bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying Genes Associated with a Quantitative Trait or Quantitative Trait Locus via Selective Transcriptional Profiling
Authors: Wang Dong , Nettleton Dan
Published: December 2005

Summary Genetical genomics is an approach that blends the mapping of quantitative trait loci (QTL) with microarray analysis. The approach can be used to identify associations between the allelic state of a genomic region and a gene's transcript abundance. However, the large number of microarrays required for adequate power results in high material and labor costs that prevent wide adoption of the genetical genomics strategy outside of some well‐funded laboratories. We present a method called selective transcriptional profiling that involves selecting an optimal subset of individuals to microarray from a larger set of individuals for which relatively inexpensive quantitative trait and molecular marker data are available. We show how to use microarray data from the selected individuals, along with the trait and marker data from all individuals, to identify genes whose transcript abundance is associated with a quantitative trait of interest through linkage to a trait QTL or correlation with the trait. Our methods for selection and analysis are derived within a missing data framework.y
A Bayesian Mixture Model for Partitioning Gene Expression Data
Authors: Zhou Chuan , Wakefield Jon
Published: December 2005

Summary In recent years there has been great interest in making inference for gene expression data collected over time. In this article, we describe a Bayesian hierarchical mixture model for partitioning such data. While conventional approaches cluster the observed data, we assume a nonparametric, random walk model, and partition on the basis of the parameters of this model. The model is flexible and can be tuned to the specific context, respects the order of observations within each curve, acknowledges measurement error, and allows prior knowledge on parameters to be incorporated. The number of partitions may also be treated as unknown, and inferred from the data, in which case computation is carried out via a birth–death Markov chain Monte Carlo algorithm. We first examine the behavior of the model on simulated data, along with a comparison with more conventional approaches, and then analyze meiotic expression data collected over time on fission yeast genes.
Polydesigns and Causal Inference
Authors: Li Fan , Frangakis Constantine E.
Published: December 2005

Summary In an increasingly common class of studies, the goal is to evaluate causal effects of treatments that are only partially controlled by the investigator. In such studies there are two conflicting features: (1) a model on the full cohort design and data can identify the causal effects of interest, but can be sensitive to extreme regions of that design's data, where model specification can have more impact; and (2) models on a reduced design (i.e., a subset of the full data), for example, conditional likelihood on matched subsets of data, can avoid such sensitivity, but do not generally identify the causal effects. We propose a framework to assess how inference is sensitive to designs by exploring combinations of both the full and reduced designs. We show that using such a “polydesign” framework generates a rich class of methods that can identify causal effects and that can also be more robust to model specification than methods using only the full design. We discuss implementation of polydesign methods, and provide an illustration in the evaluation of a needle exchange program.
Sensitivity Analyses Comparing Outcomes Only Existing in a Subset Selected Post‐Randomization, Conditional on Covariates, with Application to HIV Vaccine Trials
Authors: Shepherd Bryan E. , Gilbert Peter B. , Jemiai Yannis , Rotnitzky Andrea
Published: December 2005

Summary In many experiments, researchers would like to compare between treatments and outcome that only exists in a subset of participants selected after randomization. For example, in preventive HIV vaccine efficacy trials it is of interest to determine whether randomization to vaccine causes lower HIV viral load, a quantity that only exists in participants who acquire HIV. To make a causal comparison and account for potential selection bias we propose a sensitivity analysis following the principal stratification framework set forth by Frangakis and Rubin (2002, Biometrics58, 21–29). Our goal is to assess the average causal effect of treatment assignment on viral load at a given baseline covariate level in the always infected principal stratum (those who would have been infected whether they had been assigned to vaccine or placebo). We assume stable unit treatment values (SUTVA), randomization, and that subjects randomized to the vaccine arm who became infected would also have become infected if randomized to the placebo arm (monotonicity). It is not known which of those subjects infected in the placebo arm are in the always infected principal stratum, but this can be modeled conditional on covariates, the observed viral load, and a specified sensitivity parameter. Under parametric regression models for viral load, we obtain maximum likelihood estimates of the average causal effect conditional on covariates and the sensitivity parameter. We apply our methods to the world's first phase III HIV vaccine trial.
Response‐Adaptive Randomization for Clinical Trials with Continuous Outcomes
Authors: Zhang Lanju , Rosenberger William F.
Published: December 2005

Summary We provide an explicit asymptotic method to evaluate the performance of different response‐adaptive randomization procedures in clinical trials with continuous outcomes. We use this method to investigate four different response‐adaptive randomization procedures. Their performance, especially in power and treatment assignment skewing to the better treatment, is thoroughly evaluated theoretically. These results are then verified by simulation. Our analysis concludes that the doubly adaptive biased coin design procedure targeting optimal allocation is the best one for practical use. We also consider the effect of delay in responses and nonstandard responses, for example, Cauchy distributed response. We illustrate our procedure by redesigning a real clinical trial.
Orthonormal Transform to Decompose the Variance of a Life‐History Trait across a Phylogenetic Tree
Authors: Ollier S. , Couteron P. , Chessel D.
Published: December 2005

