bluuebunny/crossref_metadata_2025_split huggingface dataset:
A NOVEL MULTIPLEX PCR SYSTEM FOR THE DETECTION OF STAPHYLOCOCCAL ENTEROTOXIN B, TSST, NUC AND FEM GENES OF STAPHYLOCOCCUS AUREUS IN FOOD SYSTEM
Authors: SHYLAJA R. , MURALI H.S. , BATRA H.V. , BAWA A.S. 
Published: March 2010

ABSTRACTStaphylococcal enterotoxin B (SEB), toxic shock syndrome, the superantigens are responsible for diseases such as staphylococcal food poisoning and toxic shock syndrome. An easy and quick system is desirable to detect toxin‐producing strains. In this report, we described standardization of a novel multiplex‐polymerase chain reaction (PCR) assay for simultaneous detection of four important genes associated with the Staphylococcus aureus viz., SEB, Tsst, genus‐specific nuclease (nuc) and Fem genes along with an internal amplification control (IAC), which has now become mandatory in diagnostic PCRs, particularly when tested on environmental or food samples. This mPCR method is sensitive enough to detect cells as low as 103 cfu/mL or /g of the food samples. When evaluated on 136 food and environmental samples, the system detected 4 SEB‐positive S. aureus strains. The S. aureus strains that have been identified to contain the SEB gene in the mPCR were unequivocally detected for the toxin expression by the TECRA kit. mPCR produced a 100% correlation with conventional identification method. As SEB and Tsst are qualified as biowarfare molecules, this system is of immense help in detecting them during emergencies of biological war and suspected outbreaks of S. aureus food poisoning directly from the food and environmental samples.PRACTICAL APPLICATIONSThe virulence‐associated genes targeted in this study are super antigenic in nature and are responsible for diseases such as staphylococcal food poisoning and toxic shock syndrome, and these molecules are also qualified as biowarfare agents. The high throughput and cost‐effective multiplex PCR method reported here could identify all these genes successfully from both artificially spiked and natural food samples and may also find its application in detection of these toxin‐producing Staphylococcus aureus from clinical and environmental samples.
Evolutionary Computation for Remote Sensing Applications
Authors: Easson Greg , Momm H. G. 
Published: March 2010

AbstractAs the volume of available remotely sensed imagery increases so does the need to extract more specific information in a timely and cost‐effective fashion to enhance and/or update decision support systems. This manuscript provides an overview of the existing image information extraction techniques using evolutionary computation algorithms. Emphasis is given to remote sensing applications. The literature investigated is further divided into four groups based on the research objectives: image enhancement, image classification, feature extraction, and modeling. Some of the strengths of evolutionary computation are discussed, such as robust classification capabilities and ability to work with linear and non‐linear problems. Conversely, the works reviewed reveal some of the challenges in the integration of evolutionary computation and remote sensing as well as possible solutions. Limited work was found addressing the multi‐class image classification problem and assessment of the randomness involved in the generation of the first set of candidate solutions from which the algorithm begins. Based on our study, the use of evolutionary computation algorithms for information extraction from imagery is likely to grow, specifically in two areas: inverse modeling and object‐based approaches. This technology is still in its early stages of development and the capabilities of evolutionary computation are well suited to the complexities of the image processing and information extraction problems.
Role of fungal trehalose and bacterial thiamine in the improved survival and growth of the ectomycorrhizal fungus Laccaria bicolor S238N and the helper bacterium Pseudomonas fluorescens BBc6R8
Authors: Deveau A. , Brulé C. , Palin B. , Champmartin D. , Rubini P. , Garbaye J. , Sarniguet A. , Frey‐Klett P. 
Published: March 2010

