bluuebunny/crossref_metadata_2025 huggingface dataset:
Dependence of DMS global sea‐air flux distribution on transfer velocity and concentration field type
Authors: Elliott Scott
Published: April 2009

Large‐scale transport of marine reduced sulfur to the troposphere is a key to climate and global change, due to the influence of dimethyl sulfide (DMS) on aerosol/condensation nucleus fields. The sensitivity of DMS fluxes to sea‐air transfer scheme has previously been studied using established climatologies or local simulations. However, planetary level sulfur cycle models are now coming on line, and roughly coincident, eddy correlation measurements indicate that interfacial behavior of the compound may be distinct from less soluble gases. Variation of the overall sulfur flux distribution is explored here for an historical sampling of piston velocities expressed as functions of the reference height wind, plus a composite reflecting the new transfer estimates. Dissolved concentrations are derived alternately from a current generation biogeochemistry model or the standard compilation. Comparisons of simulation and data‐driven fields show that both have advantages. Modeling captures fine resolution features along frontal systems and provides a natural, biogeographic extrapolation across the general circulation. Climatology is free from physical or biotic computational biases and also is relatively strongly supported by coastal measurements. Contrast among the piston formulas includes integrated mass transfer differences as large as a factor of two. Working from the composite scheme, potential is demonstrated for improvements to shift marine DMS outputs from the Southern Ocean toward the equator. Complexities deriving from atmospheric stability, bubble enhancement, and surfactant chemistry may temper these results. Global budgets fall within the envelope of earlier work, 15 to 35 Tg S a−1.
Simulation of rain fade on arbitrary microwave link networks by the downscaling and interpolation of rain radar data
Authors: Paulson Kevin S. , Zhang Xaiobei
Published: April 2009

To predict the Quality of Service at a node in heterogeneous networks of line‐of‐sight, terrestrial, microwave links requires knowledge of the spatial and temporal statistics of rain over scales of a few meters to tens or hundreds of kilometers, and over temporal periods as short as 1 s. Meteorological radar databases provide rain rate maps over areas with a spatial resolution as fine as a few hundred meters and a sampling period of 2 to 15 min. Such two‐dimensional, rain rate map time series would have wide application in the simulation of rain scatter and attenuation of arbitrary millimeter‐wave radio networks, if the sampling period were considerably shorter, i.e., of the order of 10 s or less, and the integration volumes smaller. This paper investigates a stochastic‐numerical method to interpolate and downscale rain rate field time series to shorter sampling periods and smaller spatial integration areas, while conserving the measured and expected statistics. A series of radar derived rain maps, with a 10 min sample period, are interpolated to 10 s. The statistics of the interpolated‐downscaled data are compared to fine‐scale rain data, i.e., 10 s rain gauge data and radar data with a 300‐m resolution. The interpolated rain map time series is used to predict the fade duration statistics of a microwave link, and these are compared to a published and ITU‐R model.
Snapin associates with late endocytic compartments and interacts with late endosomal SNAREs
Authors: Lu Li , Cai Qian , Tian Jin-Hua , Sheng Zu-Hang
Published: April 2009

Late endocytic membrane trafficking delivers target materials and newly synthesized hydrolases into lysosomes and is critical for maintaining an efficient degradation process and cellular homoeostasis. Although some features of late endosome–lysosome trafficking have been described, the mechanisms underlying regulation of this event remain to be elucidated. Our previous studies showed that Snapin, as a SNAP25 (25 kDa synaptosome-associated protein)-binding protein, plays a critical role in priming synaptic vesicles for synchronized fusion in neurons. In the present study, we report that Snapin also associates with late endocytic membranous organelles and interacts with the late endosome-targeted SNARE (soluble N-ethylmaleimide-sensitive factor-attachment protein receptor) complex. Using a genetic mouse model, we further discovered that Snapin is required to maintain a proper balance of the late endocytic protein LAMP-1 (lysosome-associated membrane protein-1) and late endosomal SNARE proteins syntaxin 8 and Vti1b (vesicle transport through interaction with target SNAREs homologue 1b). Deleting the snapin gene in mice selectively led to the accumulation of these proteins in late endocytic organelles. Thus our present study suggests that Snapin serves as an important regulator of the late endocytic fusion machinery, in addition to its established role in regulating synaptic vesicle fusion.
Severe Aphasia: Possible Contributions of Using the ICF in Assessment
Authors: Threats Travis T.
Published: April 2009

Purpose: This article discusses the use of the World Health Organization's International Classification of Functioning, Disability, and Health (ICF) in the evaluation of persons with severe aphasia.

Method: Patterson and Chapey's (2008) descriptions of the hallmarks of the assessment in aphasia are presented. The ICF is described and examined in terms of whether it could be beneficial in meeting these hallmarks.