SummaryIn recent years, there has been an increased interest in studying the variability of a quantitative life‐history trait across a set of species sharing a common phylogeny. However, such studies have suffered from an insufficient development of statistical methods aimed at decomposing the trait variance with respect to the topological structure of the tree. Here we propose a new and generic approach that expresses the topological properties of the phylogenetic tree via an orthonormal basis, which is further used to decompose the trait variance. Such a decomposition provides a structure function, referred to as an “orthogram,” which is relevant to characterize in both graphical and statistical aspects the dependence of trait values on the topology of the tree (“phylogenetic dependence”). We also propose four complementary test statistics to be computed from orthogram values that help to diagnose both the intensity and the nature of phylogenetic dependence. The relevance of the method is illustrated by the analysis of three phylogenetic data sets, drawn from the literature and typifying contrasted levels and aspects of phylogenetic dependence. Freely available routines which have been programmed in the R framework are also proposed.
The Clustering of Regression Models Method with Applications in Gene Expression Data
Authors: Qin Li‐Xuan , Self Steven G.
Published: December 2005

Summary Identification of differentially expressed genes and clustering of genes are two important and complementary objectives addressed with gene expression data. For the differential expression question, many “per‐gene” analytic methods have been proposed. These methods can generally be characterized as using a regression function to independently model the observations for each gene; various adjustments for multiplicity are then used to interpret the statistical significance of these per‐gene regression models over the collection of genes analyzed. Motivated by this common structure of per‐gene models, we proposed a new model‐based clustering method—the clustering of regression models method, which groups genes that share a similar relationship to the covariate(s). This method provides a unified approach for a family of clustering procedures and can be applied for data collected with various experimental designs. In addition, when combined with per‐gene methods for assessing differential expression that employ the same regression modeling structure, an integrated framework for the analysis of microarray data is obtained. The proposed methodology was applied to two microarray data sets, one from a breast cancer study and the other from a yeast cell cycle study.
Bayesian Covariance Selection in Generalized Linear Mixed Models
Authors: Cai Bo , Dunson David B.
Published: December 2005

SummaryThe generalized linear mixed model (GLMM), which extends the generalized linear model (GLM) to incorporate random effects characterizing heterogeneity among subjects, is widely used in analyzing correlated and longitudinal data. Although there is often interest in identifying the subset of predictors that have random effects, random effects selection can be challenging, particularly when outcome distributions are nonnormal. This article proposes a fully Bayesian approach to the problem of simultaneous selection of fixed and random effects in GLMMs. Integrating out the random effects induces a covariance structure on the multivariate outcome data, and an important problem that we also consider is that of covariance selection. Our approach relies on variable selection‐type mixture priors for the components in a special Cholesky decomposition of the random effects covariance. A stochastic search MCMC algorithm is developed, which relies on Gibbs sampling, with Taylor series expansions used to approximate intractable integrals. Simulated data examples are presented for different exponential family distributions, and the approach is applied to discrete survival data from a time‐to‐pregnancy study.
Nonparametric Inference for Local Extrema with Application to Oligonucleotide Microarray Data in Yeast Genome
Authors: Song Peter X.‐K. , Gao Xin , Liu Rui , Le Wen
Published: December 2005

Summary Identifying local extrema of expression profiles is one primary objective in some cDNA microarray experiments. To study the replication dynamics of the yeast genome, for example, local peaks of hybridization intensity profiles correspond to putative replication origins. We propose a nonparametric kernel smoothing (NKS) technique to detect local hybridization intensity extrema across chromosomes. The novelty of our approach is that we base our inference procedures on equilibrium points, namely those locations at which the first derivative of the intensity curve is zero. The proposed smoothing technique provides both point and interval estimation for the location of local extrema. Also, this technique can be used to test for the hypothesis of either one or multiple suspected locations being the true equilibrium points. We illustrate the proposed method on a microarray data set from an experiment designed to study the replication origins in the yeast genome, in that the locations of autonomous replication sequence (ARS) elements are identified through the equilibrium points of the smoothed intensity profile curve. Our method found a few ARS elements that were not detected by the current smoothing methods such as the Fourier convolution smoothing.
Developmental psychopathology in adolescence: findings from a Swiss study – the NAPE Lecture 2005
Authors: Steinhausen H.‐C.
Published: December 2005

Objective:  Presentations of selective findings coming from the Zurich Adolescent Psychology and Psychopathology Study with two major aims: i) the study of the prevalence, course, and correlates of mental disorders in adolescence, and ii) the study of the determinants and processes of mental disorders in adolescence.

Method:  A representative sample of n = 1964 children and adolescents was studied in the canton of Zurich in 1994. Additional waves of data collection took place in 1997 and 2000/2001. Mean ages at these three assessments were 13, 16, and 20 years. Each wave contained a two‐stage procedure of assessment with screening by questionnaires and consecutive interviewing. The main constructs used were general and specific measures of psychopathology, life events, coping styles, self‐related cognitions, and quality of the social network.

Results:  Prevalence rates of any mental disorder in school‐age at the time of assessment was 22.5% fitting into a transcultural range of 18–26% based on DSM‐III‐R criteria. Furthermore, the derivation and validation of a four‐group adolescent drinker typology was demonstrated. Additionally, the prevalence and continuity of functional‐somatic symptoms from adolescence to young adulthood was shown. Another piece of the research tested for the identification of risk, compensatory, vulnerability, and protective factors influencing behaviour problems and found remarkably different frequencies across the four types of moderating factors.

