bluuebunny/crossref_metadata_2025 huggingface dataset:
Sci‐Fri PM: Planning‐11: Selection and optimization of angiographic roadmap images for magnetic resonance guided catheter tracking
Authors: Chen HS , Draper JN , Andersen LB , Sabati M , Frayne R
Published: July 2008

As endovascular magnetic resonance (MR) techniques for device tracking and guidance move closer to demonstrating clinical feasibility, more investigation in the generation and optimization of vascular roadmap images is need to achieve the full benefit of MR‐guided procedure. MR angiographic roadmap imaging requires high signal‐to‐noise (SNR), good vascular‐to‐background contrast and short acquisition time. These requirements not only qualify the appropriate roadmaps for therapy, but also guide in the optimization of their acquisition parameters. We hypothesize that among the well established MR angiographic techniques, low‐resolution phase‐contrast (PC) images would prove satisfactory for vascular roadmap imaging. To verify this, four potential MR angiography techniques, specifically, time‐of‐flight, contrast‐enhanced, phase‐contrast and black‐blood angiography, were explored for roadmap imaging using a canine model on a 3 T MR scanner. PC angiography was specifically performed to evaluate impact of key parameters on the SNR efficiency and vascular‐to‐background contrast efficiency in order to optimize the sequence for therapeutic use. Data were collected from five canines. Phase‐contrast angiography was found to be most suitable for generating vascular roadmap for MR‐guided endovascular therapy. It was also found that small acquisition matrix and large FOV produced satisfactory roadmap images provided that the size of the vessel of interest was more than a few times the in‐plane pixel dimension. Also, reducing the phase encoding steps had minimal effect on vessel oriented parallel to the phase encode direction.
Sci‐Sat AM(1): Imaging‐01: Tumour and normal tissue T2 and ADC distributions for a mouse model at 9.4T
Authors: Larocque M , Syme A , Fallone BG
Published: July 2008

Magnetic resonance (MR) measurements of relaxation times and diffusion coefficient in tissue have been demonstrated to be sensitive to biological changes induced by radiation therapy. We are currently using mouse models of human glioblastoma multiforme (GBM) to study tumour response to ionizing radiation by MRI at 9.4T. Utilizing conventional imaging techniques coupled with quantitative measurements of transverse relaxation time (T2) and apparent diffusion coefficient (ADC), we monitor changes during tumour growth and subsequent changes after single‐fraction radiotherapy. In addition to tumour parameters, we have measured T2 and ADC in other structures that appear in the same transverse slices as tumour tissue. Here we report the measured distributions of T2 and ADC in tumour and in normal tissues that are likely to be encountered during MR imaging of tumour xenografts in mice, including liver, kidney, fat, skeletal muscle, spinal cord, and brain. Quantitative knowledge of these distributions in normal tissue is important in optimizing the sequences used for imaging of these tissues, and in optimizing continued measurements of T2 and ADC changes. Knowledge of parameter distributions in tumour is important because recent studies have suggested that the T2 and ADC responses after therapy may be the result of large shifts in smaller isolated pockets of tumour, rather than more moderate shifts in T2 and ADC over the whole tumour volume. These distributions provide a baseline measurement of typical distributions in advance of radiation therapy.
Sci‐Sat AM(1): Imaging‐05: Analytical scatter estimation for cone‐beam computed tomography
Authors: Ingleby H , Elbakri I , Rickey D , Pistorius S
Published: July 2008

A significant challenge to the implementation of cone‐beam computed tomography (CBCT) for high‐resolution imaging is the high scatter to primary ratio. Scatter causes cupping and shading artifacts, increased noise and decreased contrast in reconstructed images. Methods to reduce the impact of scatter in CBCT are thus very desirable. We are investigating methods for computational scatter estimation and compensation for CBCT, with the goal of incorporating a scatter estimator within a statistical reconstruction algorithm. We have developed an analytical method for estimating single scatter, based on Klein‐Nishina cross‐sections. We have compared scatter estimates generated with this method with the results of high‐count EGSnrc Monte Carlo simulations. The analytical estimates compare favorably with the Monte Carlo estimates. The paper will discuss our method for analytical estimation of single scatter, including the assumptions and simplifications required to render it computationally tractable, along with the results of the comparison between the analytical method and Monte Carlo simulations. The paper will extend previous results obtained with small (40 × 40 × 40 voxel) homogeneous computational phantoms to include results for larger, more clinically relevant phantoms (128 × 128 × 128 voxels, simulated 50/50 breast tissue with inserts of varying contrast). The paper will also discuss computational acceleration obtained through the use of parallel processing via the WestGrid High‐Performance Computing network.
Sci‐Sat AM(1): Imaging‐06: Proximity‐based modification to an automatic method for tumor delineation using MRSI
Authors: Heikal AA , Wachowicz K , Fallone BG
Published: July 2008

