bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes
Authors: Sahota Gurmukh , Stormo Gary D.
Published: September 2010

Motivation: Computational techniques for microbial genomic sequence analysis are becoming increasingly important. With next-generation sequencing technology and the human microbiome project underway, current sequencing capacity is significantly greater than the speed at which organisms of interest can be studied experimentally. Most related computational work has been focused on sequence assembly, gene annotation and metabolic network reconstruction. We have developed a method that will primarily use available sequence data in order to determine prokaryotic transcription factor (TF) binding specificities.

Results: Specificity determining residues (critical residues) were identified from crystal structures of DNA–protein complexes and TFs with the same critical residues were grouped into specificity classes. The putative binding regions for each class were defined as the set of promoters for each TF itself (autoregulatory) and the immediately upstream and downstream operons. MEME was used to find putative motifs within each separate class. Tests on the LacI and TetR TF families, using RegulonDB annotated sites, showed the sensitivity of prediction 86% and 80%, respectively.

Availability:  http://ural.wustl.edu/∼gsahota/HTHmotif/

Contact:  stormo@wustl.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Labeling the Endoplasmic Reticulum with DiO-C6(3) for Imaging
Authors: Chazotte Brad
Published: September 2010

INTRODUCTION

The eukaryotic cell has evolved to compartmentalize its functions and transport various metabolites among cellular compartments. Therefore, in cell biology, the study of organization and structure/function relationships are of great importance. The endoplasmic reticulum is a highly convoluted, single membrane that is continuous with the outer nuclear membrane and is believed to form a contiguous closed sac within the cell cytosol. Although a probe specific for the endoplasmic reticulum currently does not exist, the DiO-C6(3) probe, a cationic dye, is an effective label because of the distinctive intracellular morphology of the endoplasmic reticulum that distinguishes it from other intracellular organelles. This protocol describes the labeling of the endoplasmic reticulum with DiO-C6(3).
Small-Scale Extraction of Recombinant Proteins from Bacteria
Authors: Simpson Richard J.
Published: September 2010

INTRODUCTION

Bacteria are particularly convenient for producing recombinant proteins for purification purposes. To monitor induction as well as the levels of recombinant protein expression, it is important to have a rapid, simple method for estimating bacterial protein expression. This protocol describes the preparation of small-scale bacterial extracts using cell lysis with 0.5% Triton X-100.
Voltage-Clamp Analysis of Synaptic Transmission at the Drosophila Larval Neuromuscular Junction
Authors: Zhang Bing , Stewart Bryan
Published: September 2010

INTRODUCTION

The Drosophila larval neuromuscular junction (NMJ) shares many structural and functional similarities to synapses in other animals, including humans. These include the basic feature of synaptic transmission as well as the molecular mechanisms regulating the synaptic vesicle cycle. Because of its large size, easy accessibility, and the well-characterized genetics, the fly NMJ remains an excellent model system for dissecting the cellular and molecular mechanisms of synaptic transmission. Although intracellular recording is particularly valuable in revealing membrane potential changes, it has several limitations. Primarily, it does not offer information on the kinetics of membrane currents associated with ion channels or synaptic receptors responsible for the potential change. Furthermore, the resting potential of the Drosophila body-wall muscle varies naturally such that the driving force also varies considerably, making it difficult to accurately compare the amplitude of minis (spontaneous miniature synaptic potentials) or evoked excitatory junction potentials (EJPs). Finally, accurate determination of quantal content based on minis and EJPs is possible only at low release conditions when nonlinear summation is not a major issue. The voltage-clamp technique can overcome these limitations by using negative feedback mechanisms to keep the cell membrane potential steady at any reasonable set points. In the large larval muscle cells of Drosophila, the two-electrode voltage-clamp (TEVC) method is used, in which one electrode monitors the cell membrane potential while the other electrode passes electric currents. This protocol introduces the application of TEVC in analysis of synaptic currents using the larval NMJ preparation.
Fabrication of Microelectrodes, Suction Electrodes, and Focal Electrodes
Authors: Zhang Bing , Stewart Bryan
Published: September 2010

INTRODUCTION

The Drosophila larval neuromuscular junction (NMJ) shares many structural and functional similarities to synapses in other animals, including humans. These include the basic feature of synaptic transmission, as well as the molecular mechanisms regulating the synaptic vesicle cycle. Because of its large size, easy accessibility, and well-characterized genetics, the fly NMJ remains an excellent model system for dissecting the cellular and molecular mechanisms of synaptic transmission. This protocol details some basic methods for manufacturing microelectrodes used for intracellular recording and two-electrode voltage-clamp (TEVC), and loose patch electrodes used for focal recording. In addition, a method is provided for manufacturing homemade suction electrodes used for nerve stimulation.
Methods for Expressing and Analyzing GFP-Tubulin and GFP-Microtubule-Associated Proteins
Authors: Goodson Holly V. , Dzurisin Jill S. , Wadsworth Patricia
Published: September 2010