Conclusion:  The presented findings provide further understanding of the developmental psychology and psychopathology of adolescence and the service, intervention, and prevention needs of this age‐group.
Activity Intolerance and Impaired Physical Mobility in Elders
Authors: Hur Hea‐Kung , Park So‐Mi , Kim So‐Sun , Storey Margaret J. , Kim Gi‐Yon
Published: December 2005

PURPOSE.  To clarify the use of two nursing diagnoses, activity intolerance and impaired physical mobility, with elderly patients.

METHOD.  Ninety‐two elders from a long‐term care facility in Wonju, Korea. A checklist developed by the researchers was used for data collection.

FINDINGS.  Defining characteristics from this study related to psychological components of activity intolerance are significant in differentiating between the two diagnoses. Using a decision‐making tree based on data from this study, each nursing diagnosis can be correctly identified.

CONCLUSIONS.  The results of this study are significant in broadening the defining characteristics to be used in differentiating between two nursing diagnoses.

PRACTICE IMPLICATIONS.  Clarification of nursing diagnoses serves to direct students and nurses to choosing appropriate interventions.
Nursing Diagnoses Identified During Parent Group Meetings in a Neonatal Intensive Care Unit
Authors: Do Vale Ianê Nogueira , de Souza Sandra Regina , Carmona Elenice Valentim
Published: December 2005

PURPOSE.  To identify nursing diagnoses in the reports of parents obtained during parent support group meetings in a neonatal intensive care unit.

METHODS.  An explorative descriptive study using records obtained during 29 meetings over a period of 11 months with parents and family members.

FINDINGS.  Six NANDA‐approved nursing diagnoses were identified from parent group data: fear, risk for impaired parent/infant attachment, parental role conflict, risk for ineffective breastfeeding, impaired home maintenance, and risk for caregiver role strain. Diagnoses were not validated with parents.

DISCUSSION.  Support groups helped the parents express their thoughts and feelings and provided nurses with opportunities to identify nursing diagnoses and interventions. The identification of nursing diagnoses showed that nursing interventions that are focused on improved parent outcomes should be implemented for parents and other family members.

IMPLICATIONS.  Nursing care in neonatal units should focus on interventions for parents and other family members in addition to providing the necessary care of newborns.
Viewpoint
Authors: Kelley Jane H. , Weber Janet , Sprengel Ann
Published: December 2005

PURPOSE.  To propose the addition of a fifth domain, Administrative, to the Taxonomy of Nursing Practice, and to introduce the related concept of organization nursing diagnoses.

DATA SOURCES.  The Taxonomy of Nursing Practice, organizational and nursing management/leadership literature, experience of the authors.

DATA SYNTHESIS.  Analyzing the concept of a taxonomy to capture nursing practice revealed an omission of the management/leadership roles assumed by nurses in organizational, nurse manager, and staff nurse practice levels. To incorporate this administrative practice, an additional domain, Administrative, was developed. Nursing diagnoses were oriented to the organization as client, hence the addition of organization nursing diagnoses.

CONCLUSIONS.  Including an Administrative Domain in the Taxonomy of Nursing Practice will cover the scope of nursing practice and will provide a basis for developing the diagnoses for which nurses are accountable within organizations.

IMPLICATIONS FOR PRACTICE.  Nurses’ contributions to healthcare organizational function and their effect on patient care outcomes will be made more explicit and can more readily be measured with terminology that captures the nursing administrative roles at three levels of practice.
Variant of estimation method of above‐ground plant biomass in grassland with gamma model 1. Use of an electronic capacitance probe
Authors: Tsutsumi Michio , Itano Shiro
Published: December 2005

We propose the following method for estimating above‐ground plant biomass (biomass, hereafter) in grassland as a variant of Shiyomi's (1991) second method and test its accuracy of estimation. The method proceeds thus: (i) place a given number of quadrats in the grassland of interest; (ii) an electronic capacitance probe is used to provide corrected meter reading (CMR) values within each quadrat; (iii) two sampling points with a biomass of C1 g and C2 g based on CMR values are selected to allow subdivision into three approximately equal frequency classes; (iv) quadrats are placed and CMR values are measured at the two sampling points; (v) the vegetation within the two quadrats is harvested and these samples weighed after drying; (vi) each quadrat (placed in step [i]) is divided into three categories based on the CMR values – less than C1 g, more than C1 g and less than C2 g, and more than C2 g; and (vii) biomass is estimated from the data obtained by these procedures using the gamma model. Test results suggest that the accuracy of biomass estimation of our method is equivalent to that of the cutting method using several quadrats. Thus, we propose the use of an electronic capacitance probe to rank pasture biomass and the selection of only two quadrat sites for cutting as this offers labor‐saving advantages over current methods.
The effect of temperature and daylength on heading in tetraploid cultivars of rhodesgrass (Chloris gayana Kunth)
Authors: Tarumoto Isao , Sato Hiroyasu , Horibata Toshizo
Published: December 2005