Quantifying the relative levels of Choline (Cho) to N‐Acetylaspartate (NAA) has been the method of choice by many groups as a mean to biologically identify tumors in the brain. Mcknight et al. have introduced an automatic technique for delineating tumors biologically using MRSI. A statistical model is used to separate tumors from normal tissue based on the relative concentrations of Choline and NAA in both tissue types; that method is commonly referred to as the Choline‐to‐NAA Index (CNI). In their work, it is assumed that the variation in the relative levels of Cho to NAA in normal brain is unnoticeable to within 2 standard deviations of the mean. However, developments in MRSI sequences have enabled the detectablity of more variations within the relative levels of Cho to NAA in normal tissue. With the uncertainty in the Cho to NAA levels of normal tissue increasing, it is essential to modify the CNI method to improve its specificity. This work introduces a modification to the CNI method developed by McKnight et al. that would address such increase in uncertainty. Instead of relying on an arbitrary CNI value of 2 to define the tumor boundaries, our method defines a high certainty tumor volume, surrounded by a region of uncertainty. Then based on their proximity to high certainty tumor regions, the voxels in the uncertainty region are segmented to either tumor or normal tissue. Preliminary results suggest that the proposed modified method decreases the number of false positive resulting from the original CNI method.
Sci‐Sat AM(1): Imaging‐08: Small animal APD PET detector with submillimetric resolution for molecular imaging
Authors: Bérard P , Bergeron M , Pepin CM , Cadorette J , Tétrault M‐A , Viscogliosi N , Fontaine R , Dautet H , Davies M , Lecomte R
Published: July 2008

Visualization and quantification of biological processes in mice, the preferred animal model in most preclinical studies, require the best possible spatial resolution in positron emission tomography (PET). A new 64‐channel avalanche photodiode (APD) detector module was developed to achieve submillimeter spatial resolution for this purpose. The module consists of dual 4 × 8 APD arrays mounted in a custom ceramic holder. Individual APD pixels having an active area of 1.1 × 1.1 mm2 at a 1.2 mm pitch can be fitted to an 8 × 8 LYSO scintillator block designed to accommodate one‐to‐one coupling. An analog test board with four 16‐channel preamplifier ASICs was designed to be interfaced with the existing LabPET digital processing electronics. At a standard APD operating bias, a mean energy resolution of 27.5 ± 0.6% was typically obtained at 511 keV with a relative standard deviation of 13.8% in signal amplitude for the 64 individual pixels. Crosstalk between pixels was found to be well below the typical lower energy threshold used for PET imaging applications. With two modules in coincidence, a global timing resolution of 5.0 ns FWHM was measured. Finally, an intrinsic spatial resolution of 0.8 mm FWHM was measured by sweeping a 22Na point source between two detector arrays. The proposed detector module demonstrates promising characteristics for dedicated mouse PET imaging at submillimiter resolution.
Sci‐Sat AM(2): Brachy‐05: Dosimetry effects of the TG‐43 approximations for two iodine seeds in LDR brachytherapy
Authors: Furstoss C , Bertrand MJ , Poon E , Reniers B , Pignol JP , Carrier JF , Beaulieu L , Verhaegen F
Published: July 2008

Purposes: This work consists of studying the interseed and tissue composition effects for two model iodine seeds: the IBt Interseed‐125 and the 6711 model seed. Materials & Methods: Three seeds were modeled with the MCNP MC code in a water sphere to evaluate the interseed effect. The dose calculated at different distances from the centre was compared to the dose summed when the seeds were simulated separately. The tissue composition effect was studied calculating the radial dose function for different tissues. Before carrying out post‐implant studies, the absolute dose calculated by MC was compared to experiment results: with LiF TLDs in an acrylic breast phantom and with an EBT Gafchromic film placed in a water tank. Afterwards, the TG‐43 approximation effects were studied for a prostate and breast post‐implant. Results and Discussion: The interseed effect study shows that this effect is more important for model 6711 (15%) than for IBt (10%) due to the silver rod in 6711. For both seed models the variations of the radial dose function as a function of the tissue composition are quasi similar. The absolute dose comparisons between MC calculations and experiments give good agreement (inferior to 3% in general). For the prostate and breast post‐implant studies, a 10% difference between MC calculations and the TG‐43 is found for both models of seeds. Conclusion: This study shows that the differences in dose distributions between TG43 and MC are quite similar for the two models of seeds and are about 10% for the studied post‐implant treatments.
Sci‐Sat AM(2): Brachy‐06: A Comparison of MR/CT fusion versus CT alone for assessment of implant quality in permanent prostate brachytherapy
Authors: Sasaki DK , Malkoske K , Bews J , Cho P , Drachenberg D , Chowdhury A
Published: July 2008

Low dose‐rate permanent implant brachytherapy is widely used in the management of patients with early stage prostate cancer. An assessment of the implant quality is usually carried out 30 days after the implant is delivered, using computed tomography (CT) to identify the prostate and seeds. This is difficult due to poor contrast of the prostate and the superposition of seeds in the CT images. Magnetic resonance (MR) imaging offers superior contrast but inferior visualization of seeds. At our centre, patients are imaged using both CT and T2 weighted MR 30 days after an implant, and the image sets are fused using a commercial software package. The seeds are identified on CT and the prostate volumes are contoured on MR, with fusion performed by matching seeds on CT with seed signal voids on MR. The purpose of this study was to compare standard prostate post‐implant dosimetric parameters (D90, V100, etc.) for prostates contoured on CT alone (MR blinded) versus MR/CT fusion. 25 patients were evaluated with all contouring performed by the same physician. We found that the prostate volume was overestimated using CT alone as compared to MR/CT fusion (mean: 37.2cc vs. 35.0cc respectively, p = 0.033). We also found that dosimetric parameters were underestimated for CT alone compared to MR/CT fusion, including D90 (mean: 144.3Gy vs. 150.8Gy respectively, p = 0.005) and V100 (mean: 89.2% vs. 91.0% respectively, p = 0.01). Centres using CT alone for post‐implant dosimetry may therefore be underestimating their implant quality.
Genetic and Functional Variation in Denitrifier Populations along a Short-Term Restoration Chronosequence
Authors: Smith Jason M. , Ogram Andrew
Published: July 2008