Results and Conclusions: The ICF is demonstrated to be able to contribute towards meeting the goals of this evaluation framework. It is concluded that use of the ICF by clinicians could assist in meeting the special challenges of conducting quality assessments of persons with severe aphasia.
Mental states as macrostates emerging from brain electrical dynamics
Authors: Allefeld Carsten , Atmanspacher Harald , Wackermann Jiří
Published: April 2009

Psychophysiological correlations form the basis for different medical and scientific disciplines, but the nature of this relation has not yet been fully understood. One conceptual option is to understand the mental as “emerging” from neural processes in the specific sense that psychology and physiology provide two different descriptions of the same system. Stating these descriptions in terms of coarser- and finer-grained system states (macro- and microstates), the two descriptions may be equally adequate if the coarse-graining preserves the possibility to obtain a dynamical rule for the system. To test the empirical viability of our approach, we describe an algorithm to obtain a specific form of such a coarse-graining from data, and illustrate its operation using a simulated dynamical system. We then apply the method to an electroencephalographic recording, where we are able to identify macrostates from the physiological data that correspond to mental states of the subject.
Modulational instability of dust acoustic waves in dusty plasmas with ultraviolet irradiation and nonadiabatic dust charge variation
Authors: Wang Yunliang , Zhou Zhongxiang , Jiang Xiangqian , Ni Xiaodong , Shen Jiang , Qian Ping
Published: April 2009

The combined effects of nonadiabatic dust charge fluctuation, ultraviolet irradiation, and transverse perturbation on the modulational instability of nonlinear dust acoustic (DA) waves in dusty plasma consisting of Boltzmann-distributed electrons, ions, as well as positively charged dust grain were presented here. By using the reductive perturbation technique, a three-dimensional modified Davey–Stewartson equation governing the nonlinear waves is derived. It is shown that the modulation properties of the DA waves were strongly affected by the nonadiabatic dust charge variation and photoelectrons and there was a maximum time for the modulational instability.
Restructuring of the Pt3Sn(111) surfaces induced by atomic and molecular oxygen from first principles
Authors: Dupont Céline , Jugnet Yvette , Delbecq Françoise , Loffreda David
Published: April 2009

The surface restructuring of Pt3Sn(111) induced by oxygen chemisorption is examined by means of density-functional theory calculations. Molecular and atomic oxygen chemisorption is investigated on the two available terminations of the bulk alloy—(2×2) and (3×3)R30°—these two surfaces differing by the tin content and the nature of chemical sites. An extensive geometric, energetic, and vibrational analysis is performed including the influence of oxygen coverage in the case of atomic adsorption. For molecular adsorption, regular structures have been obtained for both surfaces with a clear effect of tin on the stability of the adsorption forms. In contrast, for atomic adsorption, two oxygen chemical states are found. In particular, a peculiar surface restructuring, involving the formation of a network of SnO2 species, appears for large oxygen coverage. However the two terminations present discrepancies for the restructuring mechanism all along the oxygen coverage increase. All these results are supported by a systematic vibrational analysis.
Fast oscillatory behavior of the excited xenon density in the discharge cells of a plasma display panel
Authors: Uhm Han S. , Choi Eun H.
Published: April 2009

Fast oscillation of the excited xenon density occurs universally after an electrical discharge in the cells of a plasma display panel. A theoretical model based on ion plasma oscillation simulates this oscillatory behavior of the excited xenon density reasonably well. The magnitude and lifetime of the excited xenon density in a metastable state depend highly on the electrode configuration. Particularly, T-type electrodes provide better generation and confinement of excited xenon atoms for an abundant emission of 173 nm ultraviolet light at a high level of efficiency.
Self-organization of confined dipolar particles in a parallel field
Authors: Richardi J. , Pileni M. P. , Weis J. -J.
Published: March 2009

Monte Carlo simulations of a Stockmayer fluid confined between two parallel walls are performed to investigate self-organization of magnetic nanocrystals in a field parallel to the walls as a function of density, field strength, and wall separation. In order to study the formation of mesoscopic structures, a large number of up to 12 000 particles have to be used. The particles organize into periodically spaced cylindrical-like columns whose width typically varies between 5 and 9 particle diameters at low density. At small heights the columns are quenched due to the parallel walls, while larger wall separations can accommodate several layers of columns in good agreement with experiments. An increase in density entails a clear increase in column thickness, whereas an increase in field strength seems to have the opposite effect.
Electric multipole moment fluctuations in polar liquids
Authors: Stenhammar Joakim , Linse Per , Malmqvist Per-Åke , Karlström Gunnar
Published: April 2009

A general expression for the distribution of the fluctuating 2ℓ-pole moment Mℓ of a spherical sample of dielectric material is derived on the basis of dielectric theory combined with statistical mechanics. The formulas are compared with results from computer simulations of a weakly coupled Stockmayer fluid and the agreement is shown to be excellent. Furthermore, we calculate the size of the coupling, quantified through the free energy of solvation Asolv, of the fluctuating electric moments to a surrounding dielectric medium. It turns out that the contribution to Asolv from each fluctuating electric moment actually increases with increasing order ℓ of the moment, resulting in a formally infinite free energy of solvation. We also present a correction to Asolv for molecular media, which shows that the molecular nature of the surrounding medium effectively suppresses the divergence in the solvation free energy.
Accurate determination of subnanoscale deformation with combined laser calorimetry and surface thermal lens technique
Authors: Liu Mingqiang , Li Bincheng , Wang Yanru
Published: April 2009