The present study was conducted to clarify the effect of temperature and daylength on heading in tetraploid cultivars of rhodesgrass (Chloris gayana Kunth). Five cultivars, Tochiraku‐kei (2χ), Fords Katambora (2χ), Callide (4χ), Masaba (4χ) and Pokot (4χ), were planted on three dates at 1‐month intervals (4 May, 4 June and 4 July) in three of the Ministry of Agriculture, Forestry and Fisheries research institutions in Ishigaki (Tropical Agriculture Research Center), Nishigoshi (Kyushu National Agricultural Experiment Station) and Nishinasuno (National Grassland Research Institute) in 1978. Three tetraploid cultivars were planted on three dates at 1‐month intervals (4 May, 4 June and 4 July) under four daylength‐treatments of natural daylength (ND), 12 h daylength [12 h], ND/12 h and 12 h/ND, and changed daylength at the eighth leaf stage, in Nishinasuno in 1978. Under natural daylength, although heading was not observed for Masaba and Pokot, heading was observed in all plots for Tochiraku‐kei, Fords Katambora and Callide, and their days to heading (DH) linearly decreased with increases in daily mean temperature (DMT). The result indicated that, under natural daylength in summer, temperature was a major factor in determining DH in tetraploid Callide, which was the same as in diploid rhodesgrass cultivars. Callide reached heading under all four daylength treatments. However, Masaba and Pokot reached heading only under 12 h and ND/12 h treatments, suggesting that Masaba and Pokot have qualitative sensitivity to photoperiods that operate after the ninth leaf stage. These findings would be useful in tetraploid rhodesgrass for estimating foliage harvesting time in the field and for conducting cross‐pollination in a greenhouse during winter.
Evaluating the adaptability of herbage species to environmental variation through a long‐term grazing experiment
Authors:   Yiruhan, Shiyomi Masae , Takahashi Shigeo , Okubo Tadakatsu , Akiyama Tsuyoshi , Koyama Nobuaki , Tsuiki Mikinori
Published: December 2005

Mixtures of orchard grass, perennial ryegrass, tall fescue, redtop, Kentucky bluegrass and white clover were sown in the autumn of 1973. Two 8‐year grazing experiments were carried out at the National Grassland Research Institute (Nasushiobara, Tochigi, Japan) to determine the effects of grazing intensity and nitrogen levels on the pasture ecosystem: two different grazing intensities (1974–1981) and two different nitrogen levels (1982–1989). Large temporal and spatial variations in phytomass were observed in both experiments. To clarify the adaptability of the phytomass of the herbage species to environmental variations in year, season and treatments, we re‐examined the data obtained in these two experiments using a Finlay‐Wilkinson analysis. Orchard grass and tall fescue achieved significantly higher phytomass in a more fertile environment in that they showed a high adaptability to environmental variation. Redtop and Kentucky bluegrass showed an increase in phytomass proportional to environmental improvement. The phytomass performances of perennial ryegrass and white clover were almost independent of environmental variation in that their adaptability was low. Finally, Zoysia japonica and weeds such as Pennisetum alopecuroides and Digitaria adscendens, which were invaders from the surrounding areas to the experimental site, were not observed in the pasture during the first 8‐year period; during the second 8‐year period, they showed moderate adaptability.
Heritability estimates in contrasting environments as influenced by the adaptation level of barley germ plasm
Authors: Al‐Yassin A. , Grando S. , Kafawin O. , Tell A. , Ceccarelli S.
Published: December 2005

Low heritability estimates in marginal or stress environments have often been used as one of the main justification for conducting selection work in environments with optimum or near‐optimum conditions for plant growth and grain yield. In this study, we have examined the relationships between grain yield and broad‐sense heritability in four groups of recombinant inbred lines (RILs) obtained from four barley crosses derived from parents differing in adaptation to stress. The RILs and the parents were grown in 13 combinations of years and locations (environments) in Syria and Jordan. Grain yields ranged from about 30 kg ha−1 to nearly 4000 kg ha−1 and genotype × environment interactions explained about half of the total variance for environmentally standardised data. Broad‐sense heritability in the individual year–location combinations varied from 0 to 0.68 and both the simple correlation and the rank correlation coefficients between grain yield and heritability were not significant. Genotype × years within individual locations, which measures the repeatability of a location in discriminating between genotypes, was also independent from the yield level, confirming that low‐yielding locations can be reliable selection environments. Also, there was no relationship between the type of cross and the magnitude of heritability in the various environments, but, as expected, the magnitude of heritability was significantly associated with the genetic distance between the parents. It is concluded that, holding all other factors affecting response to selection constant, concerns about the magnitude of heritability at low‐yielding locations are not justified and should not prevent them from being used as selection sites.
Genetic diversity of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) populations and presence of the B biotype and a non‐B biotype that can induce silverleaf symptoms in squash, in Uganda
Authors: Sseruwagi P. , Legg J.P. , Maruthi M.N. , Colvin J. , Rey M.E.C. , Brown J.K.
Published: December 2005

