bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electro‐gene‐transfer as a new tool for cancer immunotherapy in animals
Authors: Impellizeri J. A. , Ciliberto G. , Aurisicchio L. 
Published: October 2012

AbstractThe concept of vaccines based on the direct inoculation of plasmid DNA gained initial proof‐of‐concept in small rodent species. Further development was hampered by the difficulty to confirm immunogenicity and efficacy in large animal species and, most importantly, in human clinical trials. These negative findings led to the search of complementary technologies which, in combination with intradermal or intramuscular plasmid DNA injection would result in more robust delivery, decreased interindividual variability, clear evidence of clinical efficacy and which would eventually lead to market approval of new vaccine products. The use of high‐pressure, needleless devices as an enhancing tool for plasmid DNA delivery led to recent approval by USDA of Oncept™, a therapeutic cancer vaccine directed against tyrosinase for the therapy of melanoma in dogs. An alternative approach to improve plasmid DNA delivery is electro‐gene‐transfer (EGT). In this article, we briefly review the principles of DNA‐EGT and the evidences for efficacy of a telomerase reverse transcriptase vaccine in a dog clinical trial, and provide perspectives for the use of this technology for broader applications in pet animals.
Assessing potential germination period of weeds with base temperatures and base water potentials
Authors: GUILLEMIN J‐P , GARDARIN A , GRANGER S , REIBEL C , MUNIER‐JOLAIN N , COLBACH N 
Published: October 2012

SummarySeed germination partly depends on both base temperature (Tb) and base water potential (Ψb), which currently are known only for a small number of species. Laboratory experiments were conducted to estimate these parameters for 14 weed species using the ‘x‐intercept’ method. Tb and Ψb (°C and MPa) for the 14 weed species were as follows: Amaranthus retroflexus (8.9 and −0.95), Ambrosia artemisiifolia (3.6 and −1.28), Avena fatua (2.2 and −1.02), Capsella bursa‐pastoris (4.5 and −0.95), Chenopodium album (5.9 and −0.80), Echinochloa crus‐galli (6.2 and −1.19), Geranium dissectum (0.6 and −3.31), Matricaria perforata (2.0 and −0.75), Picris echioides (5.2 and −0.79), Polygonum lapathifolium (5.8 and −1.55), Senecio vulgaris (2.5 and −1.23), Setaria pumila (8.6 and −0.75), Solanum nigrum (11.6 and −0.89) and Veronica hederifolia (0.2 and −1.67). The two parameters were used to determine potential germination times during expected non‐dormancy periods for three contrasting climatic years in Dijon, France. The number of potential germination days varied little among the tested climatic years, but substantially among species, ranging from 95 ± 9 days for V. hederifolia to 280 ± 7 days for M. perforata. These results may be of value for development of predictive growth models and understanding times when weed control may be most feasible.
A calibration‐free, one‐step method for quantitative photoacoustic tomography
Authors: Yuan Zhen , Jiang Huabei 
Published: October 2012

Purpose: Recently reported quantitative photoacoustic tomography (PAT) has significantly expanded the utilities of PAT because it allows for recovery of tissue optical absorption coefficient which directly correlates with tissue physiological information. However, the recovery of optical absorption coefficient by the existing quantitative PAT approaches strongly depends on the accuracy of absorbed energy density distribution, and on the knowledge of accurate strength and distribution of incident light source. The purpose of this study is to develop a new algorithm for the reconstruction of optical absorption coefficient that does not depend on these initial parameters.Methods: Here the authors propose a novel one‐step reconstruction approach that can directly recover optical absorption coefficient from photoacoustic measurements along boundary domain. The authors validate the method using simulation and phantom experiments.Results: The authors have demonstrated experimental evidence that it is possible to directly recover optical absorption coefficient maps using boundary photoacoustic measurements coupled with the photon diffusion equation in just one step. The authors found that the method described is able to quantitatively reconstruct absorbing objects with different sizes and optical contrast levels.Conclusions: Compared to the authors’ previous two‐step methods, the reconstruction results obtained here show that the one‐step scheme can significantly improve the accuracy of absorption coefficient recovery.
Low Sensitivity of NS1 Protein Tests Evidenced during a Dengue Type 2 Virus Outbreak in Santos, Brazil, in 2010
Authors: Felix Alvina Clara , Romano Camila Malta , Centrone Cristiane de Campos , Rodrigues Célia Lima , Villas-Boas Lucy , Araújo Evaldo Stanislau , de Matos Andréia Manso , Carvalho Karina Inácio , Martelli Celina Maria Turchi , Kallas Èsper Georges , Pannuti Claúdio Sérgio , Levi José Eduardo 
Published: October 2012