SummaryThe mycorrhiza helper bacterial strain Pseudomonas fluorescens BBc6R8 enhances the establishment of Laccaria bicolor S238N ectomycorrhizae by improving the pre‐symbiotic growth and survival of the fungus. Nothing is known about the effect of the ectomycorrhizal fungus on the helper bacteria or the molecules that are involved in the interaction. In this study, we have monitored the population density of the helper strain P. fluorescens BBc6R8 in soils inoculated with L. bicolor and in control soils and found that the ectomycorhizal fungus improves the survival of the helper bacteria. We investigated the identity of the fungal and bacterial metabolites involved in this reciprocal growth‐promoting effect using a combination of growth measurements, chemoattractant assays, HPLC and in silico genome analyses. We showed that trehalose, a disaccharide that accumulates to high levels in the fungal hyphae, chemoattracted and promoted the growth of the helper bacteria. Meanwhile, P. fluorescens BBc6R8 produced thiamine at concentrations that enhanced the fungal growth in vitro. Altogether our data indicate that the interaction between the two microorganisms is beneficial for both species and relies, at least in part, on trophic mutualism.
CTX‐M‐15‐type extended‐spectrum beta‐lactamases‐producing Escherichia coli from wild birds in Germany
Authors: Guenther Sebastian , Grobbel Mirjam , Beutlich Janine , Bethe Astrid , Friedrich Nicole D. , Goedecke Andreas , Lübke‐Becker Antina , Guerra Beatriz , Wieler Lothar H. , Ewers Christa 
Published: March 2010

SummaryThe isolation of Escherichia coli from wild birds in Germany revealed the occurrence of four CTX‐M‐15‐producing strains from four different birds (2.3% of 172 isolates). CTX‐M producers were recovered from two Eurasian Blackbirds, one Rock Pigeon and a Greater White‐fronted Goose. All CTX‐M‐producing E. coli revealed a clonal relationship as determined by pulsed‐field gel electrophoresis (PFGE) and were assigned to multilocus sequence type (ST) 648. Our findings suggest the emergence of a new clone with epidemiological importance and strengthen the role of wild bird species other than waterfowl as possible reservoirs of ESBL‐producing Enterobacteriaceae.
Monte Carlo calculated absorbed‐dose energy dependence of EBT and EBT2 film
Authors: Sutherland J. G. H. , Rogers D. W. O. 
Published: March 2010

Purpose:The absorbed‐dose energy dependence of GAFCHROMIC EBT and EBT2 film irradiated in photon beams is studied to understand the shape of the curves and the physics behind them.Methods:The absorbed‐dose energy dependence is calculated using the EGSnrc‐based EGS_chamber and DOSRZnrc codes by calculating the ratio of dose to water to dose to active film layers at photon energies ranging from 3 keV to 18 MeV. These data are compared to the mass energy absorption coefficient ratios and the restricted stopping power ratios of water to active film materials as well as to previous experimental results.Results:In the photon energy range of 100 keV to 18 MeV the absorbed‐dose energy dependence is found to be energy independent within ±0.6%. However, below 100 keV, the absorbed‐dose energy dependence of EBT varies by approximately 10% due to changes in mass energy absorption coefficient ratios of water to film materials, as well as an increase in the number of electrons being created and scattered in the central surface layer of the film. Results are found to disagree with previous experimental studies suggesting the possibility of an intrinsic energy dependence at lower photon energies. For EBT2 film the absorbed‐dose energy dependence at low photon energies varies by 50% or 10% depending on the manufacturing lot due to changes in the ratio of mass energy absorption coefficients of the active emulsion layers to water.Conclusions:Caution is recommended when using GAFCHROMIC EBT/EBT2 films at photon energies below 100 keV. It is recommended that the effective atomic number of future films be produced as close to that of water and that thicker active layers are advantageous.
A convolution‐superposition dose calculation engine for GPUs
Authors: Hissoiny Sami , Ozell Benoît , Després Philippe 
Published: March 2010