INTRODUCTION

Important advances in our understanding of the organization and dynamics of the cytoskeleton have been made by direct observations of fluorescently tagged cytoskeletal proteins in living cells. In early experiments, the cytoskeletal protein of interest was purified, covalently modified with a fluorescent dye, and microinjected into living cells. In the mid-1990s, a powerful new technology arose: Researchers developed methods for expressing chimeric proteins consisting of the gene of interest fused to green fluorescent protein (GFP). This approach has become a standard method for characterizing protein localization and dynamics. More recently, a profusion of “XFP” (spectral variants of GFP) has been developed, allowing researchers straightforwardly to perform experiments ranging from simultaneous co-observation of protein dynamics to fluorescence recovery after photobleaching (FRAP), fluorescence resonance energy transfer (FRET), and subresolution techniques such as stimulated emission-depletion microscopy (STED) and photoactivated localization microscopy (PALM). In this article, the methods used to express and analyze GFP- and/or XFP-tagged tubulin and microtubule-associated proteins (MAPs) are discussed. Although some details may be system-specific, the methods and considerations outlined here can be adapted to a wide variety of proteins and organisms.
ArabidopsisVILLIN1 and VILLIN3 Have Overlapping and Distinct Activities in Actin Bundle Formation and Turnover
Authors: Khurana Parul , Henty Jessica L. , Huang Shanjin , Staiger Andrew M. , Blanchoin Laurent , Staiger Christopher J.
Published: September 2010

Actin filament bundles are higher-order cytoskeletal structures that are crucial for the maintenance of cellular architecture and cell expansion. They are generated from individual actin filaments by the actions of bundling proteins like fimbrins, LIMs, and villins. However, the molecular mechanisms of dynamic bundle formation and turnover are largely unknown. Villins belong to the villin/gelsolin/fragmin superfamily and comprise at least five isovariants in Arabidopsis thaliana. Different combinations of villin isovariants are coexpressed in various tissues and cells. It is not clear whether these isovariants function together and act redundantly or whether they have unique activities. VILLIN1 (VLN1) is a simple filament-bundling protein and is Ca2+ insensitive. Based on phylogenetic analyses and conservation of Ca2+ binding sites, we predict that VLN3 is a Ca2+-regulated villin capable of severing actin filaments and contributing to bundle turnover. The bundling activity of both isovariants was observed directly with time-lapse imaging and total internal reflection fluorescence (TIRF) microscopy in vitro, and the mechanism mimics the “catch and zipper” action observed in vivo. Using time-lapse TIRF microscopy, we observed and quantified the severing of individual actin filaments by VLN3 at physiological calcium concentrations. Moreover, VLN3 can sever actin filament bundles in the presence of VLN1 when calcium is elevated to micromolar levels. Collectively, these results demonstrate that two villin isovariants have overlapping and distinct activities.
Potential consequences of replacing a retail alcohol monopoly with a private licence system: results from Sweden
Authors: Norström Thor , Miller Ted , Holder Harold , Österberg Esa , Ramstedt Mats , Rossow Ingeborg , Stockwell Tim
Published: September 2010

Aim To examine the potential effects of replacing the Swedish alcohol retail system with a private licensing system on alcohol consumption and alcohol‐related harm.

Design Two possible scenarios were analysed: (1) replacing the current alcohol retail monopoly with private licensed stores that specialize in alcohol sales or (2) making all alcohol available in grocery stores. We utilized a multiplicative model that projected effects of changes in a set of key factors including hours of sale, retail prices, promotion and advertising and outlet density. Next, we estimated the effect of the projected consumption increase on a set of harm indicators. Values for the model parameters were obtained from the research literature.

Measurements Measures of alcohol‐related harm included explicitly alcohol‐related mortality, accident mortality, suicide, homicide, assaults, drinking driving and sickness absence.

Findings According to the projections, scenario 1 yields a consumption increase of 17% (1.4 litres/capita), which in turn would cause an additional 770 deaths, 8500 assaults, 2700 drinking driving offences and 4.5 million sick days per year. The corresponding figures for scenario 2 are a consumption increase of 37.4% (3.1 litres/capita) leading to an additional annual toll of 2000 deaths, 20 000 assaults, 6600 drinking driving offences and 11.1 million days of sick leave.

Conclusions Projections based on the research literature suggest that privatization of the Swedish alcohol retail market would significantly increase alcohol consumption and alcohol‐related harm.
Centrally necrotizing carcinoma of the breast: clinicopathological analysis of 33 cases indicating its basal‐like phenotype and poor prognosis
Authors: Yu Lin , Yang Wentao , Cai Xu , Shi Daren , Fan Yuezhen , Lu Hongfen
Published: September 2010

Yu L, Yang W, Cai X, Shi D, Fan Y & Lu H (2010) Histopathology 57, 193–201

Centrally necrotizing carcinoma of the breast: clinicopathological analysis of 33 cases indicating its basal‐like phenotype and poor prognosis

Aims:  To investigate the clinicopathological features and immunophenotype of centrally necrotizing carcinoma (CNC) of the breast to ascertain its relationship to basal‐like phenotype and its prognosis.

Methods and results:  The clinical and pathological characteristics of 33 CNCs were reviewed. Immunohis‐tochemical study of oestrogen receptor, progesterone receptor, HER2, cytokeratin (CK) 8/18, high‐molecular‐weight CK (34βE12), CK5/6, CK14, CK17, smooth muscle antigen, p63, vimentin and epidermal growth factor receptor was performed. The striking feature of CNC was a central, necrotic or acellular zone surrounded by a ring‐like area of viable tumour cells. The central zone showed three morphological types: predominance of coagulative necrosis (21 cases), predominance of fibrosis and scar tissue (nine cases) and infarction (three cases). Tumour cells displayed invasive ductal carcinoma of high grade. The expression rate of basal‐like markers was higher than that of myoepithelial markers (87.9% versus 46.2%). Basal‐like subtype was shown by 63.6% of cases. The expression rate of CK5/6 (90.5%) was highest among basal‐like markers. Follow‐up data of 19 patients were available. Median progression‐free survival was 15.5 months. In 12 patients (63.2%), local recurrence and/or distant metastasis developed (median time to recurrence and/or metastasis, 14.0 months).