Complete removal of plants and soil to exposed bedrock, in order to eradicate the Hole-in-the-Donut (HID) region of the Everglades National Park, FL, of exotic invasive plants, presented the opportunity to monitor the redevelopment of soil and the associated microbial communities along a short-term restoration chronosequence. Sampling plots were established for sites restored in 1989, 1997, 2000, 2001, and 2003. The goal of this study was to characterize the activity and diversity of denitrifying bacterial populations in developing HID soils in an effort to understand changes in nitrogen (N) cycling during short-term primary succession. Denitrifying enzyme activity (DEA) was detected in soils from all sites, indicating a potential for N loss via denitrification. However, no correlation between DEA and time since disturbance was observed. Diversity of bacterial denitrifiers in soils was characterized by sequence analysis of nitrite reductase genes (
nirK
and
nirS
) in DNA extracts from soils ranging in nitrate concentrations from 1.8 to 7.8 mg kg
−1
. High levels of diversity were observed in both
nirK
and
nirS
clone libraries. Statistical analyses of clone libraries suggest a different response of
nirS
- and
nirK
-type denitrifiers to factors associated with soil redevelopment.
nirS
populations demonstrated a linear pattern of succession, with individual lineages represented at each site, while multiple levels of analysis suggest
nirK
populations respond in a grouped pattern. These findings suggest that
nirK
communities are more sensitive than
nirS
communities to environmental gradients in these soils.
Flock Health Indicators and
Campylobacter
spp. in Commercial Housed Broilers Reared in Great Britain
Authors: Bull Stephanie A. , Thomas Alastair , Humphrey Thomas , Ellis-Iversen Johanne , Cook Alasdair J. , Lovell Roger , Jorgensen Frieda
Published: July 2008

This study investigated the relationship between flock health and
Campylobacter
infection of housed commercial broilers in Great Britain. Thirty ceca were collected at slaughter from batches of broilers from 789 flocks, at either full or partial depopulation, between December 2003 and March 2006 and examined individually for
Campylobacter
by direct plating onto selective media. Management and health data were collected from each flock and included information on mortality or culling during rearing, the number of birds rejected for infectious or noninfectious causes at slaughter, the proportion of birds with digital dermatitis (also termed hock burn), and other general characteristics of the flock.
Campylobacter
spp. were isolated from 280 (35%) flocks. The relationship between bird health and welfare and
Campylobacter
status of flocks was assessed using random-effects logistic regression models, adjusting for region, month, year, and rearing regime.
Campylobacter
-positive batches of ceca were associated with higher levels of rejection due to infection (odds ratio [OR], 1.5; 95% confidence interval [CI
95%
], 0.98 to 2.30) and digital dermatitis (OR, 2.08; CI
95%
, 1.20 to 3.61). Furthermore, higher levels of these conditions were also associated with the highest-level category of within-flock
Campylobacter
prevalence (70 to 100%). These results could indicate that improving health and welfare may also reduce
Campylobacter
in broilers.
Dissemination of
Cronobacter
spp. (
Enterobacter sakazakii
) in a Powdered Milk Protein Manufacturing Facility
Authors: Mullane N. , Healy B. , Meade J. , Whyte P. , Wall P. G. , Fanning S.
Published: July 2008

The microbial contamination of air filters and possible links to contaminated product in a powdered milk protein-processing facility were investigated. Over a 10-month period, seven air filters, the environment, and powdered product were analyzed for the presence of
Cronobacter
spp. The effects of air filter installation, maintenance, and subsequent dissemination of
Cronobacter
were investigated. A total of 30 isolates were characterized by pulsed-field gel electrophoresis (PFGE). PFGE revealed the presence of three clonal populations distributed throughout the manufacturing site. This study highlights the need for proper installation of air filters to limit the dissemination of microorganisms into processing sites.
Autoaggregation of
Xylella fastidiosa
Cells Is Influenced by Type I and Type IV Pili
Authors: De La Fuente Leonardo , Burr Thomas J. , Hoch Harvey C.
Published: July 2008

Autoaggregation of widely dispersed
Xylella fastidiosa
cells into compact cell masses occurred over a period of hours following 7 to 11 days of growth in microfluidic chambers. Studies involving the use of mutants defective in polarly positioned type I (
fimA
-negative), type IV (
pilB
-negative), or both type I and IV (
fimA
- and
pilO
-negative) pili revealed the importance and role of pili in the autoaggregation process.
DjlA, a Membrane-Anchored DnaJ-Like Protein, Is Required for Cytotoxicity of Clam Pathogen
Vibrio tapetis
to Hemocytes
Authors: Lakhal Fatma , Bury-Moné Stéphanie , Nomane Yanoura , Le Goïc Nelly , Paillard Christine , Jacq Annick
Published: July 2008