Laser-induced surface deformations of optical components are measured with a combined laser calorimetry (LC) and surface thermal lens (STL) technique. The deformation is calculated from the STL amplitude by employing a simple STL model. It is also directly calculated with a rigorous deformation model by measuring the absorptance of the optical component with LC. Experimentally, the laser-induced surface deformation values of a BK7 coating sample measured by STL and Hartmann wavefront sensing techniques are in excellent agreement with that calculated with the rigorous deformation model. The measurement of subnanometer deformation with the combined LC and STL technique is demonstrated by a fused silica coating sample. The deformation measurement sensitivity and error are estimated to be 10 pm and below 10%, respectively.
Role of geranylgeranyl reductase gene in organ development and stress response in olive (Olea europaea) plants
Authors: Bruno Leonardo , Chiappetta Adriana , Muzzalupo Innocenzo , Gagliardi Cinzia , Iaria Domenico , Bruno Alessandro , Greco Maria , Giannino Donato , Perri Enzo , Bitonti Maria Beatrice
Published: April 2009

The NADPH-dependent geranylgeranyl reductase gene (OeCHLP) was characterised in olive (Olea europaea L.). OeCHLP catalyses the formation of carbon double bonds in the phytolic side chain of chlorophyll, tocopherols and plastoquinones and, therefore, is involved in metabolic pathways related to plant productivity and stress response, besides to nutritional value of its products. The nuclear OeCHLP encodes a deduced product of 51 kDa, which harbours a transit peptide for cytoplasm-to-chloroplast transport and a nicotinamide binding domain. Two estimated identical copies of gene are harboured per haploid genome of the cv. ‘Carolea’ used in the present study. Levels and cytological pattern of OeCHLP transcription were investigated by quantitative RT–PCR and in situ hybridisation. In line with the presence of ubiquitous tocopherols and/or chlorophyll, OeCHLP transcripts were present in various organs of plants. In leaves and fruits at different developmental stages, OeCHLP was differentially expressed in relation to their morpho-physiological features. An early and transient enhancement of gene transcription was detected in leaves of different age exposed to cold treatment (4°C), as well as in fruits mechanically wounded. Moreover, OeCHLP transcripts locally increased in specific cell domains of fruits severely damaged by the pathogen Bactrocera olea. Combined, these data show that OeCHLP expression early responds to biotic and abiotic stressful factors. Levels of tocopherols also increased in leaves exposed to cold conditions and fruits severely damaged by pathogen. We suggest that gene activity under stress condition could be related to tocopherol action.
KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways
Authors: Spasić Irena , Simeonidis Evangelos , Messiha Hanan L. , Paton Norman W. , Kell Douglas B.
Published: April 2009

Motivation: Most experimental evidence on kinetic parameters is buried in the literature, whose manual searching is complex, time consuming and partial. These shortcomings become particularly acute in systems biology, where these parameters need to be integrated into detailed, genome-scale, metabolic models. These problems are addressed by KiPar, a dedicated information retrieval system designed to facilitate access to the literature relevant for kinetic modelling of a given metabolic pathway in yeast. Searching for kinetic data in the context of an individual pathway offers modularity as a way of tackling the complexity of developing a full metabolic model. It is also suitable for large-scale mining, since multiple reactions and their kinetic parameters can be specified in a single search request, rather than one reaction at a time, which is unsuitable given the size of genome-scale models.

Results: We developed an integrative approach, combining public data and software resources for the rapid development of large-scale text mining tools targeting complex biological information. The user supplies input in the form of identifiers used in relevant data resources to refer to the concepts of interest, e.g. EC numbers, GO and SBO identifiers. By doing so, the user is freed from providing any other knowledge or terminology concerned with these concepts and their relations, since they are retrieved from these and cross-referenced resources automatically. The terminology acquired is used to index the literature by mapping concepts to their synonyms, and then to textual documents mentioning them. The indexing results and the previously acquired knowledge about relations between concepts are used to formulate complex search queries aiming at documents relevant to the user's information needs. The conceptual approach is demonstrated in the implementation of KiPar. Evaluation reveals that KiPar performs better than a Boolean search. The precision achieved for abstracts (60%) and full-text articles (48%) is considerably better than the baseline precision (44% and 24%, respectively). The baseline recall is improved by 36% for abstracts and by 100% for full text. It appears that full-text articles are a much richer source of information on kinetic data than are their abstracts. Finally, the combined results for abstracts and full text compared with the curated literature provide high values for relative recall (88%) and novelty ratio (92%), suggesting that the system is able to retrieve a high proportion of new documents.

Availability: Source code and documentation are available at: http://www.mcisb.org/resources/kipar/

Contact:  i.spasic@manchester.ac.uk; dbk@manchester.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum
Authors: Jurgelenaite Rasa , Dijkstra Tjeerd M. H. , Kocken Clemens H. M. , Heskes Tom
Published: April 2009

Motivation: To date, there is little knowledge about one of the processes fundamental to the biology of Plasmodium falciparum, gene regulation including transcriptional control. We use noisy threshold models to identify regulatory sequence elements explaining membership to a gene expression cluster where each cluster consists of genes active during the part of the developmental cycle inside a red blood cell. Our approach is both able to capture the combinatorial nature of gene regulation and to incorporate uncertainty about the functionality of putative regulatory sequence elements.