The extent of genetic variability and host‐plant distribution of Bemisia tabaci (Gennadius) genotypes colonising cultivated and uncultivated plant species occurring adjacent to cassava fields in selected cassava‐producing areas of Uganda in 2003/04 were investigated using the mitochondrial cytochrome oxidase I (mtCOI) gene as the molecular marker. Eight genotype clusters, Ug1–Ug8, which are supported by high bootstrap values (≥80), at 3–18% nt divergence, were revealed among the collective Ugandan B. tabaci populations. Ug1 and Ug2 (both cassava‐associated) and Ug8 (sweetpotato‐associated) have been reported previously in Uganda. Ug3 was genetically dissimilar to B. tabaci described elsewhere and colonised a single species, Ocimum gratissimum. Ug4–Ug7 formed four closely related subclusters (93–97% nt identity) and diverged by 15–18% from Ug1, Ug2, Ug3 and Ug8, respectively. Ug4 had as its closest relatives (at 97–99% nt identity) the Ivory Coast okra biotype, whereas genotypes Ug5 and Ug6 had as their closest relatives (at 95–99% and 99% nt identity, respectively) the Mediterranean–North Africa–Middle East (MED‐NAFR‐ME) biotypes, which also include the well‐studied B and Q biotypes. Ug7 was closely related (at 98–99% nt identity) to biotype Ms from the Reunion Island in the Indian Ocean. Ug4 colonised Cucurbita pepo, Cucurbita sativus, Leonotis nepetifolia and Pavonia urens, while Ug7 colonised Commelina benghalensis, Gossypium hirsutum and Phaseolus vulgaris. Ug6, the B‐biotype‐like genotype colonised Abelmoschus esculentus and C. benghalensis only. None of Ug4–Ug7 genotypes was found associated with, or colonising, cassava or sweetpotato plants. In addition to colonising sweetpotato, the Ug8 genotypes colonised Lycopersicon esculentum and L. nepetifolia. Ug6 and Ug7, both members of the B biotype/B‐like cluster, induced silverleaf symptoms on Cucurbita sp. The discovery of five previously identified B. tabaci genotype clusters, Ug3–Ug7, in Uganda, among which are some of the world's most economically important biotypes, namely B and Q, is particularly significant in the spread of geminiviruses with devastating effects to crop production in Africa.
Prospects for crop production under drought: research priorities and future directions
Authors: Parry M.A.J. , Flexas J. , Medrano H.
Published: December 2005

The efficient use of water supplies requires a systems approach that encompasses all aspects of making water available and its use within society that must recognise global issues. Increasing the efficiency of water use within agricultural systems is an essential priority in many regions including the Mediterranean. This review examines the research priorities, the prospects for crop and soil management and plant breeding and biotechnology that are needed to achieve high stable yield under drought in the Mediterranean. Research must combine the latest genomics resources including quantitative genetics, genomics and biomathematics with an ecophysiological understanding of the interactions between crop plant genotypes and the growing environment to better inform crop improvement.
Rheopheresis in Patients with Critical Limb Ischemia––Results of an Open Label Prospective Pilot Trial
Authors: Klingel Reinhard , Erdtracht Bernard , Gauss Victor , Piazolo Andreas , Mausfeld‐Lafdhiya Patrick , Diehm Curt
Published: December 2005

Abstract:  Rheopheresis is a specifically designed application of double filtration plasmapheresis, for extracorporeal treatment of microcirculatory disorders. Safety and efficacy of Rheopheresis for wound healing and skin oxygenation were investigated in patients with critical limb ischemia. Twelve patients of Fontaine stage III‐IV were treated with a series of 10 Rheopheresis sessions over 17 weeks. Transcutaneous oxygen pressure (tcpO2) and ankle‐brachial index (ABI) were repeatedly determined to monitor the effects of the Rheopheresis treatment series on microcirculation and skin blood flow. Laboratory parameters of blood rheology were measured in addition to safety parameters and course of the pain syndrome was documented. In four patients (baseline Fontaine stage III) Rheopheresis was associated with an improvement of Fontaine stage, a pronounced increase in tcpO2 and complete regression of the rest pain. As an adjunct therapeutic option, Rheopheresis may preserve a functional lower extremity, delay amputation or reduce the extent of amputation.
Therapeutic Apheresis—State of the Art in the Year 2005
Authors: Bosch Thomas
Published: December 2005

Abstract:  Therapeutic apheresis is an extracorporeal blood purification method for the treatment of diseases in which pathological proteins or cells have to be eliminated. Selective plasma processing is more efficient in pathogen removal than unselective plasma exchange and does not require a substitution fluid like albumin. This overview presents the various selective devices for the treatment of plasma (plasmapheresis) and blood cells (leukocyte apheresis). Prospective randomized trials were performed for the treatment of age‐related macular degeneration (Rheopheresis), sudden hearing loss (heparin‐induced lipoprotein precipitation [HELP]), rheumatoid arthritis (Prosorba), dilative cardiomyopathy (Ig‐Therasorb, Immunosorba), acute‐on‐chronic liver failure (molecular adsorbent recirculating system [MARS]), and ulcerative colitis (Cellsorba). Prospective non‐randomized controlled trials were carried out treating hypercholesterolemia (Liposorber) and crossmatch‐positive recipients before kidney transplantation (Immunosorba). Uncontrolled studies were done for ABO‐incompatibility in living donor kidney transplantation (KT) (Glycosorb), acute humoral rejection after KT (Immunosorba) and acute liver failure (Prometheus). According to the 2002 International Apheresis Registry covering 11428 sessions in 811 patients, 79% of the patients showed an improvement of their condition by apheresis and only a few sessions were fraught with adverse effects (AE). The major AE were blood access difficulties (3.1%) and hypotension (1.6%). In summary, therapeutic apheresis is a safe and effective procedure for the treatment of diseases refractory to drug therapy.
Long-Term Modulation of Electrical Synapses in the Mammalian Thalamus
Authors: Landisman Carole E. , Connors Barry W.
Published: December 2005