DjlA is an inner membrane cochaperone belonging to the DnaJ family, which has been shown to be involved in
Legionella
sp. pathogenesis. In this study, we explored the role of this protein in the physiology and virulence of
Vibrio tapetis
, the etiological agent of brown ring disease (BRD) in Manila clam (
Ruditapes philippinarum
). Analysis of the
djlA
locus in
V. tapetis
revealed a putative organization in an operon with a downstream gene that we designated

duf924
Vt

, which encodes a conserved protein with an unknown function and has homologues in bacteria and eukaryotes.
djlA
mutants displayed a reduced growth rate and showed an important loss of cytotoxic activity against
R. philippinarum
hemocytes in vitro, which could be restored by extrachromosomal expression of wild-type

djlA
Vt

but not

duf924
Vt

. These results are in keeping with the potential importance of DjlA for bacterial pathogenicity and open new perspectives for understanding the mechanism of action of this protein in the novel
V. tapetis-R. philippinarum
interaction model.
An Amino Acid Substitution at Position 740 in σ
70
of
Ralstonia solanacearum
Strain OE1-1 Affects Its In Planta Growth
Authors: Kanda Ayami , Tsuneishi Kazuhiro , Mori Ai , Ohnishi Kouhei , Kiba Akinori , Hikichi Yasufumi
Published: July 2008

Growth of
Ralstonia solanacearum
strain OE1-1 in roots after invasion is required for virulence. An Arg740Cys substitution in σ
70
of OE1-1 resulted in loss of in planta growth and virulence. The negative dominance of mutant σ
70
over the wild-type protein suggested that the amino acid substitution may affect the in planta growth of OE1-1, leading to a lack of virulence.
Bond Strengthening in Oral Bacterial Adhesion to Salivary Conditioning Films
Authors: van der Mei Henny C. , Rustema-Abbing Minie , de Vries Joop , Busscher Henk J.
Published: July 2008

Transition from reversible to irreversible bacterial adhesion is a highly relevant but poorly understood step in initial biofilm formation. We hypothesize that in oral biofilm formation, irreversible adhesion is caused by bond strengthening due to specific bacterial interactions with salivary conditioning films. Here, we compared the initial adhesion of six oral bacterial strains to salivary conditioning films with their adhesion to a bovine serum albumin (BSA) coating and related their adhesion to the strengthening of the binding forces measured with bacteria-coated atomic force microscopy cantilevers. All strains adhered in higher numbers to salivary conditioning films than to BSA coatings, and specific bacterial interactions with salivary conditioning films were accompanied by stronger initial adhesion forces. Bond strengthening occurred on a time scale of several tens of seconds and was slower for actinomyces than for streptococci. Nonspecific interactions between bacteria and BSA coatings strengthened twofold faster than their specific interactions with salivary conditioning films, likely because specific interactions require a closer approach of interacting surfaces with the removal of interfacial water and a more extensive rearrangement of surface structures. After bond strengthening, bacterial adhesion forces with a salivary conditioning film remained stronger than those with BSA coatings.
Dynamics of Glycolytic Regulation during Adaptation of
Saccharomyces cerevisiae
to Fermentative Metabolism
Authors: van den Brink Joost , Canelas André B. , van Gulik Walter M. , Pronk Jack T. , Heijnen Joseph J. , de Winde Johannes H. , Daran-Lapujade Pascale
Published: July 2008

The ability of baker's yeast (
Saccharomyces cerevisiae
) to rapidly increase its glycolytic flux upon a switch from respiratory to fermentative sugar metabolism is an important characteristic for many of its multiple industrial applications. An increased glycolytic flux can be achieved by an increase in the glycolytic enzyme capacities (
V
max
) and/or by changes in the concentrations of low-molecular-weight substrates, products, and effectors. The goal of the present study was to understand the time-dependent, multilevel regulation of glycolytic enzymes during a switch from fully respiratory conditions to fully fermentative conditions. The switch from glucose-limited aerobic chemostat growth to full anaerobiosis and glucose excess resulted in rapid acceleration of fermentative metabolism. Although the capacities (
V
max
) of the glycolytic enzymes did not change until 45 min after the switch, the intracellular levels of several substrates, products, and effectors involved in the regulation of glycolysis did change substantially during the initial 45 min (e.g., there was a buildup of the phosphofructokinase activator fructose-2,6-bisphosphate). This study revealed two distinct phases in the upregulation of glycolysis upon a switch to fermentative conditions: (i) an initial phase, in which regulation occurs completely through changes in metabolite levels; and (ii) a second phase, in which regulation is achieved through a combination of changes in
V
max
and metabolite concentrations. This multilevel regulation study qualitatively explains the increase in flux through the glycolytic enzymes upon a switch of
S. cerevisiae
to fermentative conditions and provides a better understanding of the roles of different regulatory mechanisms that influence the dynamics of yeast glycolysis.
Cre/
lox
System and PCR-Based Genome Engineering in
Bacillus subtilis
Authors: Yan Xin , Yu Hao-Jie , Hong Qing , Li Shun-Peng
Published: July 2008

We have developed a fast and accurate method to engineer the
Bacillus subtilis
genome that involves fusing by PCR two flanking homology regions with an antibiotic resistance gene cassette bordered by two mutant
lox
sites (
lox71
and
lox66
). The resulting PCR products were used directly to transform
B. subtilis
, and then transient Cre recombinase expression in the transformants was used to recombine
lox71
and
lox66
into a double-mutant
lox72
site, thereby excising the marker gene. The mutation process could also be accomplished in 2 days by using a strain containing a
cre
isopropyl-β-
d
-thiogalactopyranoside (IPTG)-inducible expression cassette in the chromosome as the recipient or using the
lox
site-flanked cassette containing both the
cre
IPTG-inducible expression cassette and resistance marker. The in vivo recombination efficiencies of different
lox
pairs were compared; the
lox72
site that remains in the chromosome after Cre recombination had a low affinity for Cre and did not interfere with subsequent rounds of Cre/
lox
mutagenesis. We used this method to inactivate a specific gene, to delete a long fragment, to realize the in-frame deletion of a target gene, to introduce a gene of interest, and to carry out multiple manipulations in the same background. Furthermore, it should also be applicable to large genome rearrangement.
Isolation of Sabin-Like Polioviruses from Wastewater in a Country Using Inactivated Polio Vaccine
Authors: Zurbriggen Sebastian , Tobler Kurt , Abril Carlos , Diedrich Sabine , Ackermann Mathias , Pallansch Mark A. , Metzler Alfred
Published: July 2008