ABSTRACT
In 2010, a large outbreak of dengue occurred in Santos, Brazil. The detection of the NS1 antigen was used for diagnosis in addition to the detection of IgG, IgM, and RNA. A large number of NS1 false-negative results were obtained. A total of 379 RNA-positive samples were selected for thorough evaluation. NS1 was reactive in 37.7% of cases. Most of the cases were characterized as a secondary infection by dengue 2 virus. Sequencing of NS1 positive and negative isolates did not reveal any mutation that could justify the diagnostic failure. Use of existing NS1 tests in the Brazilian population may present a low negative predictive value, and they should be used with caution, preferentially after performing a validation with samples freshly obtained during the ongoing epidemic.
Molecular Characterization of a Respiratory Syncytial Virus Outbreak in a Hematology Unit in Heidelberg, Germany
Authors: Geis Steffen , Prifert Christiane , Weissbrich Benedikt , Lehners Nicola , Egerer Gerlinde , Eisenbach Christoph , Buchholz Udo , Aichinger Elisabeth , Dreger Peter , Neben Kai , Burkhardt Ulrich , Ho Anthony D. , Kräusslich Hans-Georg , Heeg Klaus , Schnitzler Paul 
Published: October 2012

ABSTRACT

In 2011 and 2012, a large outbreak of respiratory syncytial virus (RSV) infections affecting 57 laboratory-confirmed patients occurred in an adult hematology unit in Heidelberg, Germany. During the outbreak investigation, we performed molecular genotyping of RSV strains to differentiate between single versus multiple introductions of the virus into the unit. Furthermore, we assessed the time of viral shedding of consecutive samples from the patients in order to better understand the possible impact of prolonged shedding for outbreak control management. We used subtype-specific reverse transcription-PCR on nasopharyngeal and bronchoalveolar specimens for routine diagnostics and for measuring the viral shedding period. Samples of 47 RSV-infected patients involved in the outbreak were genotyped by sequence analysis and compared to samples from RSV-infected hospitalized children representing the timing of the annual RSV epidemic in the community. Molecular investigation of the virus strains from clinical samples revealed a unique cluster with identical nucleotide sequences of RSV type A (RSV A outbreak strain) for 41 patients, while 3 patients were infected with different RSV A (nonoutbreak) strains and three other patients with RSV type B. Outbreak strains were identified in samples from November 2011 until January 2012, while nonoutbreak strains were from samples coinciding with the community epidemic in February and March 2012. Median duration of viral shedding time was 24.5 days (range, 1 to 168 days) with no difference between outbreak and nonoutbreak strains (
P
= 0.45). Our investigation suggests a single introduction of the RSV A outbreak strain into the unit that spread among the immunocompromised patients. Prolonged viral shedding may have contributed to nosocomial transmission and should be taken into account in the infection control management of RSV outbreaks in settings with heavily immunosuppressed patients.
Neonatal Herpes Encephalitis Caused by a Virologically Confirmed Acyclovir-Resistant Herpes Simplex Virus 1 Strain
Authors: Kakiuchi Satsuki , Nonoyama Shigeaki , Wakamatsu Hajime , Kogawa Kazuhiro , Wang Lixin , Kinoshita-Yamaguchi Hitomi , Takayama-Ito Mutsuyo , Lim Chang-Kweng , Inoue Naoki , Mizuguchi Masashi , Igarashi Takashi , Saijo Masayuki 
Published: October 2012

ABSTRACT

A neonate with herpes simplex virus 1 encephalitis was treated with intravenous acyclovir. During the course of therapy, the infection became intractable to the treatment and a mutation in the viral thymidine kinase gene (nucleotide G375T, amino acid Q125H) developed. This mutation was demonstrated
in vitro
to confer acyclovir resistance.
Evaluation of a Simple Blood Culture Amplification and Antigen Detection Method for Diagnosis of Salmonella enterica Serovar Typhi Bacteremia
Authors: Castonguay-Vanier Josée , Davong Viengmon , Bouthasavong Latsanyphone , Sengdetka Davanh , Simmalavong Manivone , Seupsavith Amphayvanh , Dance David A. B. , Baker Stephen , Le Thi Phuong Tu , Vongsouvath Manivanh , Newton Paul N. 
Published: October 2012