Purpose:Graphic processing units (GPUs) are increasingly used for scientific applications, where their parallel architecture and unprecedented computing power density can be exploited to accelerate calculations. In this paper, a new GPU implementation of a convolution/superposition (CS) algorithm is presented.Methods:This new GPU implementation has been designed from the ground‐up to use the graphics card's strengths and to avoid its weaknesses. The CS GPU algorithm takes into account beam hardening, off‐axis softening, kernel tilting, and relies heavily on raytracing through patient imaging data. Implementation details are reported as well as a multi‐GPU solution.Results:An overall single‐GPU acceleration factor of 908× was achieved when compared to a nonoptimized version of the CS algorithm implemented in PlanUNC in single threaded central processing unit (CPU) mode, resulting in approximatively 2.8 s per beam for a 3D dose computation on a 0.4 cm grid. A comparison to an established commercial system leads to an acceleration factor of approximately 29× or 0.58 versus 16.6 s per beam in single threaded mode. An acceleration factor of 46× has been obtained for the total energy released per mass (TERMA) calculation and a 943× acceleration factor for the CS calculation compared to PlanUNC. Dose distributions also have been obtained for a simple water‐lung phantom to verify that the implementation gives accurate results.Conclusions:These results suggest that GPUs are an attractive solution for radiation therapy applications and that careful design, taking the GPU architecture into account, is critical in obtaining significant acceleration factors. These results potentially can have a significant impact on complex dose delivery techniques requiring intensive dose calculations such as intensity‐modulated radiation therapy (IMRT) and arc therapy. They also are relevant for adaptive radiation therapy where dose results must be obtained rapidly.
Accurate brain volumetry with diffusion‐weighted spin‐echo single‐shot echo‐planar‐imaging and dual‐clustering segmentation: Comparison with volumetry‐validated quantitative magnetic resonance imaging
Authors: Watanabe Memi , Sakai Osamu , Norbash Alexander M. , Jara Hernán 
Published: March 2010

Purpose:Although the diffusion‐weighted spin‐echo single‐shot echo‐planar‐imaging (DW‐SE‐sshEPI) is an established quantitative MRI (qMRI) pulse sequence, it is known to be vulnerable to geometric distortions. The purpose of this work is to study is to study brain volumetry accuracy with DW‐SE‐sshEPI relative previously published volumetry‐validated qMRI pulse sequence, specifically the mixed turbo spin‐echo (mixed‐TSE) pulse sequence, which is robust to magnetic field inhomogeneities and affords much higher spatial resolution.Methods:Twenty‐eight subjects were imaged with both DW‐SE‐sshEPI and mixed‐TSE pulse sequences. For each subject, the intracranial structures were segmented using a single‐qMRI‐channel dual‐clustering algorithm (for DW‐SE‐sshEPI) and a three‐qMRI‐channel dual‐clustering algorithm (for mixed‐TSE). The respective intracranial volumes were calculated with both data sets and then compared.Results:The intracranial volumes derived from DW‐SE‐sshEPI and mixed‐TSE data sets are highly and linearly correlated with a slope of 0.9911, with one distorted DW‐SE‐sshEPI data set demonstrating remarkable volume underestimation. Excluding this outlier resulted in improved linear correlation with a slope of 1.0003.Conclusions:Brain volumetry with DW‐SE‐sshEPI at 1.5 T data sets can be very accurate for most patients for whom the major magnetic field inhomogeneities result from typical tissue interfaces (e.g., air‐tissue or bone‐tissue) and typical dental fillings, but not from larger metallic implants.
Detection and Genetic Analysis of Human Sapoviruses in River Water in Japan
Authors: Kitajima Masaaki , Oka Tomoichiro , Haramoto Eiji , Katayama Hiroyuki , Takeda Naokazu , Katayama Kazuhiko , Ohgaki Shinichiro 
Published: February 2010

