bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ras GTPase-Activating Protein Regulation of Actin Cytoskeleton and Hyphal Polarity in
Aspergillus nidulans
Authors: Harispe Laura , Portela Cecilia , Scazzocchio Claudio , Peñalva Miguel A. , Gorfinkiel Lisette 
Published: November 2007

ABSTRACT

Aspergillus nidulans gapA1
, a mutation leading to compact, fluffy colonies and delayed polarity establishment, maps to a gene encoding a Ras GTPase-activating protein. Domain organization and phylogenetic analyses strongly indicate that GapA regulates one or more “true” Ras proteins. A
gapA
Δ strain is viable.
gapA
colonies are more compact than
gapA1
colonies and show reduced conidiation.
gapA
Δ strains have abnormal conidiophores, characterized by the absence of one of the two layers of sterigmata seen in the wild type.
gapA
transcript levels are very low in conidia but increase during germination and reach their maximum at a time coincident with germ tube emergence. Elevated levels persist in hyphae. In germinating conidiospores,
gapA
Δ disrupts the normal coupling of isotropic growth, polarity establishment, and mitosis, resulting in a highly heterogeneous cell population, including malformed germlings and a class of giant cells with no germ tubes and a multitude of nuclei. Unlike wild-type conidia,
gapA
Δ conidia germinate without a carbon source. Giant multinucleated spores and carbon source-independent germination have been reported in strains carrying a
rasA
dominant active allele, indicating that GapA downregulates RasA.
gapA
Δ cells show a polarity maintenance defect characterized by apical swelling and subapical branching. The strongly polarized wild-type F-actin distribution is lost in
gapA
Δ cells. As GapA-green fluorescent protein shows cortical localization with strong predominance at the hyphal tips, we propose that GapA-mediated downregulation of Ras signaling at the plasma membrane of these tips is involved in the polarization of the actin cytoskeleton that is required for hyphal growth and, possibly, for asexual morphogenesis.
Target of Rapamycin and LST8 Proteins Associate with Membranes from the Endoplasmic Reticulum in the Unicellular Green Alga
Chlamydomonas reinhardtii
Authors: Díaz-Troya Sandra , Florencio Francisco J. , Crespo José L. 
Published: November 2007

ABSTRACT

The highly conserved target of rapamycin (TOR) kinase is a central controller of cell growth in all eukaryotes. TOR exists in two functionally and structurally distinct complexes, termed TOR complex 1 (TORC1) and TORC2. LST8 is a TOR-interacting protein that is present in both TORC1 and TORC2. Here we report the identification and characterization of TOR and LST8 in large protein complexes in the model photosynthetic green alga
Chlamydomonas reinhardtii
. We demonstrate that
Chlamydomonas
LST8 is part of a rapamycin-sensitive TOR complex in this green alga. Biochemical fractionation and indirect immunofluorescence microscopy studies indicate that TOR and LST8 exist in high-molecular-mass complexes that associate with microsomal membranes and are particularly abundant in the peri-basal body region in
Chlamydomonas
cells. A
Saccharomyces cerevisiae
complementation assay demonstrates that
Chlamydomonas
LST8 is able to functionally and structurally replace endogenous yeast LST8 and allows us to propose that binding of LST8 to TOR is essential for cell growth.
Profiling Bovine Antibody Responses to
Mycobacterium avium
subsp.
paratuberculosis
Infection by Using Protein Arrays
Authors: Bannantine John P. , Paustian Michael L. , Waters W. Ray , Stabel Judith R. , Palmer Mitchell V. , Li Lingling , Kapur Vivek 
Published: November 2007