Conclusions:  CNC has distinctive morphological features, which mostly exhibit a basal‐like immunophenotype and poor prognosis. CNC is a typical representative of basal‐like breast cancer.
Drought limitation of photosynthesis differs between C3 and C4 grass species in a comparative experiment
Authors: TAYLOR S. H. , RIPLEY B. S. , WOODWARD F. I. , OSBORNE C. P.
Published: September 2010

Phylogenetic analyses show that C4 grasses typically occupy drier habitats than their C3 relatives, but recent experiments comparing the physiology of closely related C3 and C4 species have shown that advantages of C4 photosynthesis can be lost under drought. We tested the generality of these paradoxical findings in grass species representing the known evolutionary diversity of C4 NADP‐me and C3 photosynthetic types. Our experiment investigated the effects of drought on leaf photosynthesis, water potential, nitrogen, chlorophyll content and mortality. C4 grasses in control treatments were characterized by higher CO2 assimilation rates and water potential, but lower stomatal conductance and nitrogen content. Under drought, stomatal conductance declined more dramatically in C3 than C4 species, and photosynthetic water‐use and nitrogen‐use efficiency advantages held by C4 species under control conditions were each diminished by 40%. Leaf mortality was slightly higher in C4 than C3 grasses, but leaf condition under drought otherwise showed no dependence on photosynthetic‐type. This phylogenetically controlled experiment suggested that a drought‐induced reduction in the photosynthetic performance advantages of C4 NADP‐me relative to C3 grasses is a general phenomenon.
Does Social Mating System Influence Nest Defence Behaviour in Great Reed Warbler (Acrocephalus arundinaceus) Males?
Authors: Trnka Alfréd , Prokop Pavol
Published: September 2010

In birds with biparental care, males and females often conflict over how much care to provide to their offspring and it may be substantially influenced by increased level of polygamy. In accordance with sexual conflict theory, males of socially polygynous bird species provide much less care to their nestlings than do males of most socially monogamous species. Most of previous studies, however, have used feeding behaviour as an index for variations in male parental care only. However, this may be skewed if polygynous males compensate for lower feeding assistance through the provision of other parental care such as protection of nests from predators. In this paper, we examine nest defence behaviour in the facultatively polygynous great reed warbler with respect to sex and type of social mating system. We recorded latency to the first arrival, distance from the predator and defensive reaction of each parent towards a human intruder. Socially polygynous males with two simultaneously active nests defended primary females’ nests less vigorously than socially monogamous males, whereas no differences were found between monogamous and primary females. Generally, however, they took a bigger role in nest defence than males in all cases. Our results support an idea that sexual conflict is driven by polygamy and that type of social mating system can influence nest defence behaviour of facultatively polygynous birds. This finding should be taken into consideration when studying nest defence parental care in polygynous mating systems.
Multiple Large Pilomatricomas in the Setting of Diffuse Epidermal Nevi
Authors: JOHNSON LANDON M. , NEWELL BRANDON
Published: September 2010

Abstract:  Epidermal nevi are hamartomas arising from the embryonic ectoderm during early embryonic stages, resulting in cutaneous mosaicism. We describe a patient with diffuse epidermal nevi and multiple large pilomatricomas arising near or within epidermal nevi.
Ablation of Atrioventricular Nodal Reentrant Tachycardia in a Patient with Reversal of Slow and Fast Pathways Inputs into the Atrioventricular Node
Authors: JIA‐FENG LIN , YUE‐CHUN LI , PENG‐LIN YANG , JI‐FEI TANG
Published: September 2010

We report a case of atrioventricular nodal reentrant tachycardia (AVNRT) coexistent with His bundle anomaly and atrial septal defects. The His‐bundle potential was recorded at the coronary sinus (CS) ostium. Fractionated atrial potentials and an A:V electrogram ratio 1:3 were recorded at the anterior septum of the tricuspid annulus approximately 2 cm from CS ostium. Radiofrequency catheter ablation at the anterior septum of the tricuspid annulus effectively eliminated AVNRT. (PACE 2012; 35:e17–e19)
Ideational Origins of Progressive Judicial Activism: The Colombian Constitutional Court and the Right to Health
Authors: Nunes Rodrigo M.
Published: September 2010

Why do some constitutional transitions trigger the emergence of progressive judicial activism? This article addresses this question through an analysis of the creation of the Colombian Constitutional Court and its subsequent activism toward rights in general and the right to health in particular. This research suggests that ideational variables are crucial to explain this outcome. On the one hand, the Constitutional Court's behavior reflects the dominance of the institutional conception that it is the judiciary's role to help fulfill the promises of the constitutional text. On the other, programmatic beliefs about the relationship between the rule of law and market-driven economic growth led powerholders to create the court and appoint judges with this orientation. The emergence of progressive judicial activism in Colombia, this analysis suggests, was the unexpected outcome of purposeful political choices made by proponents of neoliberal economics.
Nickel on the Swedish market: follow‐up 10 years after entry into force of the EU Nickel Directive
Authors: Biesterbos Jacqueline , Yazar Kerem , Lidén Carola
Published: September 2010

Background. The EU Nickel Directive, aimed at primary and secondary prevention of nickel allergy by limitation of nickel release from certain items, came fully into force in July 2001.

