bluuebunny/crossref_metadata_2025_split huggingface dataset:
TH‐C‐351‐02: Registration Based Automatic Segmentation and Wall Motion Analysis for 4D Cardiac Micro‐CT in Mice
Authors: Schreibmann E , Badea C , Fox T 
Published: July 2008

Purpose: We present an automated method for segmentation and tracking of hearth anatomy using 4D cardiac micro‐CT datasets in mice. Cardiac motion is determined and analyzed using the deformation field obtained after non‐rigidly deforming a template to all the time frames of the 4D dataset. Method and Materials: 4D micro‐CT image sets were acquired with a temporal resolution of 10 ms and 100 microns spatial resolution in four mice using the Duke in‐house developed micro‐CT scanner and cardio‐respiratory gating. Ten cardiac phases were used in the data acquisition. The images of the heart at different phases were registered using a BSpline deformable model. The contour points on the diastolic phase were automatically mapped to the corresponding points on the images of other phases following the mapping relation established by the deformable model. The method's stability to noise and artifacts in the input images was assessed using the 4D virtual mouse Moby phantom. Results: The deformable model was capable of accommodating significant variability of cardiac motion over time and across different individuals. The template was warped to the first phase of the 4D dataset with an accuracy of 0.95, 0.96 and for the left ventricle, myocardium and right ventricle as compared by the Hausdorff measure to manual segmentation. In between phases, worst segmentation accuracy was 0.93, 0.95 and 0.94 for left ventricle, myocardium and right ventricle. Additionally, the method automatically measures regional motion and deformation by probing the deformation field on the segmented contours. Conclusion: Heart wall contour evolution in 4D micro‐CT images can be easily defined and tracked using a BSpline deformable model, with no user interaction required. The method provides pre‐clinical accuracy while eliminating the labor‐intensive segmentation procedure.Image acquisition was performed at the Duke Center for In Vivo Microscopy an NCRR/NCI National Resource (R21‐CA124584‐01, 2U24‐CA092656, P41‐RR005959).
TH‐C‐332‐02: First Implementation of High‐Resolution Dual‐Detector Region‐Of‐Interest Cone‐Beam Computed Tomography (ROI‐CBCT) for a Rotating C‐Arm Gantry System
Authors: Patel V , Ionita C , Keleshis C , Sherman J , Hoffmann K , Bednarek D , Rudin S 
Published: July 2008

Purpose: Region‐of‐interest cone‐beam computed tomography (ROI‐CBCT) has the potential to reduce integral dose while providing higher‐resolution data in the ROI. Previous work used rotating object geometries. We have implemented an ROI‐CBCT system on a clinical rotating C‐arm gantry system and have developed methods for combining high‐resolution projection data within the ROI and low‐resolution, low‐dose data outside the ROI. Method and Materials: High‐resolution ROI projection data were acquired of a coronary stent placed in a rabbit using a custom‐made, high‐sensitivity, microangiographic‐fluoroscope (HSMAF) detector (35 micron pixels), attached to the C‐arm of a clinical fluoroscopic gantry. Full field‐of‐view (FFOV), low‐resolution data were acquired at the same dose as the HSMAF (standard‐dose) and at a lower dose using a commercial flat‐panel detector (FPD) (194 micron pixels). HSMAF data were spatially registered with FPD data using cross‐correlation techniques. The lower‐dose FPD pixel values were matched to the HSMAF values using linear regression. During reconstruction, HSMAF data were used within the ROI, while corrected lower‐dose FPD data were used outside the ROI. Reconstructions were performed with HSMAF/lower‐dose‐FPD and standard‐dose‐FPD data using geometric calibration data, Parker weights, a Shepp‐Logan filter, and a Feldkamp algorithm, generating 512 × 512 × 512 volumes (25 micron voxels). Results: The dual‐detector ROI‐CBCT reconstruction exhibits greater detail than that of the FPD alone. The full‐width‐at‐half‐maxima of line profiles of stent struts (100 micron diameter) are approximately 150 and 290 microns for the dual‐detector and FPD data, respectively. No truncation artifacts are visible. The integral dose of the dual‐detector system is 54% that of the standard‐dose FPD for this experiment. Conclusion: High‐resolution 3D images of stents implanted in a rabbit are successfully obtained using a new rotating‐gantry dual‐detector ROI‐CBCT system. Resolution is significantly higher and integral dose is lower with ROI‐CBCT compared to the standard FPD approach.(Support: NIH‐Grants R01‐NS43924, R01‐EB002873, Toshiba‐Medical‐Systems‐Corporation).
Genetic and Functional Variation in Denitrifier Populations along a Short-Term Restoration Chronosequence
Authors: Smith Jason M. , Ogram Andrew 
Published: July 2008

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT
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

ABSTRACTBacterial 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

ABSTRACT

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

ABSTRACT

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.