ABSTRACT

With the genome sequence of
Mycobacterium avium
subsp.
paratuberculosis
determined, technologies are now being developed for construction of protein arrays to detect the presence of antibodies against
M. avium
subsp.
paratuberculosis
in host serum. The power of this approach is that it enables a direct comparison of
M. avium
subsp.
paratuberculosis
proteins to each other in relation to their immunostimulatory capabilities. In this study, 93 recombinant proteins, produced in
Escherichia coli
, were arrayed and spotted onto nitrocellulose. These proteins include unknown hypothetical proteins and cell surface proteins as well as proteins encoded by large sequence polymorphisms present uniquely in
M. avium
subsp.
paratuberculosis
. Also included were previously reported or known
M. avium
subsp.
paratuberculosis
antigens to serve as a frame of reference. Sera from healthy control cattle (
n
= 3) and cattle infected with either
M. avium
subsp.
avium
and
Mycobacterium bovis
were exposed to the array to identify nonspecific or cross-reactive epitopes. These data demonstrated a degree of cross-reactivity with the
M. avium
subsp.
avium
proteins that was higher than the degree of cross-reactivity with the more distantly related
M. bovis
proteins. Finally, sera from naturally infected cattle (
n
= 3) as well as cattle experimentally infected with
M. avium
subsp.
paratuberculosis
(
n
= 3) were used to probe the array to identify antigens in the context of Johne's disease. Three membrane proteins were the most strongly detected in all serum samples, and they included an invasion protein, an ABC peptide transport permease, and a putative GTPase protein. This powerful combination of genomic information, molecular tools, and immunological assays has enabled the identification of previously unknown antigens of
M. avium
subsp.
paratuberculosis
.
Modulation of Pulmonary Dendritic Cell Function during Mycobacterial Infection
Authors: Anis Mursalin M. , Fulton Scott A. , Reba Scott M. , Liu Yi , Harding Clifford V. , Boom W. Henry 
Published: November 2007

ABSTRACT

We have previously reported that during mycobacterial infection, naïve CD4
+
T-cell activation is enhanced in the lungs. We investigated the role of chemokine receptor CCR7 and its ligands in the ability of CD11c
+
lung dendritic cells (DCs) to activate naïve CD4
+
T cells during pulmonary infection with
Mycobacterium bovis
bacillus Calmette-Guérin (BCG). BCG infection resulted in the accumulation and maturation in the lungs of DCs that persisted as the mycobacterial burden declined. Lung DCs from infected mice expressed more major histocompatibility complex class II (MHC-II) than those from uninfected mice. CCR7 expression levels on lung DCs were comparable among uninfected and infected mice. The gene expression of the CCR7 ligand CCL19 progressively increased throughout BCG infection, and its expression was MyD88 dependent. CD11c
+
lung cells from BCG-infected mice activated ovalbumin (OVA)-specific naïve CD4
+
T cells more than CD11c
+
lung cells from uninfected mice. Interestingly, during peak mycobacterial infection, CD11c
hi
MHC
hi
lung DCs had slightly decreased chemotaxis toward the CCR7 ligand CCL21 and less efficiency in activating naive CD4
+
T cells than DCs from mice during late-stage infection, when few bacilli are found in the lung. These findings suggest that during BCG infection, the inflammation and sustained expression of CCL19 result in the recruitment, activation, and retention in the lung of DCs that can activate naïve CD4
+
T cells in situ.
Molecular Basis of Commensalism in the Urinary Tract: Low Virulence or Virulence Attenuation?
Authors: Zdziarski Jaroslaw , Svanborg Catharina , Wullt Björn , Hacker Jörg , Dobrindt Ulrich 
Published: November 2007

ABSTRACT

In some patients,
Escherichia coli
strains establish significant bacteriuria without causing symptoms of urinary tract infection (UTI). These asymptomatic-bacteriuria (ABU) strains have been shown to express fewer virulence factors than the uropathogenic
E. coli
(UPEC) strains that cause severe, symptomatic UTI. Paradoxically, ABU strains carry many typical UPEC virulence genes, and the molecular basis of their low virulence therefore remains unclear. This study examined whether ABU strains might evolve from UPEC by genome loss and virulence gene attenuation. The presence of conserved
E. coli
K-12 genes was examined using an
E. coli
K-12 strain MG1655-specific DNA array and the distribution of UPEC virulence-related genes was examined with the
E. coli
pathoarray. Two groups of strains could be distinguished. Several ABU strains were shown by multilocus sequence typing and by comparative genomic analyses to be related to UPEC but to have smaller genome sizes. There were significant alterations in essential virulence genes, including reductive evolution by point mutations, DNA rearrangements, and deletions. Other strains were unrelated to UPEC and lacked most of the virulence-associated genes. The results suggest that some ABU strains arise from virulent strains by attenuation of virulence genes while others are nonvirulent and resemble commensal strains. We propose that virulence attenuation might constitute a general mechanism for mucosal pathogens to evolve toward commensalism.
Expression of a Uniquely Regulated Extracellular Polysaccharide Confers a Large-Capsule Phenotype to
Bacteroides fragilis
Authors: Chatzidaki-Livanis Maria , Coyne Michael J. , Roche-Hakansson Hazeline , Comstock Laurie E. 
Published: November 2007