From 2001 to 2004, Switzerland switched from routine vaccination with oral polio vaccine (OPV) to inactivated polio vaccine (IPV), using both vaccines in the intervening period. Since IPV is less effective at inducing mucosal immunity than OPV, this change might allow imported poliovirus to circulate undetected more easily in an increasingly IPV-immunized population. Environmental monitoring is a recognized tool for identifying polioviruses in a community. To look for evidence of poliovirus circulation following cessation of OPV use, two sewage treatment plants located in the Zurich area were sampled from 2004 to 2006. Following virus isolation using either RD or L20B cells, enteroviruses and polioviruses were identified by reverse transcription-PCR. A total of 20 out of 174 wastewater samples were positive for 62 Sabin-like isolates. One isolate from each poliovirus-positive sample was analyzed in more detail. Sequencing the complete viral protein 1 (VP1) capsid coding region, as well as intratypic differentiation (ITD), identified 3 Sabin type 1, 13 Sabin type 2, and 4 Sabin type 3 strains. One serotype 1 strain showed a discordant result in the ITD. Three-quarters of the strains showed mutations within the 5′ untranslated region and VP1, known to be associated with reversion to virulence. Moreover, three strains showed heterotypic recombination (S2/S1 and S3/S2/S3). The low number of synonymous mutations and the partial temperature sensitivity are not consistent with extended circulation of these Sabin virus strains. Nevertheless, the continuous introduction of polioviruses into the community emphasizes the necessity for uninterrupted child vaccination to maintain high herd immunity.
The YebC Family Protein PA0964 Negatively Regulates thePseudomonas aeruginosaQuinolone Signal System and Pyocyanin Production
Authors: Liang Haihua , Li Lingling , Dong Zhaolin , Surette Michael G. , Duan Kangmin
Published: July 2008

Bacterial pathogenicity is often manifested by the expression of various cell-associated and secreted virulence factors, such as exoenzymes, protease, and toxins. InPseudomonas aeruginosa, the expression of virulence genes is coordinately controlled by the global regulatory quorum-sensing systems, which includes thelasandrhlsystems as well as thePseudomonasquinolone signal (PQS) system. Phenazine compounds are among the virulence factors under the control of both therhland PQS systems. In this study, regulation of thephzA1B1C1D1E1(phzA1) operon, which is involved in phenazine synthesis, was investigated. In an initial study of inducing conditions, we observed thatphzA1was induced by subinhibitory concentrations of tetracycline. Screening of 13,000 mutants revealed 32 genes that alteredphzA1expression in the presence of subinhibitory tetracycline concentrations. Among them, the gene PA0964, designatedpmpR(pqsR-mediatedPQSregulator), has been identified as a novel regulator of the PQS system. It belongs to a large group of widespread conserved hypothetical proteins with unknown function, the YebC protein family (Pfam family DUF28). It negatively regulates the quorum-sensing response regulatorpqsRof the PQS system by binding at its promoter region. AlongsidephzA1expression and phenazine and pyocyanin production, a set of virulence factors genes controlled by bothrhland the PQS were shown to be modulated by PmpR. Swarming motility and biofilm formation were also significantly affected. The results added another layer of regulation in the rather complex quorum-sensing systems inP. aeruginosaand demonstrated a clear functional clue for the YebC family proteins.
Impassable YscP Substrates and Their Impact on the
Yersinia enterocolitica
Type III Secretion Pathway
Authors: Riordan Kelly E. , Sorg Joseph A. , Berube Bryan J. , Schneewind Olaf
Published: July 2008

Yersinia
type III machines secrete protein substrates across the bacterial envelope and, following assembly of their secretion needles, transport effector Yops into host cells. According to their destination during type III secretion, early, middle, and late secretion substrates can be distinguished; however, the signals and mechanisms whereby these proteins are recognized and transported by the secretion machine are not understood. Here, we examine several hybrids between secretion substrates and the impassable reporter protein glutathione
S
-transferase (GST). YscP-GST and YopR-GST blocked type III secretion; however, YscF-, YopD-, YopN-, and LcrV-GST did not. Unlike YopR-GST, which can block type III machines only during their assembly, expression of YscP-GST led to an immediate and complete block of all secretion. The secretion signal of YscP was mapped to its first 10 codons or amino acids; however, YscP
Δ2-15
-GST, lacking this secretion signal, imposed a partial blockade. YscP-GST copurified with the type III ATPase complex (YscN, YscL, and YscQ) and with YscO, suggesting that the association of specific machine components with the impassable substrate may cause the block in type III secretion.
Genomic Island 2 of
Brucella melitensis
Is a Major Virulence Determinant: Functional Analyses of Genomic Islands
Authors: Rajashekara Gireesh , Covert Jill , Petersen Erik , Eskra Linda , Splitter Gary
Published: July 2008