Results: We find a characteristic pattern where the most common motifs tend to be absent upstream of genes active in the first half of the cycle and present upstream of genes active in the second half. We find no evidence that motif's score, orientation, location and multiplicity improves prediction of gene expression. Through comparative genome analysis, we find a list of potential transcription factors and their associated motifs.

Contact:  r.jurgelenaite@cmbi.ru.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
Hooke: an open software platform for force spectroscopy
Authors: Sandal Massimo , Benedetti Fabrizio , Brucale Marco , Gomez-Casado Alberto , Samorì Bruno
Published: April 2009

Summary:  Hooke is an open source, extensible software intended for analysis of atomic force microscope (AFM)-based single molecule force spectroscopy (SMFS) data. We propose it as a platform on which published and new algorithms for SMFS analysis can be integrated in a standard, open fashion, as a general solution to the current lack of a standard software for SMFS data analysis. Specific features and support for file formats are coded as independent plugins. Any user can code new plugins, extending the software capabilities. Basic automated dataset filtering and semi-automatic analysis facilities are included.

Availability: Software and documentation are available at http://code.google.com/p/hooke. Hooke is a free software under the GNU Lesser General Public License.

Contact:  massimo.sandal@unibo.it
Coping with environmental uncertainty: dynamic bet hedging as a maternal effect
Authors: Crean Angela J , Marshall Dustin J
Published: April 2009

Mothers in a range of taxa manipulate the phenotype of their offspring in response to environmental change in order to maximize their own fitness. Most studies have focused on changes in the mean phenotype of offspring. Focusing on mean offspring phenotypes is appropriate for species in which mothers are likely to successfully predict the environment their offspring will experience, but what happens when the offspring's environment is unpredictable? Theory suggests that when mothers face uncertainty regarding their offspring's environment, they should increase within-clutch variation in the offspring phenotype (i.e. they should bet hedge). While comparative analyses support the idea that mothers do bet hedge in response to environmental unpredictability, empirical tests are very rare and it remains unclear whether mothers adaptively adjust variance in offspring traits (a phenomenon we call dynamic bet hedging). As a first step towards examining dynamic bet hedging, we reanalysed data from five previously published studies. These studies were across a range of taxa, but all manipulated the maternal environment/phenotype and then examined changes in mean offspring size. We found some support for the theoretical predictions that mothers should increase within-clutch offspring size variation when faced with unpredictable environments. We predict that dynamic bet hedging is more common than previously anticipated and suggest that it has some interesting implications for the studies that focus on shifts in mean offspring traits alone. Hence, future studies should examine maternal effects on both the mean and the variance of offspring traits.
Comparative analysis of Caulobacter chromosome replication origins
Authors: Shaheen S. M. , Ouimet Marie-Claude , Marczynski Gregory T.
Published: March 2009

Caulobacter crescentus (CB15) initiates chromosome replication only in stalked cells and not in swarmers. To better understand this dimorphic control of chromosome replication, we isolated replication origins (oris) from freshwater Caulobacter (FWC) and marine Caulobacter (MCS) species. Previous studies implicated integration host factor (IHF) and CcrM DNA methylation sites in replication control. However, ori IHF and CcrM sites identified in the model FWC CB15 were only conserved among closely related FWCs. DnaA boxes and CtrA binding sites are established CB15 ori components. CtrA is a two-component regulator that blocks chromosome replication selectively in CB15 swarmers. DnaA boxes and CtrA sites were found in five FWC and three MCS oris. Usually, a DnaA box and a CtrA site were paired, suggesting that CtrA binding regulates DnaA activity. We tested this hypothesis by site-directed mutagenesis of an MCS10 ori which contains only one CtrA binding site overlapping a critical DnaA box. This overlapping site is unique in the whole MCS10 genome. Selective DnaA box mutations decreased replication, while selective CtrA binding site mutations increased replication of MCS10 ori plasmids. Therefore, both FWC and MCS oris use CtrA to repress replication. Despite this similarity, phylogenetic analysis unexpectedly shows that CtrA usage evolved separately among these Caulobacter oris. We discuss consensus oris and convergent ori evolution in differentiating bacteria.
Purification of Recombinant Drosophila ACF
Authors: Peterson Craig L.
Published: April 2009

INTRODUCTION

The goal of chromatin assembly procedures is to prepare extended nucleosomal arrays from cloned DNA templates and purified core and linker histones. The assembled chromatin should be highly defined in its protein content and resemble bulk chromatin isolated from living cell nuclei in terms of periodicity and nucleosome positioning. This protocol describes the preparation of Drosophila ACF (ATP-utilizing chromatin assembly and remodeling factor) for use in chromatin assembly reactions. In this method, ACF is prepared by the coexpression of the carboxyl-terminally FLAG-tagged Acf1 subunit with the untagged ISWI subunit in baculovirus. The complex is then purified in one step by FLAG immunoaffinity chromatography. This procedure typically results in a stoichiometric complex of Acf1 and ISWI.
Obtaining Ilyanassa Snail Embryos
Authors: Gharbiah Maey , Cooley James , Leise Esther M. , Nakamoto Ayaki , Rabinowitz Jeremy S. , Lambert J. David , Nagy Lisa M.
Published: April 2009