Objectives. To assess the prevalence on the market of items with nickel release and to compare the outcome with previous studies performed in Sweden in 1999 and 2002–2003.

Materials and Methods. Nickel release from 659 items covered by the EU Nickel Directive was assessed with the dimethylglyoxime (DMG) test. Special attention, as compared with the previous surveys, was given to cheap jewellery in street markets and sewing materials in haberdashery shops.

Results. Nickel release was shown for 9% of the tested items, all of which were intended for direct and prolonged contact with the skin. A high proportion of items bought at haberdashery shops and street markets, 34% and 61%, respectively, showed nickel release.

Conclusions. The Swedish market for products intended for direct and prolonged contact with the skin has largely adapted to the Nickel Directive. It is suggested that authorities should monitor the market regularly and give attention to areas where compliance with the requirements is poor, for protection of public health.
Frontal affinity chromatography analysis of constructs of DC‐SIGN, DC‐SIGNR and LSECtin extend evidence for affinity to agalactosylated N‐glycans
Authors: Yabe Rikio , Tateno Hiroaki , Hirabayashi Jun
Published: September 2010

Dendritic cell‐specific intracellular adhesion molecule‐3‐grabbing nonintegrin (DC‐SIGN) is a member of the C‐type lectin family selectively expressed on immune‐related cells. In the present study, we performed a systematic interaction analysis of DC‐SIGN and its related receptors, DC‐SIGN‐related protein (DC‐SIGNR) and liver and lymph node sinusoidal endothelial cell C‐type lectin (LSECtin) using frontal affinity chromatography (FAC). Carbohydrate‐recognition domains of the lectins, expressed as Fc–fusion chimeras, were immobilized to Protein A–Sepharose and subjected to quantitative FAC analysis using 157 pyridylaminated glycans. Both DC‐SIGN–Fc and DC‐SIGNR–Fc showed similar specificities for glycans containing terminal mannose and fucose, but great difference in affinity under the given experimental conditions. By contrast, LSECtin–Fc showed no affinity to these glycans. As a common feature, the DC‐SIGN‐related lectin–Fc chimeras, including LSECtin, exhibited binding affinity to mono‐ and/or bi‐antennary agalactosylated N‐glycans. The detailed FAC analysis further implied that the presence of terminal GlcNAc at the N‐acetylglucosaminyltransferase I position is a key determinant for the binding of these lectins to agalactosylated N‐glycans. By contrast, none of the lectins showed significant affinity to highly branched agalactosylated N‐glycans. All of the lectins expressed on the cells were able to mediate cellular adhesion to agalactosylated cells and endocytosis of a model glycoprotein, agalactosylated α1‐acid glycoprotein. In this context, we also identified three agalactosylated serum glycoproteins recognized by DC‐SIGN‐Fc (i.e. α‐2‐macroglobulin, serotransferrin and IgG heavy chain), by lectin blotting and MS analysis. Hence, we propose that ‘agalactosylated N‐glycans’ are candidate ligands common to these lectins.
Thermoelastic Modeling of Rotor Response With Shaft Rub
Authors: Ziaei-Rad S. , Kouchaki E. , Imregun M.
Published: September 2010

This paper studies the effects of shaft rub on a rotating system’s vibration response with emphasis on heat generation at the contact point. A 3D heat transfer code, coupled to a 3D vibration code, was developed to predict the dynamic response of a rotor in the time domain. The shaft bow is represented by an equivalent bending moment and the contact forces by rotating external forces. The seal ring is modeled as a linear spring, which exerts a normal force to the rotor. The tangential force is then calculated as the product of the normal force with the friction coefficient. Stable or unstable spiraling and oscillating modes were seen to occur in well defined shaft speed zones. In the main, for the configurations studied, the shaft vibration was found to be unstable for speeds below the first critical speed and stable for speeds above the first critical speed. Limit cycle behavior was observed when the phase angle between the unbalance force and the response was around 90 deg. The vibration behavior with rub during startup and shutdown was studied by considering the effects of acceleration/deceleration rate, friction coefficient, and mass unbalance. It was found that friction coefficient and increasing mass unbalance amplified the rub effects while acceleration/deceleration rate reduced it.
Precombustion Chamber Design for Emissions Reduction From Large Bore NG Engines
Authors: Simpson Dean J. , Olsen Daniel B.
Published: September 2010

Precombustion chambers (PCCs) are an ignition technology for large bore, natural gas engines, which can extend the lean operating limit through improved combustion stability. Previous research indicates that the PCC is responsible for a significant portion of engine-out emissions, especially near the lean limit of engine operation. In this work, six concept PCC designs are developed with the objective of reducing engine-out emissions, focusing on oxides of nitrogen (NOx). The design variables include chamber geometry, chamber volume, fuel delivery, nozzle geometry, and material thermal conductivity. The concepts are tested on a single cylinder of a large bore, two-stroke cycle, lean burn, natural gas compressor engine, and the results are compared with stock PCC performance. The pollutants of interest include NOx, carbon monoxide, total hydrocarbons, and volatile organic compounds (VOCs). The results indicate that PCC volume has the largest effect on the overall NOx–CO tradeoff. Multiple nozzles and electronic PCC fuel control were found to enhance main chamber combustion stability, particularly at partial load conditions. The PCC influence on VOCs was insignificant; rather, VOCs were found to be heavily dependent on fuel composition.
Effect of CO2 Dilution on Flame Structure and Soot and NO Formations in CH4-Air Nonpremixed Flames
Authors: Samanta Arindam , Ganguly Ranjan , Datta Amitava
Published: September 2010