Brucella
genomic islands (GIs) share similarities in their genomic organization to pathogenicity islands from other bacteria and are likely acquired by lateral gene transfer. Here, we report the identification of a GI that is important for the pathogenicity of
Brucella melitensis
. The deletion of GI-1, GI-5, or GI-6 did not affect bacterial growth in macrophages as well as their virulence in interferon regulatory factor 1-deficient (IRF-1
−/−
) mice, suggesting that these islands do not contribute to
Brucella
virulence. However, the deletion of GI-2 resulted in the attenuation of bacterial growth in macrophages and virulence in IRF-1
−/−
mice. The GI-2 mutant also displayed a rough lipopolysaccharide (LPS) phenotype indicated by acriflavin agglutination, suggesting that in vitro and in vivo attenuation is a result of LPS alteration. Further, systematic analysis of the entire GI-2 revealed two open reading frames (ORFs), BMEI0997 and I0998, that encode hypothetical sugar transferases and contribute to LPS alteration, as the deletion of either of these ORFs resulted in a rough phenotype similar to that of the GI-2 mutant. Complementation analyses indicated that in addition to I0997 and I0998, I0999 is required to restore the smooth LPS in the GI-2 mutant as well as its full in vitro and in vivo virulence. The I0999 sequence analysis suggested that it might function as a transporter to help facilitate the transport or linking of the O antigen to the LPS. Our study also indicated that the rough LPS resulting from the GI-2 deletion may affect pathogen-associated molecular pattern recognition by Toll-like receptors.
Molecular Mechanisms Underlying the Positive Stringent Response of the
Bacillus subtilis ilv-leu
Operon, Involved in the Biosynthesis of Branched-Chain Amino Acids
Authors: Tojo Shigeo , Satomura Takenori , Kumamoto Kanako , Hirooka Kazutake , Fujita Yasutaro
Published: July 2008

Branched-chain amino acids are the most abundant amino acids in proteins. The
Bacillus subtilis ilv-leu
operon is involved in the biosynthesis of branched-chain amino acids. This operon exhibits a RelA-dependent positive stringent response to amino acid starvation. We investigated this positive stringent response upon lysine starvation as well as decoyinine treatment. Deletion analysis involving various
lacZ
fusions revealed two molecular mechanisms underlying the positive stringent response of
ilv-leu
, i.e., CodY-dependent and -independent mechanisms. The former is most likely triggered by the decrease in the in vivo concentration of GTP upon lysine starvation, GTP being a corepressor of the CodY protein. So, the GTP decrease derepressed
ilv-leu
expression through detachment of the CodY protein from its
cis
elements upstream of the
ilv-leu
promoter. By means of base substitution and in vitro transcription analyses, the latter (CodY-independent) mechanism was found to comprise the modulation of the transcription initiation frequency, which likely depends on fluctuation of the in vivo RNA polymerase substrate concentrations after stringent treatment, and to involve at least the base species of adenine at the 5′ end of the
ilv-leu
transcript. As discussed, this mechanism is presumably distinct from that for
B. subtilis rrn
operons, which involves changes in the in vivo concentration of the initiating GTP.
The pathology of placenta accreta, a worldwide epidemic
Authors: Khong T Y
Published: July 2008

The incidence of placenta accreta, defined as the abnormal adherence of the placenta to the uterine wall, has been increasing alarmingly in the developed as well as the developing world. There is considerable maternal morbidity and mortality related to the condition. The pathophysiology focuses on the balance between decidualisation on the one hand and trophoblast invasion on the other. Pathological diagnosis relies on the finding of placental villi in direct apposition to myometrium, either in hysterectomy specimens or in placental basal plates.
The placenta in pre-eclampsia and intrauterine growth restriction
Authors: Roberts D J , Post M D
Published: July 2008

Placental examination in pregnancies with complications such as pre-eclampsia/toxaemia of pregnancy (PET) or intrauterine growth restriction (IUGR) can provide insight into specific diagnoses, recurrence risk and chronicity. Placental findings have clinical significance as they can identify the aetiology of the IUGR (as in inborn errors of metabolism) and predict recurrence (as in maternal floor infarcts). Evaluation of obstetric pathology in such pregnancies should be an integral part of clinical care. This review will highlight the placental findings in IUGR and PET.
Cryptococcus meningitis and skin lesions in an HIV negative child
Authors: Swe Swe K , Bekker A , Greeff S , Perkins D R
Published: July 2008

Disseminated cryptococcosis is an uncommon occurrence in immunocompetent populations and occurs mainly in immunocompromised patients. The first case of cryptococcus meningitis and skin lesions in a 4-year-old confirmed HIV negative boy who presented with fever, meningism and skin lesions is reported. On examination the child was confused, uncooperative, and had neck stiffness and raised skin lesions. A septic screen, including skin scraping, was performed; the child was treated with penicillin and ceftriaxone for suspected meningococcal meningitis. The cerebrospinal fluid (CSF) had normal protein, glucose and chloride levels; yeasts were observed on Gram stain from the CSF and skin scraping. The India ink stain andCryptococcus neoformanslatex agglutination test on the CSF were both positive. Bacterial culture of the skin biopsy, CSF and blood culture specimens was negative. The child was treated with amphotericin B based on preliminary results, and had a gradual recovery with no neurological sequelae. The child continued oral fluconazole.
Analysis of microsatellite instability in colorectal carcinoma by microfluidic-based chip electrophoresis
Authors: Odenthal M , Barta N , Lohfink D , Drebber U , Schulze F , Dienes H P , Baldus S E
Published: July 2008