INTRODUCTION

The marine gastropod Ilyanassa obsoleta is a long-standing and very useful model for studies of embryonic development. It is an especially important model for spiralian development, and for studies of asymmetric cell division. The embryos are amenable to classic embryological manipulation techniques as well as a growing number of molecular approaches. Ilyanassa is also an important model for studies of metamorphosis, the ecology of parasitism, the effects of environmental contaminants on morphology and sexual function, and comparative neurobiology. Ilyanassa adults are readily obtainable and easy to keep in the laboratory. Although the normal spawning season for Ilyanassa is during early summer, they can produce high-quality embryos nearly year-round in the laboratory. Snails collected in the late fall, winter, or spring can be induced to deposit zygotes before the natural spawning season by warming them to room temperature, and snails collected before the natural spawning season can be made to postpone zygote deposition until needed (up to at least 6 mo) by maintaining them in tanks in a cold room at 4°C-8°C. This protocol describes how to induce embryo production in Ilyanassa snails, collect the embryos, and rear them to the stage required for study.
Microinjection of Helobdella (Leech) Embryos: Figure 1.
Authors: Weisblat David A. , Kuo Dian-Han
Published: April 2009

INTRODUCTION

One advantage of using Helobdella (leech) embryos as an experimental system is their amenability for microinjection. Blastomeres ranging in size from the zygote (400 μm diameter) down to micromeres and primary blast cells (~20 μm diameter) can be injected by pressure under a dissecting microscope. Smaller cells can be injected by iontophoresis under a compound microscope. Microinjection is useful for studying embryonic development. For example, developmental fates of a cell can be followed by injecting a lineage tracer. A specific cell can be killed by injecting a toxic substance. Furthermore, cells can be killed at a given developmental stage by directing intense fluorescence illumination or a blue laser beam on fluorescein-labeled cells. Finally, gene expression can be manipulated in leech embryos by injecting zygotes or selected blastomeres with synthetic mRNA, morpholino antisense oligo, or a plasmid construct. Molecules <1500 Da can diffuse freely among early blastomeres via gap junctions. When intercellular diffusion of an injected substance is undesirable, small molecules should be conjugated to larger molecules such as dextran (10 kDa). Different commercial microinjection setups can be adopted for Helobdella embryos. This article describes how to microinject embryos using a versatile homemade pressure injection system. Under a dissecting microscope, embryos are immobilized by suction in a custom-fabricated chamber with the target cell facing upward. Cells are visualized using transillumination via a long-working-distance, dark-field condenser. The tip of a micropipette is brought into the target cell with a micromanipulator, and the injectant is delivered into the cell by pressure.
Devitellinization of Living Helobdella (Leech) Embryos
Authors: Weisblat David A. , Kuo Dian-Han
Published: April 2009

INTRODUCTION

Embryos of glossiphoniid leeches are enclosed in a thin vitelline envelope until “hatching” (stage 10). This protocol describes the procedure for removing the vitelline envelope from Helobdella robusta and H. sp. (Austin) embryos. This protocol is applicable to embryos of stages 1-9 but is probably more useful for early stages. With careful culturing, the devitellinized embryos can develop normally.
Arnolds’ Silver Staining of Helbodella (Leech) Embryos
Authors: Weisblat David A. , Kuo Dian-Han
Published: April 2009

INTRODUCTION

Arnolds’ silver staining is used to visualize the boundaries of epidermal cells at the surface of embryos. As described in this article, silver staining can be performed on either living or fixed Helbodella (leech) embryos. To preserve the cell junction in fixed embryos, a special fixation procedure is used.
tDNA-PCR Followed by Automated Fluorescent Capillary Electrophoresis for Identification of Bacterial Species
Authors: Baele Margo , Stakenborg Tim , Lopes dos Santos Santiago Guido , Haesebrouck Freddy , Vaneechoutte Mario
Published: April 2009

INTRODUCTION

Transfer RNA intergenic spacer length polymorphism analysis (tDNA-PCR) is a simple and reproducible polymerase chain reaction (PCR) technique for identification of bacteria at the species or even subspecies level. The primers used in the PCR are based on conserved sequences located at the edges of the tRNA genes. Because the selected consensus primers are directed outwardly, the intergenic spacers are amplified rather than the genes themselves. With each PCR, several amplicons of different lengths are obtained, because several intergenic spacers are present in each bacterial genome. The patterns thus obtained are identical within species, but differ between distinct species, and as a result, can be used for identification of bacterial species. The amplicons are separated using high-resolution (1 bp) electrophoresis (e.g., fluorescent capillary electrophoresis) and immediately digitized as tables composed of numerical lengths (expressed in base pairs) and peak intensities. For identification, the resulting peak pattern can be compared with a large database of patterns of well-identified bacterial strains, using an in-house-developed software package that is available online. New patterns (linked to the correct species name, which can be obtained, e.g., after 16S rRNA gene sequence determination) can be added to expand the database further. This protocol describes tDNA-PCR, followed by automated fluorescent capillary electrophoresis to identify bacterial species.
The glutamic acid decarboxylase 65 immunoglobulin G subclass profile differs between adult-onset type 1 diabetes and latent autoimmune diabetes in adults (LADA) up to 3 years after clinical onset
Authors: Hillman M , Törn C , Landin-Olsson M
Published: April 2009