ABSTRACTWe investigated the prevalence of sapoviruses (SaVs) in the Tamagawa River in Japan from April 2003 to March 2004 and performed genetic analysis of the SaV genes identified in river water. A total of 60 river water samples were collected from five sites along the river, and 500 ml was concentrated using the cation-coated filter method. By use of a real-time reverse transcription (RT)-PCR assay, 12 (20%) of the 60 samples were positive for SaV. SaV sequences were obtained from 15 (25%) samples, and a total of 30 SaV strains were identified using six RT-PCR assays followed by cloning and sequence analysis. A newly developed nested RT-PCR assay utilizing a broadly reactive forward primer showed the highest detection efficiency and amplified more diverse SaV genomes in the samples. SaV sequences were frequently detected from November to March, whereas none were obtained in April, July, September, or October. No SaV sequences were detected in the upstream portion of the river, whereas the midstream portion showed high positive rates. Based on phylogenetic analysis, SaV strains identified in the river water samples were classified into nine genotypes, namely, GI/1, GI/2, GI/3, GI/5, GI/untyped, GII/1, GII/2, GII/3, and GV/1. To our knowledge, this is the first study describing seasonal and spatial distributions and genetic diversity of SaVs in river water. A combination of real-time RT-PCR assay and newly developed nested RT-PCR assay is useful for identifying and characterizing SaV strains in a water environment.
Siderophores Are Not Involved in Fe(III) Solubilization during Anaerobic Fe(III) Respiration by
Shewanella oneidensis
MR-1
Authors: Fennessey Christine M. , Jones Morris E. , Taillefert Martial , DiChristina Thomas J. 
Published: February 2010

ABSTRACT

Shewanella oneidensis
MR-1 respires a wide range of anaerobic electron acceptors, including sparingly soluble Fe(III) oxides. In the present study,
S. oneidensis
was found to produce Fe(III)-solubilizing organic ligands during anaerobic Fe(III) oxide respiration, a respiratory strategy postulated to destabilize Fe(III) and produce more readily reducible soluble organic Fe(III). In-frame gene deletion mutagenesis, siderophore detection assays, and voltammetric techniques were combined to determine (i) if the Fe(III)-solubilizing organic ligands produced by
S. oneidensis
during anaerobic Fe(III) oxide respiration were synthesized via siderophore biosynthesis systems and (ii) if the Fe(III)-siderophore reductase was required for respiration of soluble organic Fe(III) as an anaerobic electron acceptor. Genes predicted to encode the siderophore (hydroxamate) biosynthesis system (SO3030 to SO3032), the Fe(III)-hydroxamate receptor (SO3033), and the Fe(III)-hydroxamate reductase (SO3034) were identified in the
S. oneidensis
genome, and corresponding in-frame gene deletion mutants were constructed. ΔSO3031 was unable to synthesize siderophores or produce soluble organic Fe(III) during aerobic respiration yet retained the ability to solubilize and respire Fe(III) at wild-type rates during anaerobic Fe(III) oxide respiration. ΔSO3034 retained the ability to synthesize siderophores during aerobic respiration and to solubilize and respire Fe(III) at wild-type rates during anaerobic Fe(III) oxide respiration. These findings indicate that the Fe(III)-solubilizing organic ligands produced by
S. oneidensis
during anaerobic Fe(III) oxide respiration are not synthesized via the hydroxamate biosynthesis system and that the Fe(III)-hydroxamate reductase is not essential for respiration of Fe(III)-citrate or Fe(III)-nitrilotriacetic acid (NTA) as an anaerobic electron acceptor.
Multilocus Sequence Type Analysis Reveals both Clonality and Recombination in Populations of Candida glabrata Bloodstream Isolates from U.S. Surveillance Studies
Authors: Lott Timothy J. , Frade João P. , Lockhart Shawn R. 
Published: February 2010