Microsatellite analysis is an important tool in clinical research and molecular diagnostics because microsatellite instability (MSI) occurs frequently in various types of cancer. Approximately 10–15% of colorectal, gastric and endometrial carcinomas are associated with MSI, and this has an impact on clinical prognosis. The microsatellite loci Bat25, Bat26, D2S123, D5S346 and D17S250, recommended by the Bethesda guidelines, were analysed by microfluidic-based on-chip electrophoresis in 40 cases of colon carcinoma with known MSI status. In all cases, microfluidic separation of the PCR amplicons resulted in highly resolved, distinct patterns of each of the five microsatellite loci. Detection of MSI could be demonstrated by microsatellite-loci-associated, well-defined deviations in the electropherogram profiles of tumour and non-tumour material, and confirmed the classification of MSI cases performed by conventional technology. In conclusion, microfluidic chip technology is a simple and reliable approach for MSI detection that allows label-free and very fast analysis of microsatellite amplicons.
Cardiac botryomycosis: an autopsy report
Authors: Gupta K , Das A , Radotra B D , Bhalla A
Published: July 2008

Visceral botryomycosis is rare, and documented sites are lung, brain, kidney, liver and prostate. This report describes a rare autopsy case of disseminated visceral botryomycosis, with bulky, grape-like botryomycotic vegetations in the heart, and similar abscesses in the lungs and bone marrow. This is the first such report in the literature to the best of our knowledge.
Analysis of mucins: role in laboratory diagnosis
Authors: Mall A S
Published: July 2008

Mucins are high molecular weight glycoproteins with complex oligosaccharide side chains attached to the apomucin protein backbone byO-glycosidic linkage; they are found in crude mucus gels that protect epithelial surfaces in the major tracts of the body and as transmembrane proteins expressed on the apical cell surface of glandular and ductal epithelia of various organs. Changes in the sequence of glycosylation of mucins in different settings generate a variety of epitopes in the oligosaccharide side chains of mucins, including newly expressed blood-group antigens, distinguishing between normal and diseased states. Tumour-associated epitopes on mucins and their antigenicity make them suitable as immunotargets on malignant epithelial cells and their secretions, creating a surge of interest in mucins as diagnostic and prognostic markers for various diseases, and even influencing the design of mucin-based vaccines. This review discusses the emerging roles of mucins such as MUC1 and MUC4 in cancer and some other diseases, and stresses how underglycosylated and truncated mucins are exploited as markers of disease and to monitor widespread metastasis, making them useful in patient management. Furthermore the type, pattern and amount of mucin secreted in some tissues have been considered in the classification and terminology of neoplasia and in specific organs such as the pancreas. These factors have been instrumental in pathological classification, diagnosis and prognostication of neoplasia.
Systemic mastocytosis with associated myeloproliferative disease and precursor B lymphoblastic leukaemia with t(13;13)(q12;q22) involvingFLT3
Authors: Tzankov A , Sotlar K , Muhlematter D , Theocharides A , Went P , Jotterand M , Horny H-P , Dirnhofer S
Published: July 2008

Systemic mastocytoses represent neoplastic proliferations of mast cells. In about 20% of cases systemic mastocytoses are accompanied by clonal haematopoietic non-mast cell-lineage disorders, most commonly myeloid neoplasms. A case of systemic mastocytosis carrying the characteristic mutation at codon 816 (D816V) in theKITgene of mast cells, with two concurrent accompanying clonal haematopoietic non-mast cell-lineage disorders, chronic myeloproliferative disease, unclassifiable and precursor B lymphoblastic leukaemia is documented. Both accompanying clonal haematopoietic non-mast cell-lineage disorders carried the wild-typeKITgene, but had a novel t(13;13)(q12;q22) involving theFLT3locus at 13q12. The chronic myeloproliferative disease, unclassifiable and the precursor B lymphoblastic leukaemia were cured by syngenous stem cell transplantation, but the systemic mastocytosis persisted for more than 10 years. The additional impact of molecular techniques on the correct diagnosis in haematological malignancies is highlighted, and evidence is provided that, apart from internal tandem duplications and mutations,FLT3can be activated by translocations.
Use of tissue ink to maintain identification of individual cores on needle biopsies of the prostate
Authors: Singh P B , Saw N K , Haq A , Blades R A , Martin F L , Matanhelia S S , Nicholson C M
Published: July 2008

Background:

There is an increasing necessity to extract the maximum amount of information, beyond even a cancer diagnosis, from prostate biopsies. Thus, maintaining site-specific information regarding individual biopsy cores might be critical.

Aim:

To evaluate the applicability of employing tissue ink to maintain the identity of individual prostatic biopsy cores.

Method:

In this ongoing study, 12 core prostate biopsy specimens are sent to the laboratory in individual pots labelled according to anatomical site. The specimens are placed in two separate multi-compartment cassettes. They are inked with different colours to identify the site of origin from each lobe. The cassettes are then processed with a single paraffin block for each side; the six cores from each side can be mounted on a single slide.

Results:

The different colours used adhere well to the biopsy cores, thus maintaining the identity of each core. Six cores from each side are embedded in a single paraffin block and examined on a single slide, making it cost-effective, while maintaining high quality, accurate histopathological information.