In the present work, a numerical analysis has been presented to show the variations in flame structure, flame radiation, and formations of soot and NO in methane-air laminar nonpremixed flames with different CO2 dilutions of fuel. It is observed that the flame length reduces as the dilution of the fuel stream by CO2 increases while maintaining constant fuel jet velocity at the burner tip. However, the flame length remains almost unchanged with different blends of CH4 and CO2 if the burner loading (i.e., fuel flow rate×heating value of fuel) is kept constant. Both soot and NO formations decrease monotonically when the CO2 fraction in the fuel is increased. The radiation from the flame also decreases when CO2 dilution of the fuel is increased, particularly, when the fuel jet velocity is maintained constant.
Spy vs. Spy: Recruiting Stem Cells to the War on Cancer
Authors: Ng Kenneth W.
Published: September 2010

Mesenchymal stem cells can home in and deliver drug-carrying nanoparticles to brain tumors.
Morphological and anatomical characterization of ectomycorrhizas and ectendomycorrhizas on Pinus strobus seedlings in a southern Ontario nursery
Authors: Ursic Margot , Peterson R. Larry
Published: September 2010

A morphological and anatomical study of the mycorrhizas on Pinus strobus L. was conducted on seedlings excavated from St.-Williams nursery in southern Ontario. Micro- and macro-scopic characters were used to classify the morphotypes into complexes and, when possible, genera and species. An E-strain fungus, fungi from the Mycelium radicis atrovirens (MRA) complex, and an unidentified ascomycetous "red-type" fungus formed ectendomycorrhizal (EECM) associations, while Tuber sp., Hebeloma sp., and Thelephora terrestris formed ectomycorrhizal (ECM) associations in the nursery. Cultures of Hebeloma sp., the E-strain fungus, Tuber sp., and two morphologically distinct MRA fungi (MRA1, later identified as Phialophora finlandia Wang & Wilcox, and MRA2, unidentified) were isolated from field-collected morphotypes and re-inoculated onto Pinus strobus seedlings grown in semisterile pot cultures for 4 months. In the resynthesis experiment, the E-strain fungus formed EECM with sparse intracellular colonization, and Tuber sp. formed ECM with characteristic cystidia and densely packed mantles, as they had in the field. However, unlike the MRA field specimens, Phialophora finlandia formed ECM in pot culture. Hebeloma sp., normally an ECM former with conifer seedlings, did not form mycorrhizal structures under the given culture conditions, and neither did the MRA2 isolate. Key words: ectomycorrhiza, ectendomycorrhiza, Pinus strobus, Tuber sp., Phialophora finlandia, E-strain.
Puccinia recondita causing leaf rust on cultivated wheats, wild wheats, and rye
Authors: Anikster Y. , Bushnell W. R. , Roelfs A. P. , Eilam T. , Manisterski J.
Published: September 2010

Aecial and telial host range, interfertility, teliospore dimensions, and amount of nuclear DNA were determined for Puccinia recondita collected either worldwide from species of cultivated wheats (Triticum aestivum and Triticum turgidum ssp. durum and rye (Secale cereale), or from wild emmer (Triticum turgidum ssp. dicoccoides) and four species of wild wheat (Aegilops) in Israel. The results indicate that the collections belong in two major groups: Group I (from cultivated wheats and wild emmer), which has Thalictrum speciosissimum (in the Ranunculaceae) as principal aecial host; and Group II (principally from wild wheats or rye), which has several species in the Boraginaceae, such as Anchusa aggregata, Anchusa italica, Echium glomeratum, and Lycopsis arvensis as aecial hosts. In glasshouse experiments, intercrosses could be made readily among collections within Groups I and II but not between the two groups. Group I consisted of all collections from Triticum aestivum, Triticum turgidum ssp. dicoccoides, and most collections from Triticum turgidum ssp. durum. For Group I collections, four species of Aegilops, Hordeum maritimum, S. cereale, as well as Triticum aestivum and Triticum turgidum ssp. durum and ssp. dicoccoides could all serve as telial host in glasshouse experiments. Group II consisted of four types, all clearly different from Group I. Type A was from Triticum turgidum ssp. durum found in fields near Anchusa italica, which was its only aecial host; Triticum aestivum, Triticum turgidum ssp. durum, and Triticum turgidum ssp. dicoccoides could serve as telial hosts. Type B was from Aegilops ovata and had E. glomeratum, Anchusa undulata, and L. arvensis as aecial hosts. Type C was from Aegilops longissima, Aegilops sharonensis, and Aegilops variabilis and had Anchusa aggregata, Anchusa undulata and L. arvensis as aecial hosts. Type D was from S. cereale and had L. arvensis and Anchusa undulata as aecial hosts. In addition to differences in host range, teliospores were wider and bigger in cross sectional area, and nuclear DNA content of pycniospores was 1.3–1.6 times greater in Group II than in Group I. The results suggest that Groups I and II have evolved separately for an extended period and are now morphologically distinct and genetically isolated from each other. Furthermore, differences in both telial and aecial host species, in teliospore dimensions, and in amount of nuclear DNA indicate that subgroups within Group II are beginning to show genetic divergence. Key words: aecial hosts, Aegilops, Anchusa, Echium, Hordeum, leaf rust, Lycopsis, Puccinia recondita, Puccinia triticina, Secale, Thalictrum, Triticum.
Biogeographic relationships between the macrofungi of temperate eastern Asia and eastern North America
Authors: Wu Qiuxin , Mueller Gregory M.
Published: September 2010