Autoantibodies against glutamic acid decarboxylase 65 (GADA) are found frequently in patients with autoimmune diabetes. Immunoglobulin (Ig)G1 is the most frequent subclass among the GADA IgG subclasses. IgG4 is a more common subclass in latent autoimmune diabetes in adults (LADA) at clinical onset compared to type 1 diabetes. The aim of this work was to study the different GADA-IgG subclass profiles during a 3-year follow-up in these groups of autoimmune diabetes. Adult-onset subjects, classified as either type 1 (n = 40) or LADA (n = 43), were included in the study. New samples were collected every year from these patients. In addition to conventional GADA analyses, GADA-IgG subclasses were also analysed with a radioimmunoprecipitation assay using biotin-conjugated antibodies (directed against human IgG subclasses and IgM) and streptavidin Sepharose. During 3 years' follow-up, all the IgG subclass levels decreased in type 1 diabetes – IgG1: P < 0·001; IgG2: P < 0·001; IgG3: P < 0·001; IgG4: P < 0·05 (Friedman's’ test) – while levels remained stable for all four subclasses in LADA. GADA IgM, however, decreased in both groups (P < 0·001). Patients with LADA have higher GADA IgG3 and IgG4 at clinical onset and seem to maintain the levels and profile of their IgG subclasses up to 3 years after clinical onset, while all the GADA IgG subclass levels decrease in type 1 diabetic patients. This indicates a persistent different immune response in LADA compared to type 1 diabetes and further indicates the difference in pathogenesis.
Improving clinical outcome in patients with intestinal failure using individualised nutritional advice
Authors: Culkin A. , Gabe S. M. , Madden A. M.
Published: April 2009

Background: Patients with intestinal failure are required to adhere to a complex regimen. Written information may increase knowledge leading to improvements in clinical outcomes. The present study aimed to evaluate the effectiveness of nutrition advice incorporating the use of a booklet.

Methods: Each patient completed a questionnaire evaluating their knowledge of the regime and quality of life and kept a diet and gastrointestinal output diary. The diary was assessed and they were given the booklet with a verbal explanation tailored to individual requirements. The booklet explained the causes of intestinal failure, diet and fluid recommendations in relation to intestinal anatomy, information on medications and long‐term monitoring. Patients were reassessed at their next appointment using the same tools. The primary endpoint was an improvement in knowledge. Secondary endpoints were an improvement in oral nutritional intake, nutritional status, quality of life and the content of home parenteral nutrition.

Results: Forty‐eight patients completed the study. Knowledge improved significantly after dietetic intervention in association with the provision of the booklet (P < 0.001). Oral energy (P = 0.04) and fat (P = 0.003) intake increased with an improvement in body mass index (P = 0.02). Patients on home parenteral nutrition showed a reduction in parenteral energy (P = 0.02), nitrogen (P = 0.003), volume (P = 0.02) and frequency (P = 0.003).

Conclusions: A booklet for patients with intestinal failure in conjunction with personalised dietary counselling improves knowledge and clinical outcomes.
Modelling evolutionary processes in small populations: not as ideal as you think
Authors: WAPLES ROBIN S. , FAULKNER JAMES R.
Published: March 2009

Evolutionary processes are routinely modelled using ‘ideal’ Wright–Fisher populations of constant size N in which each individual has an equal expectation of reproductive success. In a hypothetical ideal population, variance in reproductive success (Vk) is binomial and effective population size (Ne) = N. However, in any actual implementation of the Wright–Fisher model (e.g., in a computer), Vk is a random variable and its realized value in any given replicate generation () only rarely equals the binomial variance. Realized effective size () thus also varies randomly in modelled ideal populations, and the consequences of this have not been adequately explored in the literature. Analytical and numerical results show that random variation in  and  can seriously distort analyses that evaluate precision or otherwise depend on the assumption that  is constant. We derive analytical expressions for Var(Vk) [4(2N – 1)(N – 1)/N3] and Var(Ne) [N(N – 1)/(2N – 1) ≈ N/2] in modelled ideal populations and show that, for a genetic metric G = f(Ne), Var(Ĝ) has two components: VarGene (due to variance across replicate samples of genes, given a specific ) and VarDemo (due to variance in ). Var(Ĝ) is higher than it would be with constant Ne = N, as implicitly assumed by many standard models. We illustrate this with empirical examples based on F (standardized variance of allele frequency) and r2 (a measure of linkage disequilibrium). Results demonstrate that in computer models that track multilocus genotypes, methods of replication and data analysis can strongly affect consequences of variation in . These effects are more important when sampling error is small (large numbers of individuals, loci and alleles) and with relatively small populations (frequently modelled by those interested in conservation).
Sputum eosinophilia: an early marker of bronchial response to occupational agents
Authors: Vandenplas O. , D’Alpaos V. , Heymans J. , Jamart J. , Thimpont J. , Huaux F. , Lison D. , Renauld J‐C.
Published: April 2009

Background:  False‐negative responses to specific inhalation challenge (SIC) with occupational agents may occur. We explored whether assessing changes in sputum cell counts would help improve the identification of bronchial reactivity to occupational agents during SICs.