Electrical synapses are common between inhibitory neurons in the mammalian thalamus and neocortex. Synaptic modulation, which allows flexibility of communication between neurons, has been studied extensively at chemical synapses, but modulation of electrical synapses in the mammalian brain has barely been examined. We found that the activation of metabotropic glutamate receptors, via endogenous neurotransmitter or by agonist, causes long-term reduction of electrical synapse strength between the inhibitory neurons of the rat thalamic reticular nucleus.
Drought, Snails, and Large-Scale Die-Off of Southern U.S. Salt Marshes
Authors: Silliman Brian R. , van de Koppel Johan , Bertness Mark D. , Stanton Lee E. , Mendelssohn Irving A.
Published: December 2005

Salt marshes in the southeastern United States have recently experienced massive die-off, one of many examples of widespread degradation in marine and coastal ecosystems. Although intense drought is thought to be the primary cause of this die-off, we found snail grazing to be a major contributing factor. Survey of marsh die-off areas in three states revealed high-density fronts of snails on die-off edges at 11 of 12 sites. Exclusion experiments demonstrated that snails actively converted marshes to exposed mudflats. Salt addition and comparative field studies suggest that drought-induced stress and grazers acted synergistically and to varying degrees to cause initial plant death. After these disturbances, snail fronts formed on die-off edges and subsequently propagated through healthy marsh, leading to cascading vegetation loss. These results, combined with model analyses, reveal strong interactions between increasing climatic stress and grazer pressure, both potentially related to human environmental impacts, which amplify the likelihood and intensity of runaway collapse in these coastal systems.
Multistep Synthesis of a Radiolabeled Imaging Probe Using Integrated Microfluidics
Authors: Lee Chung-Cheng , Sui Guodong , Elizarov Arkadij , Shu Chengyi Jenny , Shin Young-Shik , Dooley Alek N. , Huang Jiang , Daridon Antoine , Wyatt Paul , Stout David , Kolb Hartmuth C. , Witte Owen N. , Satyamurthy Nagichettiar , Heath James R. , Phelps Michael E. , Quake Stephen R. , Tseng Hsian-Rong
Published: December 2005

Microreactor technology has shown potential for optimizing synthetic efficiency, particularly in preparing sensitive compounds. We achieved the synthesis of an [
18
F]fluoride-radiolabeled molecular imaging probe, 2-deoxy-2-[
18
F]fluoro-
d
-glucose ([
18
F]FDG), in an integrated microfluidic device. Five sequential processes—[
18
F]fluoride concentration, water evaporation, radiofluorination, solvent exchange, and hydrolytic deprotection—proceeded with high radio-chemical yield and purity and with shorter synthesis time relative to conventional automated synthesis. Multiple doses of [
18
F]FDG for positron emission tomography imaging studies in mice were prepared. These results, which constitute a proof of principle for automated multistep syntheses at the nanogram to microgram scale, could be generalized to a range of radiolabeled substrates.
Comment on "Characterization of Excess Electrons in Water-Cluster Anions by Quantum Simulations"
Authors: Verlet J. R. R. , Bragg A. E. , Kammrath A. , Cheshnovsky O. , Neumark D. M.
Published: December 2005

The conclusion by Turi
et al
. (Reports, 5 August 2005, p. 914) that all experimental spectral and energetic data on water-cluster anions point toward surface-bound electrons is overstated. Comparison of experimental vertical detachment energies with their calculated values for (H
2
O)
n
–
clusters with surface-bound and internalized electrons supports previous arguments that both types of clusters exist.
Response to Comment on "Characterization of Excess Electrons in Water-Cluster Anions by Quantum Simulations"
Authors: Turi László , Sheu Wen-Shyan , Rossky Peter J.
Published: December 2005

We reiterate that the conclusions of our original report are based on identifiable characteristic trends in several observables with cluster size. The numerical comparison between simulated and experimental vertical detachment energies emphasized by Verlet
et al
. reflect quantitative limitations of our atomistic model, but, in our opinion, do not undermine these conclusions.
Chitin Induces Natural Competence in
Vibrio cholerae
Authors: Meibom Karin L. , Blokesch Melanie , Dolganov Nadia A. , Wu Cheng-Yen , Schoolnik Gary K.
Published: December 2005

The mosaic-structured
Vibrio cholerae
genome points to the importance of horizontal gene transfer (HGT) in the evolution of this human pathogen. We showed that
V. cholerae
can acquire new genetic material by natural transformation during growth on chitin, a biopolymer that is abundant in aquatic habitats (e.g., from crustacean exoskeletons), where it lives as an autochthonous microbe. Transformation competence was found to require a type IV pilus assembly complex, a putative DNA binding protein, and three convergent regulatory cascades, which are activated by chitin, increasing cell density, and nutrient limitation, a decline in growth rate, or stress.
Developmental Plasticity in the Life History of a Prosauropod Dinosaur
Authors: Sander P. Martin , Klein Nicole
Published: December 2005