Eastern North America and temperate eastern Asia reportedly share a relatively high number of taxa of macrofungi (mushrooms and relatives), including a number of taxa that have putative eastern North America – temperate eastern Asia disjunct distributions. These reports have been used to imply an affinity between the mycota (fungal equivalent of flora and fauna) of the two regions. To date, however, this affinity has not been examined in detail. A comparison of north temperate macrofungal mycotas was undertaken to examine the similarity between these regions. We used two methods in this study: (i) direct comparison of taxon lists and (ii) calculation of the Simpson Coefficient of similarity from lists of selected taxa. These analyses were based on field work, herbarium records, and published taxonomic treatments for Amanita, Lactarius, Ramaria, and Boletaceae. Results of these analyses document that taxonomic similarity between eastern North America and temperate eastern Asia mycotas can be quite high. In all cases, the calculated similarity values for eastern North America – temperate eastern Asia comparisons are higher than those between either region of North America and Europe or between western North America and eastern Asia. Furthermore, the eastern North American and temperate eastern Asian disjunct distributions of macrofungi are usually limited to the level of species or lower. Key words: biogeography, China, disjunct distribution, macrofungi, North America, Simpson Coefficient.
THE INFLUENCE OF TIBIAL PROSTHESIS DESIGN FEATURES ON STRESSES RELATED TO ASEPTIC LOOSENING AND STRESS SHIELDING
Authors: CHONG DESMOND Y. R. , HANSEN ULRICH N. , AMIS ANDREW A.
Published: September 2010

Aseptic loosening caused by mechanical factors is a recognized failure mode for tibial components of knee prostheses. This parametric study investigated the effects of prosthesis fixation design changes, which included the presence, length and diameter of a central stem, the use of fixation pegs beneath the tray, all-polyethylene versus metal-backed tray, prosthesis material stiffness, and cement mantle thickness. The cancellous bone compressive stresses and bone–cement interfacial shear stresses, plus the reduction of strain energy density in the epiphyseal cancellous bone, an indication of the likelihood of component loosening, and bone resorption secondary to stress shielding, were examined. Design features such as longer stems reduced bone and bone–cement interfacial stresses thus the risk of loosening is potentially minimized, but at the expense of an increased tendency for bone resorption. The conflicting trend suggested that bone quality and fixation stability have to be considered mutually for the optimization of prosthesis designs. By comparing the bone stresses and bone–cement shear stresses to reported fatigue strength, it was noted that fatigue of both the cancellous bone and bone–cement interface could be the driving factor for long-term aseptic loosening for metal-backed tibial trays.
DYNAMICAL FINITE ELEMENT MODELING OF SOFT TISSUES AS CHEMOELECTRIC POROUS MEDIA
Authors: YANG ZHAOCHUN , SMOLINSKI PATRICK , LIN JEEN-SHANG , GILBERTSON LARS G.
Published: September 2010

An implicit mixed finite element formulation of hydrated soft biological tissues, based on the Simon model, is presented that incorporates the coupling of solid, fluid, and ion phases as well as the viscoelasticity of soft tissue in the dynamical process. The tissues are modeled as a multi-field viscoelastic body subject to finite deformation. In addition to a three-field (u-w-p) modeling of the porous matrix, the study also includes an ion phase for the ionic solution. After presenting the formulation, an efficient staggered solution scheme is presented: within each time step, the ion charge equation is solved first to give the distribution of the charge concentration, the charge induced osmotic water pressure is then employed in solving the u-w-p equations. The resulting u field becomes a forcing term to the solution of the ion charge concentration equations for iteration. This methodology and codes developed for the study have been verified with one-dimensional (1D) analytical solutions. A 2D chemical electric swelling model illustrates the important role of viscoelasticity. A brain tissue impact example demonstrates the potential application of the model.
First Trial Postural Reactions to Unexpected Balance Disturbances: A Comparison With the Acoustic Startle Reaction
Authors: Oude Nijhuis Lars B. , Allum John H. J. , Valls-Solé Josep , Overeem Sebastiaan , Bloem Bastiaan R.
Published: September 2010

Unexpected support-surface movements delivered during stance elicit “first trial” postural reactions, which are larger and cause greater instability compared with habituated responses. The nature of this first trial reaction remains unknown. We hypothesized that first trial postural reactions consist of a generalized startle reaction, with a similar muscle synergy as the acoustic startle response, combined with an automatic postural reaction. Therefore we compared acoustic startle responses to first trial postural reactions. Eight healthy subjects stood on a support surface that unexpectedly rotated backwards 10 times, followed by 10 startling acoustic stimuli, or vice versa. Outcome measures included full body kinematics and surface EMG from muscles involved in startle reactions or postural control. Postural perturbations and startling acoustic stimuli both elicited a clear first trial reaction, as reflected by larger kinematic and EMG responses. The ensuing habituation rate to repeated identical stimuli was comparable for neck and trunk muscles in both conditions. Onset latencies in neck muscles occurred significantly later for first trial perturbations compared with startle responses, but earlier in trunk muscles. Our results show that platform tilting initially induces reactions larger than needed to maintain equilibrium. For neck and trunk muscles, these first trial postural reactions resembled acoustic startle reflexes. First trial postural reactions may be triggered by interaction of afferent volleys formed by somatosensory and vestibular inputs. Acoustic startle reactions may also be partially triggered by vestibular inputs. Similar muscle activation driven by vestibular inputs may be the common element of first trial postural responses and acoustic startle reactions.
Influence of Biopsychosocial Factors on the Survival of the Elderly in Northeast Brazil—A Prospective Study
Authors: Maciel Álvaro Campos Cavalcanti , Oliveira Guerra Ricardo
Published: September 2010