Methods:  The predictive value of the changes in sputum cell counts after a negative FEV1 response to a first challenge exposure to an occupational agent was determined using the changes in airway calibre observed during repeated challenges as the ‘gold standard’. The study included 68 subjects investigated for work‐related asthma in a tertiary centre. After a control day, the subjects were challenged with the suspected occupational agent(s) for up to 2 h. All subjects who did not show an asthmatic reaction were re‐challenged on the following day. Additional challenges were proposed to those who demonstrated a ≥ 2% increase in sputum eosinophils or an increase in nonspecific bronchial hyperresponsiveness to histamine after the second challenge day.

Results:  Six of the 35 subjects without changes in FEV1 on the first challenge developed an asthmatic reaction on subsequent challenges. ROC analysis revealed that a >3% increase in sputum eosinophils at the end of the first challenge day was the most accurate parameter for predicting the development of an asthmatic response on subsequent challenges with a sensitivity of 67% and a specificity of 97%.

Conclusions:  An increase in sputum eosinophils is an early marker of specific bronchial reactivity to occupational agents, which may help to identify subjects who will develop an asthmatic reaction only after repeated exposure.
IgG4‐related inflammatory aneurysm of the aortic arch
Authors: Ishida Mitsuaki , Hotta Machiko , Kushima Ryoji , Asai Tohru , Okabe Hidetoshi
Published: March 2009

IgG4‐related sclerosing disease can occur in the cardiovascular system and some inflammatory abdominal aortic aneurysms have been shown to belong to IgG4‐related sclerosing disease. Herein is reported a case of IgG4‐related inflammatory aortic aneurysm of the aortic arch. A 71‐year‐old Japanese man was found to have an aneurysm of the aortic arch with maximum dimension of 5.5 cm. The surgically resected aneurysm wall had conspicuous fibrosclerotic changes, dense lymphoplasmacytic infiltration and occasional obliterative phlebitis in the adventitia; the thickness of the adventitia was 6.5 mm. Immunohistochemistry indicated numerous IgG4‐positive plasma cell infiltrates; 84% of the IgG‐bearing cells were IgG4 positive. The diagnosis of IgG4‐related inflammatory aortic aneurysm of the aortic arch was made. Although previously reported IgG4‐related inflammatory aortic aneurysms were confined to the abdominal aorta, the present case report demonstrates that IgG4‐related inflammatory aortic aneurysm can occur in the aortic arch, thereby extending the spectrum of IgG4‐related periaortitis. Further studies are needed to clarify the spectrum of IgG4‐related sclerosing disease in the cardiovascular system.
Lower urinary tract symptoms in relation to lifestyle and medical conditions in Japanese workers
Authors: Tomita Kentaro , Mizoue Tetsuya , Matsumoto Tetsuro
Published: April 2009

Objectives:  To examine the association of medical conditions and lifestyle with lower urinary tract symptoms (LUTS) in a population of Japanese male workers.

Methods:  A questionnaire survey on LUTS was conducted at the time of a periodic health examination among workers of a group of engineering and shipbuilding companies in Southern Kanto, Japan. A total of 1278 (85%) men responded. LUTS were assessed by using a modified International Prostate Symptom Score questionnaire. Men having at least one point of the score were regarded as positive. Logistic regression analysis was used to examine the relation of the LUTS to age, smoking, drinking, body mass index, and medical treatment of diabetes mellitus, hypertension, and dyslipidemia.

Results:  Age was a strong determinant of LUTS. Men undergoing medical treatment for diabetes mellitus were significantly more likely to have LUTS than men without treatment (multivariate‐adjusted odds ratio, 1.8; 95% confidence interval, 1.0–3.2). Increased odds of LUTS were also observed in men undergoing medical treatment for hypertension or dyslipidemia. Smoking, drinking alcohol, and obesity were not related to LUTS.

Conclusions:  Our present findings, together with previous epidemiological and experimental evidence, suggest that LUTS might share common etiological factors with diabetes mellitus, hypertension, and dyslipidemia.
Style timing with the value spread in Australia
Authors: Hyde Charles E. , Beggs David
Published: April 2009

The value spread is shown to be positively related to the value premium in the Australian market. The relationship is especially strong for small cap portfolios and typically stronger when using the book‐to‐price ratio than other value metrics. In small cap portfolios, the positive value premium–spread relationship is primarily driven by the short side. Our results are consistent with previous findings in US and Asian markets. We also show that the small cap–large cap value spread differential is positively related to the corresponding value premium differential, suggesting the value spread can also be used for timing the large/small cap tilt.
SPATIAL EFFECTS ON PROVINCIAL CONVERGENCE AND INCOME DISTRIBUTION IN SPAIN: 1985–2003
Authors: MAZA ADOLFO , VILLAVERDE JOSÉ
Published: April 2009

This paper examines the role of space (geographical location) in provincial income convergence and income distribution in Spain. To do that, and after showing the presence of spatial dependence in our income data, the paper compares two sample series: actual versus filtered (spaceless) data. The comparison of these two series comes out to two important differences: first, the speed of convergence is higher and, second, the income distribution is more concentrated (less biased) around the national average with filtered data. Besides this, the paper also shows that geographical location particularly explains relative income improvement in provinces with per capita income slightly above average. These results confirm that, as for Spain, space does indeed matter.
Trichobezoar Obstruction after Stapled Jejunal Anastomosis in a Dog
Authors: CAROBBI BARBARA , FOALE ROBERT D. , WHITE RICHARD A. S.
Published: April 2009

Objective— To describe an unusual long‐term complication of circular end‐to‐end anastomosis (CEEA) stapling in a dog.