Long-bone histology indicates that the most common early dinosaur, the prosauropod
Plateosaurus engelhardti
from the Upper Triassic of Central Europe, had variable life histories. Although
Plateosaurus
grew at the fast rates typical for dinosaurs, as indicated by fibrolamellar bone, qualitative (growth stop) and quantitative (growth-mark counts) features of its histology are poorly correlated with body size. Individual life histories of
P. engelhardti
were influenced by environmental factors, as in modern ectothermic reptiles, but not in mammals, birds, or other dinosaurs.
Island Biogeography of Populations: An Introduced Species Transforms Survival Patterns
Authors: Schoener Thomas W. , Losos Jonathan B. , Spiller David A.
Published: December 2005

Population phenomena, which provide much of the underlying basis for the theoretical structure of island biogeography, have received little direct study. We determined a key population trait—survival—in the Bahamian lizard
Anolis sagrei
on islands with an experimentally introduced predatory lizard and on neighboring unmanipulated islands. On unmanipulated islands, survival declined with several variables, most notably vegetation height: The island with the shortest vegetation had nearly the highest survival recorded for any lizard. On islands with the introduced predator, which forages mostly on the ground,
A. sagrei
shifted to taller vegetation; unlike on unmanipulated islands, its survival was very low on islands with the shortest vegetation but was higher on the others. Thus, species introduction radically changed a resident species' relation of survival to a key island-biogeographical variable.
Direct Experimental Evidence of a Growing Length Scale Accompanying the Glass Transition
Authors: Berthier L. , Biroli G. , Bouchaud J.-P. , Cipelletti L. , Masri D. El , L'Hôte D. , Ladieu F. , Pierno M.
Published: December 2005

Understanding glass formation is a challenge, because the existence of a true glass state, distinct from liquid and solid, remains elusive: Glasses are liquids that have become too viscous to flow. An old idea, as yet unproven experimentally, is that the dynamics becomes sluggish as the glass transition approaches, because increasingly larger regions of the material have to move simultaneously to allow flow. We introduce new multipoint dynamical susceptibilities to estimate quantitatively the size of these regions and provide direct experimental evidence that the glass formation of molecular liquids and colloidal suspensions is accompanied by growing dynamic correlation length scales.
Two-Dimensional Science
Authors: Labinger Jay A.
Published: December 2005

Mad, Bad and Dangerous?
. The Scientist and the Cinema.
By Christopher Frayling
. Reaktion, London, 2005. 239 pp. $35, £19.95. ISBN 1-86189-255-1.

The author explores the ways scientists have been portrayed in films and what those portrayals suggest about society's ambivalent relation to science.
The Psychopathology and Treatment of Bipolar Disorder
Authors: Miklowitz David J. , Johnson Sheri L.
Published: December 2005

In this chapter we review research on the diagnosis, course, etiology, and pharmacological and psychosocial treatment of bipolar disorder (BD). BD is a highly recurrent and severe illness, with high rates of suicidality and functional impairment. The disorder is heritable and appears to share susceptibility genes with schizophrenia. It is characterized by dysregulation in the dopamine and serotonin systems and by pathology in the brain systems involved in regulating emotion. Psychosocial stressors, notably life events and familial expressed emotion, significantly influence the course of the illness in the context of these vulnerabilities. Findings of randomized clinical trials indicate that psychosocial interventions enhance long-term outcomes when added to pharmacotherapy. Much remains to be clarified about the interactive contributions of genetic, neurobiological, and psychosocial factors to the course of the disorder, and the moderators and mediators of treatment effects.
CONNECTING CHEMICAL DYNAMICS IN GASES AND LIQUIDS
Authors: Elles Christopher G. , Crim F. Fleming
Published: December 2005

▪ Abstract  Modern ultrafast spectroscopic techniques provide new opportunities to study chemical reaction dynamics in liquids and hold the possibility of obtaining much of the same detailed information available in gases. Vibrational energy transfer studies are the most advanced of the investigations and demonstrate that it is possible to observe state-specific pathways of energy flow within a vibrationally excited molecule (intramolecular vibrational relaxation) and into the surrounding solvent molecules (intermolecular energy transfer). Energy transfer in liquids and gases share many common aspects, but the presence of the solvent also alters the relaxation in both obvious and subtle ways. Photodissociation is amenable to similarly detailed study in liquids, and there are informative new measurements. Bimolecular reactions have received the least attention in state-resolved measurements in liquids, but the means to carry them much further now exist. Studying photodissociation and bimolecular reaction of molecules prepared with initial vibrational excitation in liquids is a realistic, but challenging, goal.
Nitric oxide attenuates IGF-I-induced aortic smooth muscle cell motility by decreasing Rac1 activity: essential role of PTP-PEST and p130cas
Authors: Ceacareanu Alice-Corina , Ceacareanu Bogdan , Zhuang Daming , Chang Yingzi , Ray Ramesh M. , Desai Leena , Chapman Kenneth E. , Waters Christopher M. , Hassid Aviv
Published: December 2005