ABSTRACT

Bacteroides fragilis
synthesizes eight distinct capsular polysaccharides, more than any described bacterium outside the order
Bacteroidales
. Here, we show that this organism also produces a high-molecular-weight extracellular polysaccharide (EPS). Expression of the EPS results in the formation of a large polysaccharide layer around the bacteria which prevents them from forming a tight pellet upon centrifugation and from entering a Percoll density gradient. Like expression of the capsular polysaccharides, expression of the EPS is phase variable and dictated by DNA inversion of its promoter. EPS expression is regulated at one level by the DNA invertase Tsr19, which is encoded by a gene immediately upstream of the EPS locus and inverts the EPS promoter, causing an on or off phenotype. Expression of the EPS is also regulated at another level, which dictates the amount of EPS produced. By analyzing a panel of
tsr19
deletion mutants, we found that the number of inverted repeats (IRs) flanking the promoter is variable. Transcription into the EPS genes is greater in mutants with a single IR between the promoter and the downstream EPS genes than in mutants with more than one IR in this region, correlating with the synthesis of more EPS. By analyzing the relative orientations of the EPS promoter of bacteria obtained from human fecal samples, we showed that both DNA inversion and variation in the number of IRs are active processes of
B. fragilis
in the endogenous human intestinal ecosystem.
Priscian on Divine Ideas and Mental Conceptions: The Discussions in the Glosulae in Priscianum, the Notae Dunelmenses, William of Champeaux and Abelard
Authors: Rosier-Catach Irène 
Published: November 2007

AbstractPriscian's Institutiones Grammaticae, which rely on Stoic and Neoplatonic sources, constituted an important, although quite neglected, link in the chain of transmission of ancient philosophy in the Middle Ages. There is, in particular, a passage where Priscian discusses the vexed claim that common names can be proper names of the universal species and where he talks about the ideas existing in the divine mind. At the beginning of the 12th century, the anonymous Glosulae super Priscianum and the Notae Dunelmenses, which heavily quote William of Champeaux (as master G.), interpret the passage in the context of a growing interest in the problem of universals, raising semantic as well as ontological questions, and introducing a Platonic view on universals in the discussions on the signification of the noun. Moreover, this same passage will be used by Abelard to elaborate one of his opinions about the signification of universal or common names—that they signify "mental conceptions".
Symbolism and Linguistic Semantics. Some Questions (and Confusions) from Late Antique Neoplatonism up to Eriugena
Authors: Bonfiglioli Stefania , Marmo Costantino 
Published: November 2007

AbstractThe notion of 'symbol' in Eriugena's writing is far from clear. It has an ambiguous semantic connection with other terms such as 'signification', 'figure', 'allegory', 'veil', 'agalma', 'form', 'shadow', 'mystery' and so on. This paper aims to explore into the origins of such a semantic ambiguity, already present in the texts of the pseudo-Dionysian corpus which Eriugena translated and commented upon. In the probable Neoplatonic sources of this corpus, the Greek term symbolon shares some aspects of its meaning with other words inherited from the ancient tradition, such as synthēma , eikōn , homoiotēs. Some of them, such as eikōn and homoiotēs, belong to the field of images and are associated with linguistic semantics in the Neoplatonic commentaries not only to Plato but also to Aristotle's logical works. Among the late ancient Neoplatonists, particular attention is paid to Proclus and to his use of the term agalma. In fact, the textual history of this word seems to be a privileged perspective from which to reconstruct the Neoplatonic semantic blending of symbol and image, as well as the main role played by linguistic issues in this conflation.
Theory of Supposition vs. Theory of Fallacies in Ockham
Authors: Novaes Catarina Dutilh 
Published: November 2007

