , Hsu Clarissa , Starks Helene , Sales Anne E.
Published: May 2004

Objective: To identify barriers and facilitators to implementation of pilot interventions designed to improve measurement and management of low‐density lipoprotein cholesterol (LDL‐c) levels in coronary heart disease patients using the evidence/context/facilitation model of implementation of evidence‐based practice.

Design: Theory‐based conceptual content analysis of structured interviews conducted between January and April 2001.

Setting: Six medical centers in the United States Veterans Health Administration Northwest Network.

Participants: Fifty‐one of 64 individuals (physicians, nurses, pharmacists, dieticians, quality managers, and other clinical and nonclinical staff) who participated in planning and/or implementing pilot interventions.

Main Findings: Barriers to successful implementation related primarily to the intervention process and secondarily to characteristics of the intervention context. Interview responses indicated that planning, including identification of resources and assessment of potential barriers and facilitators, was a critical and universally underutilized step in the intervention process.

Conclusions: Organized team process, documented plans for intervention activities, and ongoing evaluation are essential for sustaining intervention activities. A top priority for facilitating interventions should be the development of educational materials, such as “how to” guides, that teach intervention teams how to anticipate barriers and make plans to address them, as well as identifying and fostering local experts in planning and implementing interventions.
In Vitro Interactions between Amphotericin B, Itraconazole, and Flucytosine against 21 Clinical
Aspergillus
Isolates Determined by Two Drug Interaction Models
Authors: Te Dorsthorst D. T. A. , Verweij P. E. , Meis J. F. G. M. , Punt N. C. , Mouton J. W.
Published: May 2004

Combination therapy of flucytosine (5FC) with other antifungal agents could be of use for the treatment of invasive aspergillosis. However, interpretation of the results of in vitro interactions is problematic. The fractional inhibitory concentration (FIC) index is the most commonly used method, but it has several major drawbacks in characterizing antifungal drug interaction. Alternatively, a response surface approach using the concentration-effect relationship over the whole concentration range instead of just the MIC can be used. We determined the in vitro interactions between amphotericin B (AMB), itraconazole, and 5FC against 21
Aspergillus
isolates with a broth microdilution checkerboard method that employs the dye MTT [3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2
H
-tetrazolium bromide]. FIC indices based on three different MIC endpoints (MIC-0, MIC-1, and MIC-2) and the interaction coefficient alpha were determined, the latter by estimation from the response surface approach described by Greco et al. (W. R. Greco, G. Bravo, and J. C. Parsons, Pharmacol. Rev. 47:331-385, 1995). The value obtained for the FIC index was found to be dependent on the MIC endpoint used and could be either synergistic, indifferent, or antagonistic. The response surface approach gave more consistent results. Of the three combinations tested, the AMB-5FC combination was the most potent in vitro against
Aspergillus
spp. We conclude that the use of the response surface approach for the interpretation of in vitro interaction studies of antifungals may be helpful in order to predict the nature and intensity of the drug interaction. However, the correlation of these results with clinical outcome remains difficult and needs to be further investigated.
Effects of Voriconazole on
Cryptococcus neoformans
Authors: van Duin David , Cleare Wendy , Zaragoza Oscar , Casadevall Arturo , Nosanchuk Joshua D.
Published: May 2004

Voriconazole is a broad-spectrum triazole that offers extended activity against molds and yeasts that are not susceptible to earlier azole-type drugs. Recent studies indicate that melanization can severely reduce the susceptibility of certain antifungal drugs, but there is no information as to whether voriconazole is vulnerable to this effect. The activity of voriconazole on
C. neoformans
was assessed by MIC analysis and time-kill assays for melanized and nonmelanized cells. Cell morphology, capsule release, and phagocytosis of
C. neoformans
were studied in the presence or absence of subinhibitory concentrations of voriconazole. Voriconazole was fungicidal at concentrations of ≥8 μg/ml in vitro against the strains of
C. neoformans
examined, and its efficacy was not diminished by melanization. Cells grown in subinhibitory concentrations of voriconazole had smaller cellular and capsular volumes than cells grown in the absence of drug. The induction of the capsule by serum was not affected by voriconazole. Cells grown in subinhibitory concentrations of voriconazole released their capsule and were phagocytosed at rates comparable with yeast grown without the antifungal. The high activity of voriconazole against both melanized and nonmelanized cells results suggest that voriconazole may be a particularly valuable drug for cryptococcosis.
In Vitro Activities of Garenoxacin and Levofloxacin against
Chlamydia pneumoniae
Are Not Affected by Presence of
Mycoplasma
DNA
Authors: Smith Raymond P. , Baltch Aldona L. , Ritz William J. , Carpenter Andrea N. , Halse Tanya A. , Bopp Lawrence H.
Published: May 2004