Recent data support the hypothesis that reactive oxygen species (ROS) play a central role in the initiation and progression of vascular diseases. An important vasoprotective function related to the regulation of ROS levels appears to be the antioxidant capacity of nitric oxide (NO). We previously reported that treatment with NO decreases phosphotyrosine levels of adapter protein p130cas by increasing protein tyrosine phosphatase-proline, glutamate, serine, and threonine sequence protein (PTP-PEST) activity, which leads to the suppression of agonist-induced H2O2 elevation and motility in cultured rat aortic smooth muscle cells (SMCs). The present study was performed to investigate the hypotheses that 1) IGF-I increases the activity of the small GTPase Rac1 as well as H2O2 levels and 2) NO suppresses IGF-I-induced H2O2 elevation by decreasing Rac1 activity via increased PTP-PEST activity and dephosphorylation of p130cas. We report that IGF-I induces phosphorylation of p130cas and activation of Rac1 and that NO attenuates these effects. The effects of NO are mimicked by the overexpression of PTP-PEST or dominant-negative (dn)-p130cas and antagonized by the expression of dn-PTP-PEST or p130cas. We conclude that IGF-I induces rat aortic SMC motility by increasing phosphotyrosine levels of p130cas and activating Rac1 and that NO decreases motility by activating PTP-PEST, inducing dephosphorylating p130cas, and decreasing Rac1 activity. Decreased Rac1 activity lowers intracellular H2O2 levels, thus attenuating cell motility.
Regulation of the mouse organic solute transporter α-β, Ostα-Ostβ, by bile acids
Authors: Frankenberg Tamara , Rao Anuradha , Chen Frank , Haywood Jamie , Shneider Benjamin L. , Dawson Paul A.
Published: December 2005

The mechanisms responsible for bile acid regulation of mouse intestinal organic solute transporter α-β (Ostα-Ostβ) expression were investigated. Expression of Ostα-Ostβ mRNA was increased in cecum and proximal colon of cholic acid-fed mice and in chenodeoxycholate-treated mouse CT26 colon adenocarcinoma cells. Sequence analysis revealed potential cis-acting elements for farnesoid X receptor (FXR) and liver receptor homolog-1 (LRH-1) in the mouse Ostα and Ostβ promoters and reporter constructs containing Ostα and Ostβ 5′-flanking sequences were positively regulated by bile acids. Expression of a dominant-negative FXR, reduction of FXR with interfering small RNA (siRNA), or mutation of the potential FXR elements decreased Ostα and Ostβ promoter activity and abolished the induction by chenodeoxycolic acid. Negative regulation of the Ostα and Ostβ promoters by bile acids was mediated through LRH-1 elements. Ostα and Ostβ promoter activities were increased by coexpression of LRH-1 and decreased by coexpression of SHP. Mutation of the potential LRH-1 elements and siRNA-mediated reduction of LRH-1 expression decreased basal promoter activity. As predicted from the promoter analyses, ileal Ostα and Ostβ mRNA expressions were increased in wild-type mice administered the FXR agonist GW4064 and decreased in FXR-null mice. Immunoblotting analysis revealed that Ostα and Ostβ intestinal protein expressions correlated with mRNA expression. The mouse Ostα and Ostβ promoters are unusual in that they contain functional FXR and LRH elements, which mediate, respectively, positive and negative feedback regulation by bile acids. Although the positive regulatory pathway appears to be dominant, this arrangement provides a mechanism to finely titrate Ostα-Ostβ expression to the bile acid flux.
Dead space: Simplicity to complexity
Authors: Klocke Robert A.
Published: December 2005

This essay looks at the historical significance of an APS classic paper that is freely available online:

Fowler WS. Lung function studies. II. The respiratory dead space. Am J Physiol 154: 405-416, 1948. ( http://ajplegacy.physiology.org/cgi/reprint/154/3/405 ).
Effects of nasal continuous positive airway pressure and oxygen supplementation on norepinephrine kinetics and cardiovascular responses in obstructive sleep apnea
Authors: Mills Paul J. , Kennedy Brian P. , Loredo Jose S. , Dimsdale Joel E. , Ziegler Michael G.
Published: December 2005

Obstructive sleep apnea (OSA) is characterized by noradrenergic activation. Nasal continuous positive airway pressure (CPAP) is the treatment of choice and has been shown to effectively reduce elevated norepinephrine (NE) levels. This study examined whether the reduction in NE after CPAP is due to an increase in NE clearance and/or a decrease of NE release rate. Fifty CPAP-naive OSA patients with an apnea-hypopnea index >15 were studied. NE clearance and release rates, circulating NE levels, urinary NE excretion, and blood pressure and heart rate were determined before and after 14 days of CPAP, placebo CPAP (CPAP administered at ineffective pressure), or oxygen supplementation. CPAP led to a significant increase in NE clearance ( P ≤ 0.01), as well as decreases in plasma NE levels ( P ≤ 0.018) and daytime ( P < 0.001) and nighttime ( P < 0.05) NE excretion. NE release rate was unchanged with treatment. Systolic ( P ≤ 0.013) and diastolic ( P ≤ 0.026) blood pressure and heart rate ( P ≤ 0.014) were decreased in response to CPAP but not in response to oxygen or placebo CPAP treatment. Posttreatment systolic blood pressure was best predicted by pretreatment systolic blood pressure and posttreatment NE clearance and release rate ( P < 0.01). The findings indicate that one of the mechanisms through which CPAP reduces NE levels is through an increase in the clearance of NE from the circulation.