ABSTRACT

The human commensal yeast
Candida glabrata
is becoming increasingly important as an agent of nosocomial bloodstream infection. However, relatively little is known concerning the genetics and population structure of this species. We have analyzed 230 incident bloodstream isolates from previous and current population-based surveillance studies by using multilocus sequence typing (MLST). Our results show that in the U.S. cities of Atlanta, GA; Baltimore, MD; and San Francisco, CA during three time periods spanning 1992 to 2009, five populations of
C. glabrata
bloodstream isolates are defined by a relatively small number of sequence types. There is little genetic differentiation in the different
C. glabrata
populations. We also show that there has been a significant temporal shift in the prevalence of one major subtype in Atlanta. Our results support the concept that both recombination and clonality play a role in the population structure of this species.
Kinetic Characterization of the WalRKSpn(VicRK) Two-Component System ofStreptococcus pneumoniae: Dependence of WalKSpn(VicK) Phosphatase Activity on Its PAS Domain
Authors: Gutu Alina D. , Wayne Kyle J. , Sham Lok-To , Winkler Malcolm E. 
Published: February 2010

ABSTRACTThe WalRK two-component system plays important roles in maintaining cell wall homeostasis and responding to antibiotic stress in low-GC Gram-positive bacteria. In the major human pathogen,Streptococcus pneumoniae, phosphorylated WalRSpn(VicR) response regulator positively controls the transcription of genes encoding the essential PcsB division protein and surface virulence factors. WalRSpnis phosphorylated by the WalKSpn(VicK) histidine kinase. Little is known about the signals sensed by WalK histidine kinases. To gain information about WalKSpnsignal transduction, we performed a kinetic characterization of the WalRKSpnautophosphorylation, phosphoryltransferase, and phosphatase reactions. We were unable to purify soluble full-length WalKSpn. Consequently, these analyses were performed using two truncated versions of WalKSpnlacking its single transmembrane domain. The longer version (Δ35 amino acids) contained most of the HAMP domain and the PAS, DHp, and CA domains, whereas the shorter version (Δ195 amino acids) contained only the DHp and CA domains. The autophosphorylation kinetic parameters of Δ35 and Δ195 WalKSpnwere similar [Km(ATP) ≈ 37 μM;kcat≈ 0.10 min−1] and typical of those of other histidine kinases. The catalytic efficiency of the two versions of WalKSpn∼P were also similar in the phosphoryltransfer reaction to full-length WalRSpn. In contrast, absence of the HAMP-PAS domains significantly diminished the phosphatase activity of WalKSpnfor WalRSpn∼P. Deletion and point mutations confirmed that optimal WalKSpnphosphatase activity depended on the PAS domain as well as residues in the DHp domain. In addition, these WalKSpnDHp domain and ΔPAS mutations led to attenuation of virulence in a murine pneumonia model.
GEOMETRIC STREAMING ALGORITHM WITH A SORTING PRIMITIVE
Authors: CHEN ERIC Y. 
Published: March 2010

We solve several fundamental geometric problems under a new streaming model recently proposed by Ruhl et al.2,15In this model, in one pass the input stream can be scanned to generate an output stream or be sorted based on a user-defined comparator; all intermediate streams must be of size O(n). We obtain the following geometric results for any fixed constant ϵ > 0:• We can construct 2D convex hulls in O(1) passes with O(nϵ) extra space.• We can construct 3D convex hulls in O(1) expected number of passes with O(nϵ) extra space.• We can construct a triangulation of a simple polygon in O(1) expected number of passes with O(nϵ) extra space, where n is the number of vertices on the polygon.• We can report all k intersections of a set of 2D line segments in O(1) passes with O(nϵ) extra space, if an intermediate stream of size O(n + k) is allowed.We also consider a weaker model, where we do not have the sorting primitive but are allowed to choose a scan direction for every scan pass. Here we can construct a 2D convex hull from an x-ordered point set in O(1) passes with O(nϵ) extra space.
Normal Structure and Common Fixed Point Properties for Semigroups of Nonexpansive Mappings in Banach Spaces
Authors: Lau AnthonyTo-Ming 
Published: February 2010