AbstractI propose to examine the issue of whether the ancient tradition in logic continued to be developed in the later medieval period from the vantage point of the relations between two specific groups of theories, namely the medieval theories of supposition and the (originally) ancient theories of fallacies. More specifically, I examine whether supposition theories absorbed and replaced theories of fallacies, or whether the latter continued to exist, with respect to one particular author, William of Ockham. I compare different parts of Ockham's Summa Logicae, namely III-4 (on fallacies), and the final chapters of part I and first chapters of part II (on supposition). I conclude that there is overlap of conceptual apparatus and of goals (concerning propositions that must be distinguished) in Ockham's theories of supposition and of fallacies, but that the respective conceptual apparatuses also present substantial dissimilarities. Hence, theories of supposition are better seen as an addition to the general logical framework that medieval authors had inherited from ancient times, rather than the replacement of an ancient tradition by a medieval one. Indeed, supposition theories and fallacy theories had different tasks to fulfil, and in this sense both had their place in fourteenth century logic.
Relationship between Vegetation Biophysical Properties and Surface Temperature Using Multisensor Satellite Data
Authors: Hong Seungbum , Lakshmi Venkat , Small Eric E. 
Published: November 2007

Abstract
Vegetation is an important factor in global climatic variability and plays a key role in the complex interactions between the land surface and the atmosphere. This study focuses on the spatial and temporal variability of vegetation and its relationship with land–atmosphere interactions. The authors have analyzed the vegetation water content (VegWC) from the Advanced Microwave Scanning Radiometer for EOS (AMSR-E), the leaf area index (LAI), the normalized difference vegetation index (NDVI), the land surface temperature (Ts), and the Moderate Resolution Imaging Spectroradiometer (MODIS). Three regions, which have climatically differing characteristics, have been selected: the North America Monsoon System (NAMS) region, the Southern Great Plains (SGP) region, and the Little River Watershed in Tifton, Georgia. Temporal analyses were performed by comparing satellite observations from 2003 and 2004. The introduction of the normalized vegetation water content (NVegWC) derived as the ratio of VegWC and LAI corresponding to the amount of water in individual leaves has been estimated and this yields significant correlation with NDVI and Ts. The analysis of the NVegWC–NDVI relationship in the above listed three regions displays a negative exponential relation, and the Ts–NDVI relationship (TvX relationship) is inversely proportional. The correlation between these variables is higher in arid areas such as the NAMS region, and becomes less correlated in the more humid and more vegetated regions such as the area of eastern Georgia. A land-cover map is used to examine the influence of vegetation types on the vegetation biophysical and surface temperature relationships. The regional distribution of vegetation reflects the relationship between the vegetation biological characteristics of water and the growing environment.
Fifty-Seven-Year California Reanalysis Downscaling at 10 km (CaRD10). Part I: System Detail and Validation with Observations
Authors: Kanamitsu Masao , Kanamaru Hideki 
Published: November 2007

Abstract
For the purpose of producing datasets for regional-scale climate change research and application, the NCEP–NCAR reanalysis for the period 1948–2005 was dynamically downscaled to hourly, 10-km resolution over California using the Regional Spectral Model.
This is Part I of a two-part paper, describing the details of the downscaling system and comparing the downscaled analysis [California Reanalysis Downscaling at 10 km (CaRD10)] against observation and global analysis. An extensive validation of the downscaled analysis was performed using station observations, Higgins gridded precipitation analysis, and Precipitation-Elevation Regression on Independent Slopes Model (PRISM) precipitation analysis.
In general, the CaRD10 near-surface wind and temperature fit better to regional-scale station observations than the NCEP–NCAR reanalysis used to force the regional model, supporting the premise that the regional downscaling is a viable method to attain regional detail from large-scale analysis. This advantage of CaRD10 was found on all time scales, ranging from hourly to decadal scales (i.e., from diurnal variation to multidecadal trend).
Dynamically downscaled analysis provides ways to study various regional climate phenomena of different time scales because all produced variables are dynamically, physically, and hydrologically consistent. However, the CaRD10 is not free from problems. It suffers from positive bias in precipitation for heavy precipitation events. The CaRD10 is inaccurate near the lateral boundary where regional detail is damped by the lateral boundary relaxation. It is important to understand these limitations before the downscaled analysis is used for research.
Robot model validation
Authors: Gawthrop P.J. , Li X. 
Published: November 2007