ABSTRACT

In most areas where typhoid is endemic, laboratory diagnosis is not possible due to the lack of appropriate facilities. We investigated whether the combination of blood culture amplification of
Salmonella enterica
serovar Typhi with an
S. Typhi
antigen rapid diagnostic test (RDT) could be an accurate and inexpensive tool for the accelerated diagnosis of patients with acute typhoid in Laos. For a panel of 23 Gram-negative reference pathogens, the Standard Diagnostics (catalog no. 15FK20; Kyonggi-do, South Korea) RDT gave positive results for
S. Typhi
NCTC 8385,
S. Typhi
NCTC 786 (Vi negative),
Salmonella enterica
serovar Enteritidis (ATCC 13076), and
Salmonella enterica
serovar Ndolo NCTC 8700 (all group D). In a prospective study of 6,456 blood culture bottles from 3,028 patients over 15 months, 392 blood culture bottles (6.1%) from 221 (7.3%) patients had Gram-negative rods (GNRs) seen in the blood culture fluid. The sensitivity, negative predictive value, specificity, and positive predictive value were 96.7%, 99.5%, 97.9%, and 87.9%, respectively, for patients with proven
S. Typhi
bacteremia and 91.2%, 98.4%, 98.9%, and 93.9% for patients with group D
Salmonella
. The median (range) number of days between diagnosis by RDT and reference assays was 1 (−1 to +2) day for those with confirmed
S. Typhi
. The use of antigen-based pathogen detection in blood culture fluid may be a useful, relatively rapid, inexpensive, and accurate technique for the identification of important causes of bacteremia in the tropics.
Detection of SPM-1-Producing Pseudomonas aeruginosa and Class D β-Lactamase-Producing Acinetobacter baumannii Isolates by Use of Liquid Chromatography-Mass Spectrometry and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Carvalhaes Cecilia G. , Cayô Rodrigo , Assis Diego M. , Martins Evelin R. , Juliano Luiz , Juliano Maria A. , Gales Ana C. 
Published: October 2012

ABSTRACT

This study evaluates the accuracy of liquid chromatography-mass spectrometry (LC-MS) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) for detecting carbapenem hydrolytic activity among SPM-1-, GIM-1-, and GES-5-producing
Pseudomonas aeruginosa
isolates and OXA-143-, IMP-10-, and OXA-58-producing
Acinetobacter baumannii
isolates. Class A and B carbapenemase activities were rapidly detected by MALDI-TOF in a 2-h assay. However, an extended incubation time was necessary for detection of carbapenem-hydrolyzing class D β-lactamase (CHDL) activity in
Acinetobacter
spp.
Rapid Intracellular Competition between Hepatitis C Viral Genomes as a Result of Mitosis
Authors: Webster Brian , Wissing Silke , Herker Eva , Ott Melanie , Greene Warner C. 
Published: October 2012

ABSTRACT

Cells infected with hepatitis C virus (HCV) become refractory to further infection by HCV (T. Schaller et al., J. Virol. 81:4591–4603, 2007; D. M. Tscherne et al., J. Virol. 81:3693–3703, 2007). This process, termed superinfection exclusion, does not involve downregulation of surface viral receptors but instead occurs inside the cell at the level of RNA replication. The originally infecting virus may occupy replication niches or sequester host factors necessary for viral growth, preventing effective growth of viruses that enter the cell later. However, there appears to be an additional level of intracellular competition between viral genomes that occurs at or shortly following mitosis. In the setting of cellular division, when two viral replicons of equivalent fitness are present within a cell, each has an equal opportunity to exclude the other. In a population of dividing cells, the competition between viral genomes proceeds apace, randomly clearing one or the other genome from cells in the span of 9 to 12 days. These findings demonstrate a new mechanism of intracellular competition between HCV strains, which may act to further limit HCV's genetic diversity and ability to recombine
in vivo
.
Mutations in Multiple Domains of Gag Drive the Emergence of
In Vitro
Resistance to the Phosphonate-Containing HIV-1 Protease Inhibitor GS-8374
Authors: Stray Kirsten M. , Callebaut Christian , Glass Bärbel , Tsai Luong , Xu Lianhong , Müller Barbara , Kräusslich Hans-Georg , Cihlar Tomas 
Published: October 2012