Study Design— Clinical case report.

Animal— An 11‐year‐old, female neutered, Labrador Retriever.

Methods— The dog was referred for clinical signs of bowel obstruction. An enterectomy was performed 2 years before presentation using a CEEA stapling device. Palpation, plain radiographs, and ultrasound of the abdomen confirmed the presence of a mass in the bowel, causing obstruction, and requiring surgical approach.

Results— An exploratory celiotomy revealed a 5 cm mass in the jejunum, involving the site of the previous surgery. The mass was removed by enterectomy. Dissection of the mass revealed the presence of many staples at the previous enterectomy site, and a trichobezoar entangled in the exposed parts of the staples.

Conclusions— An enterectomy was required to treat an intestinal obstruction caused by a trichobezoar entangled in a CEEA‐stapled anastomosis.

Clinical Relevance— Development of trichobezoar and subsequent bowel obstruction should be considered an unusual but potential long‐term complication of CEEA‐stapled anastomosis.
Rate Reduction by Overdrive Stimulation at the Origin of an Ectopic Ventricular Tachycardia in the Intact Pig Heart‐Evidence of Vagal Activation
Authors: WEISMÜLLER PETER , MAYER ULRICH , LIPPERT RAINER , HOMBACH VINZENZ , STAUCH MARTIN
Published: April 2009

Overdrive stimulation is used in the treatment of tachycardias. In this study, the effect of overdrive stimulation on a focal ventricular tachycardia was investigated. In 12 landrace pigs thoracotomy was performed. Stable ectopic ventricular tachycardias with a rate of 120–170/min were induced by subepicardial infusion of a solution of norepinephrine (10−4 M). Unipolar cathodal stimulation was carried out by an epicardial screw‐in electrode. During tachycardia, overdrive stimulation was undertaken in different distances to the ectopic focus, with different stimulus amplitude and duration. A significant rate reduction of the ventricular tachycardia was observed after stimulation. When stimulated directly at the focus the extent of rate reduction was larger than after stimulation in a distance of 10–40 mm. At the infusion site the rate of the tachycardia was lowered in direct relation to the stimulation amplitude and stimulus width. The marked reduction in rate after overdrive stimulation (18%) was nearly completely antagonized by atropine. This indicates that rate reduction caused by local overdrive stimulation is due to local acetylcholine liberation caused by vagal stimulation in the ventricular working myocardium in this experimental model.
The Prognostic Significance of Inducing Nonsustained Ventricular Tachycardia in Patients Presenting with Sustained Ventricular Tachycardia or Cardiac Arrest
Authors: BONNET CHRISTOPHER A. , ELSON JAMES J. , FIEDLER SUSAN B. , FOGOROS RICHARD N.
Published: April 2009

The significance of inducing nonsustained ventricular tachycardia during baseline electrophysiological testing in patients presenting with sustained ventricular arrhythmias is unclear. In this study, 145 consecutive patients presenting with cardiac arrest or sustained ventricular tachycardia underwent electrophysiological study. Twenty five (17%) had no inducible ventricular tachycardia (group I), 33 (23%) had inducible nonsustained ventricular tachycardia (group II), and 87 (60%) had inducible sustained ventricular tachycardia (group 111). Group I was not treated with antiarrhythmic therapy. Groups II and III underwent serial drug trials guided by electrophysiological testing. Mean follow‐up for all three groups was 31 ± 18 months. The actuarial rate of arrhythmia recurrence for group 1 at 12, 24, and 36 months of follow‐up was 0%, 6%, and 17%, respectively. This actuarial arrhythmia recurrence rate for group I was significantly lower (P < 0.05) than that of group II (16%, 27%, and 32%) and group III (32%, 39%, and 44%). There was no significant difference between the arrhythmia recurrence rates in groups 11 and III. When groups II and III were broken down into drug responders and nonresponders, drug responders in both groups had significantly fewer arrhythmia recurrences than nonresponders (P < 0.05). The overall incidence of sudden death was low (11 of 145, 8%) and not significantly different between groups I, II, and III. In summary, among patients who present with sustained ventricular arrhythmias, those who have nonsustained ventricular tachycardia induced during baseline electrophysiological testing respond to serial drug testing and have long‐term outcomes similar to those with inducible sustained ventricular tachycardia.
Management of Patients with Supra ventricular Tachycardia Using Amiodarone Therapy
Authors: GRABOYS THOMAS B. , BLATT CHARLES M.
Published: April 2009

Amiodarone has emerged as a potent agent for the management of patietits with reentrant supra ventricular tachycardias, atrial flutter, atrial fibrillation, and dysrhythmias associated with the preexcitation syndromes. Efficacy is reported betiveen 50 and 90% dependent upon the nature of the primary rhythm disturbance and population studied. Electrophysiological studies have not in general been helpful in predicting outcome with this agent. The drug may produce a wide array of toxic side effects, requiring cessation of therapy in less than 10% of patients. Our approach to the use of this agent relegates it to a second or third line of therapy in view of its complex pharmacokinetics and wide array of side effects.