Background. Identifying the risk factors peculiar to each population has a great relevance, because it enables health policy formulators to analyze information accurately and by doing so, define objectives and action programs aimed at a qualitative and economically feasible solution to the problem. Thus, this study aimed at identifying the risk factors for survival in elderly in a city in the state of Rio Grande do Norte (RN), Brazil.Methods. A prospective study was carried out, where 310 elderly persons were selected to form a baseline. The follow-up was 53 months. The predictive variables were divided into sociodemographic, physical health, neuropsychiatric and functional capacity. Statistical analysis was performed using bivariate analysis, survival analysis, followed by Cox regression in the multivariate analysis.Results. A total of 60 (19.3%) elderly individuals died during the follow-up. The survival mean was 24.8 months. In the Cox analysis, dependence in basic activities of daily living (HR = 3.55), cognitive deficit (HR = 4.22) and stroke (HR = 3.35) continued as independent risk factors for death.Discussion. The risk factors found in the study can be interpreted as the primary predictors for death among elderly members of the community.
Health Monitoring for a Structure Using Its Nonstationary Vibration
Authors: Hirata Yoshimutsu , Tohyama Mikio , Matsumoto Mitsuo , Gotoh Satoru
Published: September 2010

The frequency distribution of a short interval period, the SIP distribution, obtained
from the vibration of a structure that is excited by the force of non‐stationary vibration is available for the robust estimation of the dynamic property of the structure. This paper shows experiments of the health monitoring of a model structure using the SIP distribution. Comparisons of SIP distributions with average DFT spectra are also shown.
Myxoglobulosis of the Appendix: A Case Associated with Ruptured Diverticulum
Authors: Aroukatos Panagiotis , Verras Dionysios , Vandoros Gerassimos P. , Repanti Maria
Published: September 2010

We describe a case of the extremely rare entity of myxoglobulosis of the appendix from a 45-year-old white man who was operated urgently with the clinical diagnosis of acute appendicitis. Sectioning of the appendix revealed the presence in the dilated appendiceal lumen of numerous whitish opaque globules ranging in size from 0.2 to 0.7 cm in diameter. A ruptured diverticulum and several smaller ones were also found. On microscopic examination, the globules consisted of faintly eosinophilic laminations of mucin surrounding an amorphous granular core. The mucin was identified by positivity with histochemical mucin stains. After thorough microscopic examination of the appendix, our case was diagnosed as myxoglobulosis due to mucosal hyperplasia, associated with ruptured diverticulum and acellular extra-appendiceal mucin deposits.
Refsum's Disease—Use of the Intestinal Lipase Inhibitor, Orlistat, as a Novel Therapeutic Approach to a Complex Disorder
Authors: Perera Nimalie J. , Lewis Barry , Tran Huy , Fietz Michael , Sullivan David R.
Published: September 2010

Refsum's Disease is an inherited metabolic disorder in which a metabolite of branched chain fatty acids accumulates due to lack of appropriate oxidative enzymes. Patients have elevated plasma phytanic acid levels and high concentrations of phytanic acid in a variety of tissues leading to progressive tissue damage. Besides retinal degeneration or retinal dystrophy associated with adult onset retinitis pigmentosa, additional symptoms include chronic polyneuropathy, cerebellar ataxia, sensorineural hearing loss, anosmia, ichthyosis, as well as skeletal, cardiac, hepatic, and renal abnormalities. Current management includes avoidance of dietary sources of branched chain fatty acids and regular plasmapheresis to prevent accumulation of these compounds to ameliorate progressive neurological deficits. Two brothers with Refsum's disease who experienced progressive symptoms despite optimal diet and plasmapheresis were commenced on a novel therapy. We report the effect of the intestinal lipase inhibitor, Orlistat, which led to significant reduction (P-value<0.001on 2-sample unpairedt-test) of mean preplasmapheresis phytanic acid levels with retardation of the progression of most of their dermatological and neurological symptoms.
Ultrabroadband Electro-Optic Modulator Based on Hybrid Silicon-Polymer Dual Vertical Slot Waveguide
Authors: Shi Shouyuan , Prather Dennis W.
Published: September 2010

We present a novel hybrid silicon-polymer dual slot waveguide for high speed and ultra-low driving voltage electro-optic (EO) modulation. The proposed design utilizes the unique properties of ferroelectric materials such as LiNbO3 to achieve dual RF and optical modes within a low index nanoslot. The tight mode concentration and overlap in the slot allow the infiltrated organic EO polymers to experience enhanced nonlinear interaction with the applied electric field. Half-wavelength voltage-length product and electro-optic response are rigorously simulated to characterize the proposed design, which reveals ultrabroadband operation, up to 250 GHz, and subvolt driving voltage for a 1 cm long modulator.
Deregulated Semantic Cognition Follows Prefrontal and Temporo-parietal Damage: Evidence from the Impact of Task Constraint on Nonverbal Object Use
Authors: Corbett Faye , Jefferies Elizabeth , Lambon Ralph Matthew A.
Published: September 2010