Some initial results arising from a project involving robot validation are described. A theme of the project is that control, whether adaptive or non-adaptive, should be model-based; that is, the controller should contain a model of the dynamic system describing the robotic manipulator. Good control requires a good model, and obtaining such a model is the aim of the validation exercise. The paper focuses on validating models of three components of the robot system: link flexibility, DC motors, and manipulator dynamics. In each case, algorithms, simulation and experimental results are presented. The use of symbolic algebra techniques is emphasised. Relationships with other area of control and systems theory are explored. In particular, the relationships with parameter identification and fault detection are noted.
A prognostic maintenance system based on the Hough Transformation
Authors: Flint A.D. 
Published: November 2007

An automated predictive maintenance system has been developed based on the Hough Transform. The Hough Transform, used in image processing to extract geometrical primitives from image data, has been adapted to extract linear trend features from monitored data. The predictive maintenance system uses the extracted trend features to diagnose incipient fault conditions. It then predicts the time for the system to reach a critical fault condition. The transform provides an early warning of a developing fault allowing operating staff to anticipate the types of maintenance required before secondary damage and complete breakdown occurs. It can also deal robustly with noisy data, including impulsive noise. It is proposed that logistic curves may be useful for the empirical description of wear failure. A multi-point generalisation of the Hough Transform (Flint et al, 1992) was developed for extracting logistic features from developing fault signatures. The new generalisation of the Hough Transform differs from earlier generalisations by incorporating early data fusion to reduce the size of previously large cumbersome arrays. A brief description is given of the Hough Transform's application to two predictive maintenance case studies. The first case study is the uni-feature problem of providing predictive maintenance decisions for a diesel-engine lubricating oil system. The subject of the second case study is a pneumatic sliding-door system. Here a multivariate generalisation of the Hough Transform is required. The proposed generalisation involves the accumulation of vector rather than scalar votes in an array.
Modular system for control experimentation
Authors: Mitchell R.J. 
Published: November 2007

A modular system has recently been developed which allows many experiments to be performed studying various control problems. Experimenters can use software provided for them which demonstrates the appropriate principles, as well as developing their own programs. The system is user friendly, allows the development of a variety of algorithms, and its modularity has enabled the system to be used in many applications both for teaching and research. This paper describes the philosophy behind the system, the components used in its implementation and some of the ways in which it has been used. These include control of a motor, interfacing to microprocessors, analysis and control of a flexible arm, and measurement and control in a mobile robot.
Application of an extended Kalman filter for high-performance current regulation of a vector-controlled induction machine drive
Authors: Hardan F. , Zhang L. , Shepherd W. 
Published: November 2007

Variable frequency AC drives using voltage-source inverters to supply induction motors are increasingly used in industry for high-performance speed response. Such a drive usually employs a vector-controller at the outer speed-loop which will generate the required torque-current signal. An inner current control loop is incorporated to ensure that an appropriate reference current is impressed on the stator circuit. However, due to nonlinearity and time varying characteristics of the machine circuit, a fixed-parameter regulator cannot give good current control performance in the transient state. The paper presents a model-based predictive current regulator for a vector-con trolled induction motor drive. An extended Kalman filter is employed to estimate the back-EMF of the machine stator circuit model used by the inner current regulator loop. This also estimates the rotor resistance for slip angular velocity calculation in the outer speed-loop. The adaptive feature of this controller leads to improved speed-response performance from the induction machine.
Neural network identification and control of an underwater vehicle
Authors: Lisboa P.J.G. , Kodogiannis V.S. , Lucas J. 
Published: November 2007

Real-time predictive control requires a forward model that is both accurate and fast. This paper introduces two nonlinear internal memory network architectures and compares their performance with a Multi-layer Perceptron (MLP) augmented with the use of spread encoding. The test plant is a single component from an Underwater Robotic Vehicle (URV), comprising a thruster encased in a steel frame and provided with buoyancy. This assemblv is free to move under water and is controlled for depth. The internal memory networks are of comparable accuracy to the MLP but more parsimonious, resulting, in a faster response which makes them better suited for on-line control. Although a particular case study is presented as the focus of this paper, the algorithms and methods developed have generic applicability.