Conclusion:

Differential inking of prostate biopsy cores is an easily applicable method that is cost-effective and provides tumour location information. Prostate biopsy data archived to maintain individual core information might be used to determine applicability of such information to predict extra-capsular extension by correlating with imaging and radical prostatectomy findings, and for treatment planning.
Quantitative assessment of the degree of villous atrophy in patients with coeliac disease
Authors: Ciaccio E J , Bhagat G , Naiyer A J , Hernandez L , Green P H R
Published: July 2008

Background:

Endoscopy and biopsy are used to diagnose coeliac disease. There are, however, observer-dependent interpretations of the degree of villous atrophy in biopsies. A pilot study using quantitative image-processing procedures was performed to quantify the degree of villous atrophy in patients with coeliac disease.

Method:

The degree of villous atrophy in duodenal biopsy images was quantified by calculating the ratio of villous edge-to-piecewise arc length (E/P ratio), and this value was compared with the blinded assessment of Marsh score for degree of villous atrophy.

Results:

Mean E/P ratios for n = 31 biopsy images, 2.76 (SD 0.44) (Marsh IIIa), 1.91 (0.50) (Marsh IIIb) and 1.18 (0.22) (Marsh IIIc), were significantly different (p = 0.006). Based on non-parametric testing, the E/P ratios were inversely correlated with Marsh scores (Spearman coefficient ρ = −0.798, Kendall τ = −0.681; p<0.0001).

Conclusions:

Biopsy images quantified by image analysis correlated exceedingly well with the histopathological grade of villous atrophy. Since quantified measurements are real-numbered values and lack observer bias, measurement of villous atrophy based on image analysis lends itself to standardisation of histological grading.
Nestin is expressed in basal-like and triple negative breast cancers
Authors: Parry S , Savage K , Marchiò C , Reis-Filho J S
Published: July 2008

Aims:

To analyse the distribution of nestin expression in different breast tumours and to determine the prognostic impact of nestin expression.

Methods:

Nestin expression was immunohistochemically analysed in a cohort of 245 invasive breast cancer patients treated with therapeutic surgery followed by anthracycline-based chemotherapy using a semi-quantitative scoring system.

Results:

Nestin was exclusively expressed in grade III breast carcinoma and preferentially expressed in basal-like and triple negative cancers. Nestin-positive tumours displayed high proliferation rates and p53 nuclear expression. Lymph-node positive patients with nestin-positive cancers had a shorter breast cancer specific survival; however nestin was not an independent prognostic factor on multivariate analysis.

Conclusions:

Nestin expression is preferentially found in basal-like and triple negative breast carcinomas. Further studies are warranted to define the biological role played by nestin in these subgroups of breast cancers.
Chronic daily headache
Authors: Weatherall Mark W
Published: July 2008

Headache is a relatively neglected neurological disorder. Indeed, many neurologists find outpatient headache management—particularly of chronic daily headache—one of the least engaging parts of their job. The neglect of headache as a research problem has been reversed by the relatively recent emergence of strong programmes in centres such as Copenhagen, London, Philadelphia, New York, Liege and Leiden. Partly as a result of this, the pejorative attitude to headache as a clinical problem is less than it was, but many neurologists are still bemused by the intrusion of headache, both at a local level when headache patients occupy scarce specialist beds, and at a global level where the World Health Organization ranks migraine in the top 20 causes of global disability. This article reviews one of the commonest headache syndromes encountered by neurologists—chronic daily headache.
Viral encephalitis: a clinician’s guide
Authors: Solomon Tom , Hart Ian J , Beeching Nicholas J
Published: July 2008

The management of patients with suspected viral encephalitis has been revolutionised in recent years with improved imaging and viral diagnostics, better antiviral and immunomodulatory therapies, and enhanced neurointensive care. Despite this, disasters in patient management are sadly not uncommon. While some patients are attacked with all known antimicrobials with little thought to investigation of the cause of their illness, for others there are prolonged and inappropriate delays before treatment is started. Although viral encephalitis is relatively rare, patients withsuspectedcentral nervous system (CNS) infections, whomighthave viral encephalitis, are not. In addition, the increasing number of immunocompromised patients who may have viral CNS infections, plus the spread of encephalitis caused by arthropod-borne viruses, present new challenges to clinicians. This article discusses the Liverpool approach to the investigation and treatment of adults with suspected viral encephalitis, and introduces the Liverpool algorithm for investigation and treatment of immunocompetent adults with suspected viral encephalitis (available atwww.liv.ac.uk/braininfections).
Neurological complications of coeliac disease: what is the evidence?
Authors: Grossman G
Published: July 2008

Coeliac disease is a chronic immune-mediated disorder that primarily affects the gastrointestinal tract. There is an inflammatory response in the intestine to the ingestion of gluten which improves with a gluten-free diet. Many patients, especially adults, may be asymptomatic or have only extraintestinal symptoms at onset without any of the classical coeliac symptoms. In the last two decades there have been increasing numbers of reports describing neurological complications of coeliac disease, especially ataxia, peripheral neuropathy and epilepsy. This literature has become quite controversial, with disputes over the definition of coeliac disease and gluten sensitivity, whether neurological complications are caused by coeliac disease or are epiphenomena, and whether the proposed complications respond to a gluten-free diet. This review uses an evidence-based approach to critically assess this literature and provides guidelines for the evaluation and management of these patients.