Semantic cognition, which encompasses all conceptually based behavior, is dependent on the successful interaction of two key components: conceptual representations and regulatory control. Qualitatively distinct disorders of semantic knowledge follow damage to the different parts of this system. Previous studies have shown that patients with multimodal semantic impairment following CVA—a condition referred to as semantic aphasia (SA)—perform poorly on a range of conceptual tasks due to a failure of executive control following prefrontal and/or temporo-parietal infarction [Jefferies, E., & Lambon Ralph, M. A. Semantic impairment in stroke aphasia versus semantic dementia: A case-series comparison. Brain, 129, 2132–2147, 2006]. Although a deficit of core semantic control would be expected to impair all modalities in parallel, most research exploring this condition has focused on tasks in the verbal domain. In a novel exploration of semantic control in the nonverbal domain, therefore, we assessed eight patients with SA on two experiments that examined object use knowledge under different levels of task constraint. Patients exhibited three key characteristics of semantic deregulation: (a) difficulty using conceptual knowledge flexibly to support the noncanonical uses of everyday objects; (b) poor inhibition of semantically related distractor items; and (c) improved object use with the provision of more tightly constraining task conditions following verbal and pictorial cues. Our findings are consistent with the notion that a neural network incorporating the left inferior prefrontal and temporo-parietal areas (damaged in SA) underpins regulation of semantic activation across both verbal and nonverbal modalities.
African signatures of recent positive selection in human FOXI1
Authors: Moreno-Estrada Andrés , Aparicio-Prat Estel , Sikora Martin , Engelken Johannes , Ramírez-Soriano Anna , Calafell Francesc , Bosch Elena
Published: September 2010

Background

The human FOXI1 gene codes for a transcription factor involved in the physiology of the inner ear, testis, and kidney. Using three interspecies comparisons, it has been suggested that this may be a gene under human-specific selection. We sought to confirm this finding by using an extended set of orthologous sequences. Additionally, we explored for signals of natural selection within humans by sequencing the gene in 20 Europeans, 20 East Asians and 20 Yorubas and by analysing SNP variation in a 2 Mb region centered on FOXI1 in 39 worldwide human populations from the HGDP-CEPH diversity panel.

Results

The genome sequences recently available from other primate and non-primate species showed that FOXI1 divergence patterns are compatible with neutral evolution. Sequence-based neutrality tests were not significant in Europeans, East Asians or Yorubas. However, the Long Range Haplotype (LRH) test, as well as the iHS and XP-Rsb statistics revealed significantly extended tracks of homozygosity around FOXI1 in Africa, suggesting a recent episode of positive selection acting on this gene. A functionally relevant SNP, as well as several SNPs either on the putatively selected core haplotypes or with significant iHS or XP-Rsb values, displayed allele frequencies strongly correlated with the absolute geographical latitude of the populations sampled.

Conclusions

We present evidence for recent positive selection in the FOXI1 gene region in Africa. Climate might be related to this recent adaptive event in humans. Of the multiple functions of FOXI1, its role in kidney-mediated water-electrolyte homeostasis is the most obvious candidate for explaining a climate-related adaptation.
Genetic divergence of influenza A NS1 gene in pandemic 2009 H1N1 isolates with respect to H1N1 and H3N2 isolates from previous seasonal epidemics
Authors: Campanini Giulia , Piralla Antonio , Paolucci Stefania , Rovida Francesca , Percivalle Elena , Maga Giovanni , Baldanti Fausto
Published: September 2010

Background

The Influenza A pandemic sustained by a new H1N1 variant (H1N1v) started in Mexico and the USA at the end of April 2009 spreading worldwide in a few weeks. In this study we investigate the variability of the NS1 gene of the pandemic H1N1v strain with respect to previous seasonal strains circulating in humans and the potential selection of virus variants through isolation in cell culture.

Methods

During the period April 27th 2009-Jan 15th 2010, 1633 potential 2009 H1N1v cases have been screened at our center using the CDC detection and typing realtime RT-PCR assays. Virus isolation on MDCK cells was systematically performed in 1/10 positive cases. A subset of 51 H1N1v strains isolated in the period May-September 2009 was selected for NS1 gene sequencing. In addition, 15 H1N1 and 47 H3N2 virus isolates from three previous seasonal epidemics (2006-2009) were analyzed in parallel.

Results

A low variability in the NS1 amino acid (aa) sequence among H1N1v isolates was shown (aa identity 99.5%). A slightly higher NS1 variability was observed among H1N1 and H3N2 strains from previous epidemics (aa identity 98.6% and 98.9%, respectively). The H1N1v strains were closely related (aa identity 92.1%) to swine reference strain (A/swine/Oklahoma/042169/2008). In contrast, substantial divergence (aa identity 83.4%) with respect to human reference strain A/Brevig Mission/1/1918 and previous epidemic strains H1N1 and H3N2 (aa identity 78.9% and 77.6%, respectively) was shown. Specific sequence signatures of uncertain significance in the new virus variant were a C-terminus deletion and a T215P substitution.

Conclusions

The H1N1v NS1 gene was more conserved than that of previous epidemic strains. In addition, a closer genetic identity of H1N1v with the swine than the human reference strains was shown. Hot-spots were shown in the H1N1v NS1 aa sequence whose biologic relevance remains to be investigated.