ABSTRACT

GS-8374 is a potent HIV protease inhibitor (PI) with a unique diethyl-phosphonate moiety. Due to a balanced contribution of enthalpic and entropic components to its interaction with the protease (PR) active site, the compound retains activity against HIV mutants with high-level multi-PI resistance. We report here the
in vitro
selection and characterization of HIV variants resistant to GS-8374. While highly resistant viruses with multiple mutations in PR were isolated in the presence of control PIs, an HIV variant displaying moderate (14-fold) resistance to GS-8374 was generated only after prolonged passaging for >300 days. The isolate showed low-level cross-resistance to darunavir, atazanavir, lopinavir, and saquinavir, but not other PIs, and contained a single R41K mutation in PR combined with multiple genotypic changes in the Gag matrix, capsid, nucleocapsid, and SP2 domains. Mutations also occurred in the transframe peptide and p6* domain of the Gag-Pol polyprotein. Analysis of recombinant HIV variants indicated that mutations in Gag, but not the R41K in PR, conferred reduced susceptibility to GS-8374. The Gag mutations acted in concert, since they did not affect susceptibility when introduced individually. Analysis of viral particles revealed that the mutations rendered Gag more susceptible to PR-mediated cleavage in the presence of GS-8374. In summary, the emergence of resistance to GS-8374 involved a combination of substrate mutations without typical resistance mutations in PR. These substrate changes were distributed throughout Gag and acted in an additive manner. Thus, they are classified as primary resistance mutations indicating a unique mechanism and pathway of resistance development for GS-8374.
Kaposi's Sarcoma-Associated Herpesvirus Suppression of DUSP1 Facilitates Cellular Pathogenesis following
De Novo
Infection
Authors: Qin Zhiqiang , Dai Lu , Defee Michael , Findlay Victoria J. , Watson Dennis K. , Toole Bryan P. , Cameron Jennifer , Peruzzi Francesca , Kirkwood Keith , Parsons Chris 
Published: October 2012

ABSTRACT

Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi's sarcoma (KS), and KSHV activation of mitogen-activated protein kinases (MAPKs) initiates a number of key pathogenic determinants of KS. Direct inhibition of signal transduction as a therapeutic approach presents several challenges, and a better understanding of KSHV-induced mechanisms regulating MAPK activation may facilitate the development of new treatment or prevention strategies for KS. MAPK phosphatases, including dual-specificity phosphatase-1 (DUSP1), negatively regulate signal transduction and cytokine activation through MAPK dephosphorylation or interference with effector molecule binding to MAPKs, including the extracellular signal-regulated kinase (ERK). We found that ERK-dependent latent viral gene expression, the induction of promigratory factors, and cell invasiveness following
de novo
infection of primary human endothelial cells are in part dependent on KSHV suppression of DUSP1 expression during
de novo
infection. KSHV-encoded miR-K12-11 upregulates the expression of xCT (an amino acid transporter and KSHV fusion/entry receptor), and existing data indicate a role for xCT in the regulation of 14-3-3β, a transcriptional repressor of DUSP1. We found that miR-K12-11 induces endothelial cell secretion of promigratory factors and cell invasiveness through upregulation of xCT-dependent, 14-3-3β-mediated suppression of DUSP1. Finally, proof-of-principle experiments revealed that pharmacologic upregulation of DUSP1 inhibits the induction of promigratory factors and cell invasiveness during
de novo
KSHV infection. These data reveal an indirect role for miR-K12-11 in the regulation of DUSP1 and downstream pathogenesis.
A STATIC OPTIMALITY TRANSFORMATION WITH APPLICATIONS TO PLANAR POINT LOCATION
Authors: IACONO JOHN , MULZER WOLFGANG 
Published: October 2012

Over the last decade, there have been several data structures that, given a planar subdivision and a probability distribution over the plane, provide a way for answering point location queries that is fine-tuned for the distribution. All these methods suffer from the requirement that the query distribution must be known in advance. We present a new data structure for point location queries in planar triangulations. Our structure is asymptotically as fast as the optimal structures, but it requires no prior information about the queries. This is a 2-D analogue of the jump from Knuth's optimum binary search trees (discovered in 1971) to the splay trees of Sleator and Tarjan in 1985. While the former need to know the query distribution, the latter are statically optimal. This means that we can adapt to the query sequence and achieve the same asymptotic performance as an optimum static structure, without needing any additional information.
COMPRESSIVE SENSING WITH LOCAL GEOMETRIC FEATURES
Authors: GUPTA RISHI , INDYK PIOTR , PRICE ERIC , RACHLIN YARON 
Published: October 2012