AbstractIn 1965, Kirk proved that if "Equation missing" is a nonempty weakly compact convex subset of a Banach space with normal structure, then every nonexpansive mapping "Equation missing" has a fixed point. The purpose of this paper is to outline various generalizations of Kirk's fixed point theorem to semigroup of nonexpansive mappings and for Banach spaces associated to a locally compact group.
p53 Regulates the Ras Circuit to Inhibit the Expression of a Cancer-Related Gene Signature by Various Molecular Pathways
Authors: Buganim Yosef , Solomon Hilla , Rais Yoach , Kistner Daria , Nachmany Ido , Brait Mariana , Madar Shalom , Goldstein Ido , Kalo Eyal , Adam Nitzan , Gordin Maya , Rivlin Noa , Kogan Ira , Brosh Ran , Sefadia-Elad Galit , Goldfinger Naomi , Sidransky David , Kloog Yoel , Rotter Varda 
Published: March 2010

Abstract
In this study, we focus on the analysis of a previously identified cancer-related gene signature (CGS) that underlies the cross talk between the p53 tumor suppressor and Ras oncogene. CGS consists of a large number of known Ras downstream target genes that were synergistically upregulated by wild-type p53 loss and oncogenic H-RasG12V expression. Here we show that CGS expression strongly correlates with malignancy. In an attempt to elucidate the molecular mechanisms underling the cooperation between p53 loss and oncogenic H-RasG12V, we identified distinguished pathways that may account for the regulation of the expression of the CGS. By knocking-down p53 or by expressing mutant p53, we revealed that p53 exerts its negative effect by at least two mechanisms mediated by its targets B-cell translocation gene 2 (BTG2) and activating transcription factor 3 (ATF3). Whereas BTG2 binds H-RasG12V and represses its activity by reducing its GTP loading state, which in turn causes a reduction in CGS expression, ATF3 binds directly to the CGS promoters following p53 stabilization and represses their expression. This study further elucidates the molecular loop between p53 and Ras in the transformation process. Cancer Res; 70(6); 2274–84
Antibody-Maytansinoid Conjugates Designed to Bypass Multidrug Resistance
Authors: Kovtun Yelena V. , Audette Charlene A. , Mayo Michele F. , Jones Gregory E. , Doherty Heather , Maloney Erin K. , Erickson Hans K. , Sun Xiuxia , Wilhelm Sharon , Ab Olga , Lai Katharine C. , Widdison Wayne C. , Kellogg Brenda , Johnson Holly , Pinkas Jan , Lutz Robert J. , Singh Rajeeva , Goldmacher Victor S. , Chari Ravi V.J. 
Published: March 2010

Abstract
Conjugation of cytotoxic compounds to antibodies that bind to cancer-specific antigens makes these drugs selective in killing cancer cells. However, many of the compounds used in such antibody-drug conjugates (ADC) are substrates for the multidrug transporter MDR1. To evade the MDR1-mediated resistance, we conjugated the highly cytotoxic maytansinoid DM1 to antibodies via the maleimidyl-based hydrophilic linker PEG4Mal. Following uptake into target cells, conjugates made with the PEG4Mal linker were processed to a cytotoxic metabolite that was retained by MDR1-expressing cells better than a metabolite of similar conjugates prepared with the nonpolar linker N-succinimidyl-4-(maleimidomethyl)cyclohexane-1-carboxylate (SMCC). In accord, PEG4Mal-linked conjugates were more potent in killing MDR1-expressing cells in culture. In addition, PEG4Mal-linked conjugates were markedly more effective in eradicating MDR1-expressing human xenograft tumors than SMCC-linked conjugates while being tolerated similarly, thus showing an improved therapeutic index. This study points the way to the development of ADCs that bypass multidrug resistance. Cancer Res; 70(6); 2528–37