We studied 20
Chlamydia pneumoniae
isolates obtained from respiratory sites and atheroma tissue of patients from various geographic areas to determine the susceptibilities of these isolates to a new des-fluoroquinolone, garenoxacin, and to levofloxacin. In addition, we assessed the cultures with these isolates by PCR for the presence or absence of
Mycoplasma
sp. DNA. Both the MIC at which 90% of isolates are inhibited (MIC
90
) and the minimal bactericidal concentration at which 90% of isolates are killed (MBC
90
) for garenoxacin were 0.06 μg/ml, and both the MIC
90
and the MBC
90
for levofloxacin were 2.0 μg/ml. The activity of garenoxacin against
C. pneumoniae
was 32-fold greater than that of levofloxacin.
Mycoplasma
sp. DNA was detected by PCR in 17 of 20 cultures.
Mycoplasma
amplicons from five
Mycoplasma
DNA-positive
C. pneumoniae
cultures were sequenced and found to represent four
Mycoplasma
species. Our data demonstrate that
C. pneumoniae
cultures frequently contain
Mycoplasma
DNA and that its presence in
C. pneumoniae
cultures does not appear to affect the susceptibility results for the two fluoroquinolones that we tested.
Effects of Efflux Transporter Genes on Susceptibility of
Escherichia coli
to Tigecycline (GAR-936)
Authors: Hirata Takahiro , Saito Asami , Nishino Kunihiko , Tamura Norihisa , Yamaguchi Akihito
Published: May 2004

The activity of tigecycline, 9-(
t
-butylglycylamido)-minocycline, against
Escherichia coli
KAM3 (
acrB
) strains harboring plasmids encoding various tetracycline-specific efflux transporter genes,
tet
(B),
tet
(C), and
tet
(K), and multidrug transporter genes,
acrAB
,
acrEF
, and
bcr
, was examined. Tigecycline showed potent activity against all three Tet-expressing, tetracycline-resistant strains, with the MICs for the strains being equal to that for the host strain. In the Tet(B)-containing vesicle study, tigecycline did not significantly inhibit tetracycline efflux-coupled proton translocation and at 10 μM did not cause proton translocation. This suggests that tigecycline is not recognized by the Tet efflux transporter at a low concentration; therefore, it exhibits significant antibacterial activity. These properties can explain its potent activity against bacteria with a Tet efflux resistance determinant. Tigecycline induced the Tet(B) protein approximately four times more efficiently than tetracycline, as determined by Western blotting, indicating that it is at least recognized by a TetR repressor. The MICs for multidrug efflux proteins AcrAB and AcrEF were increased fourfold. Tigecycline inhibited active ethidium bromide efflux from intact
E. coli
cells overproducing AcrAB. Therefore, tigecycline is a possible substrate of AcrAB and its close homolog, AcrEF, which are resistance-modulation-division-type multicomponent efflux transporters.
Regulatory Regions of
smeDEF
in
Stenotrophomonas maltophilia
Strains Expressing Different Amounts of the Multidrug Efflux Pump SmeDEF
Authors: Sanchez Patricia , Alonso Ana , Martinez Jose L.
Published: May 2004

The
smeT-smeDEF
region and the
smeT
gene, which encodes
the
smeDEF
repressor, are highly polymorphic. Few changes in
smeT
might be associated with
smeDEF
overexpression.
The results obtained with cellular extracts suggest that mutant SmeT
proteins cannot bind to the operator and that other transcription
factors besides SmeT are involved in the regulation of
smeDEF
expression.
Nosocomial Outbreak of Extended-Spectrum β-Lactamase SHV-5-Producing Isolates ofPseudomonas aeruginosain Athens, Greece
Authors: Poirel Laurent , Lebessi Evangelia , Castro Marisa , Fèvre Cindy , Foustoukou Maria , Nordmann Patrice
Published: May 2004

Seven nonrepetitivePseudomonas aeruginosaisolates producing the clavulanic acid-inhibited extended-spectrum β-lactamase SHV-5 were isolated in the same hospital in Athens, Greece, from 1998 to 2002. All isolates except one were clonally related, and theblaSHV-5gene was chromosomally located. This study underlined that this gene, which is widespread inEnterobacteriaceaein Greece, may disseminate also inP. aeruginosa.
ELVIRA HSV, a Yield Reduction Assay for Rapid Herpes Simplex Virus Susceptibility Testing
Authors: Stránská Růžena , Schuurman Rob , Scholl David R. , Jollick Joseph A. , Shaw Carl J. , Loef Caroline , Polman Merjo , van Loon Anton M.
Published: May 2004

A colorimetric yield reduction assay, ELVIRA (enzyme-linked virus inhibitor reporter assay) HSV, was developed to determine the antiviral drug susceptibilities of herpes simplex virus (HSV). It uses an HSV-inducible reporter cell line. This simple and rapid assay has an objective readout, low inoculum size, and good reproducibility. The results correlate well with those of the plaque reduction assay.