We propose a framework for compressive sensing of images with local distinguishable objects, such as stars, and apply it to solve a problem in celestial navigation. Specifically, let x ∈ ℝNbe an N pixel image, consisting of a small number of local distinguishable objects plus noise. Our goal is to design an m × Nmeasurement matrix A with m ≪ N, such that we can recover an approximation to x from the measurements Ax.We construct a matrix A and recovery algorithm with the following properties: (i) if there are k objects, the number of measurements m is O((k log N)/( log k)), undercutting the best known bound of O(k log (N/k)) (ii) the matrix A is very sparse, which is important for hardware implementations of compressive sensing algorithms, and (iii) the recovery algorithm is empirically fast and runs in time polynomial in k and log (N).We also present a comprehensive study of the application of our algorithm to attitude determination, or finding one's orientation in space. Spacecraft typically use cameras to acquire an image of the sky, and then identify stars in the image to compute their orientation. Taking pictures is very expensive for small spacecraft, since camera sensors use a lot of power. Our algorithm optically compresses the image before it reaches the camera's array of pixels, reducing the number of sensors that are required.
A Tumorigenic MLL-Homeobox Network in Human Glioblastoma Stem Cells
Authors: Gallo Marco , Ho Jenny , Coutinho Fiona J. , Vanner Robert , Lee Lilian , Head Renee , Ling Erick K. M. , Clarke Ian D. , Dirks Peter B. 
Published: October 2012

Abstract
Glioblastoma growth is driven by cancer cells that have stem cell properties, but molecular determinants of their tumorigenic behavior are poorly defined. In cancer, altered activity of the epigenetic modifiers Polycomb and Trithorax complexes may contribute to the neoplastic phenotype. Here, we provide the first mechanistic insights into the role of the Trithorax protein mixed lineage leukemia (MLL) in maintaining cancer stem cell characteristics in human glioblastoma. We found that MLL directly activates the Homeobox gene HOXA10. In turn, HOXA10 activates a downstream Homeobox network and other genes previously characterized for their role in tumorigenesis. The MLL–Homeobox axis we identified significantly contributes to the tumorigenic potential of glioblastoma stem cells. Our studies suggest a role for MLL in contributing to the epigenetic heterogeneity between tumor-initiating and non–tumor-initiating cells in glioblastoma. Cancer Res; 73(1); 417–27. ©2012 AACR.
Relative Roles of Circumnavigating Waves and Extratropics on the MJO and Its Relationship with the Mean State*
Authors: Ray Pallav , Li Tim 
Published: October 2012

Abstract
A set of atmospheric general circulation model (GCM) experiments is designed to explore the relative roles of the circumnavigating waves and the extratropics on the Madden–Julian oscillation (MJO). In a “control” simulation, the model is forced by the climatological monthly sea surface temperature for 20 yr. In the first sensitivity experiment, model prognostic variables are relaxed in the tropical Atlantic region (20°S–20°N, 80°W–0°) toward the “controlled” climatological annual cycle to suppress the influences from the circumnavigating waves. In the second sensitivity experiment, model prognostic variables are relaxed in the 20°–30° latitude zones toward the controlled climatological annual cycle to suppress the influences from the extratropics (or the tropics–extratropics interactions). The numerical results demonstrate that the extratropics play a more important role in maintaining the MJO variance than the circumnavigating waves.
The simulations further show that both the tropical mean precipitation and the intraseasonal precipitation variability are reduced when the extratropical influences are suppressed. The in-phase relationship is primarily attributed to the effect of the mean state on perturbations. A moisture budget analysis indicates that a positive feedback to the mean precipitation by the anomalous moisture convergence is offset by a negative feedback due to the anomalous moisture advection. The change in the mean precipitation in the absence of extratropical influences is primarily determined by the change in the mean moisture convergence, which in turn is due to the change in circulation. This study is the first attempt to quantitatively separate the effects of the circumnavigating waves and the extratropics on the MJO. Implications and limitations of this study are discussed.