bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of Transformation Parameters Between Centre‐Line Vector Road Maps and High Resolution Satellite Images
Authors: Lu Luping , Zhang Yong , Tao Pengjie , Zhang Zuxun , Zhang Yongjun 
Published: April 2013

AbstractA method for automatically estimating the transformation parameters between road centre‐line vector maps and high resolution satellite images is proposed. The advantages of the method are that global image feature extraction is avoided and feature extraction and matching are achieved simultaneously by using the vector data as guidance. The road width, as estimated by the algorithm, together with the road direction are used as constraints to refine the matching results. Arbitrarily chosen road nodes contribute to improving the adjustment. Map‐to‐image matching has advantages over image‐to‐image matching and could be a good method for the rapid updating of geographical information system (GIS) data.
Locked Plate Fixation of Proximal Humerus Fractures Using Cannulated Subchondral Support Pegs
Authors: Raphael James S. , Booker M. Rashad , Saing Minn H. , Beaver Andrew B. , Marvil Sean C. , Puglisi Anthony S. , Samuel Solomon P. 
Published: April 2013

Background In severely osteoporotic proximal humerus fractures, the biomechanics of fixed-angle fracture fixation with locked smooth pegs may be improved by using polymethyl methacrylate (PMMA) augmentation. Commercially available smooth pegs were modified (added a central cannula and two distal side ports) to accommodate bone cement injection around the pegs. The failure strength and stiffness of proximal humerus fracture fixation with modified pegs and PMMA augmentation was evaluated. Methods Nineteen fresh-frozen cadaveric humeri were fixated with a locked plate using: (i) smooth pegs (seven specimens), (ii) threaded pegs (six specimens) or (iii) modified smooth pegs with PMMA augmentation (six specimens). The osteotomized humeri constructs were subjected to an axial compressive load to failure at loading rate of 5 mm/minute. The maximum failure load and slope for each specimen was calculated. Results There was no difference ( p > 0.31) between the failure strength of constructs containing smooth or threaded pegs. However, the mean failure strength and stiffness of modified smooth pegs with PMMA augmentation was higher than the constructs containing either the smooth or threaded pegs. Conclusions The results obtained in the present study show that the use of PMMA augmentation along with smooth pegs may benefit humerus fracture patients with severe osteoporosis.
Fungal‐specific transcription factor AbPf2 activates pathogenicity in Alternaria brassicicola
Authors: Cho Yangrae , Ohm Robin A. , Grigoriev Igor V. , Srivastava Akhil 
Published: April 2013

SummaryAlternaria brassicicola is a successful saprophyte and necrotrophic plant pathogen. To identify molecular determinants of pathogenicity, we created non‐pathogenic mutants of a transcription factor‐encoding gene, AbPf2. The frequency and timing of germination and appressorium formation on host plants were similar between the non‐pathogenic ∆abpf2 mutants and wild‐type A. brassicicola. The mutants were also similar in vitro to wild‐type A. brassicicola in terms of vegetative growth, conidium production, and responses to a phytoalexin, reactive oxygen species and osmolites. The hyphae of the mutants grew slowly but did not cause disease symptoms on the surface of host plants. Transcripts of the AbPf2 gene increased exponentially soon after wild‐type conidia contacted their host plants . A small amount of AbPf2 protein, as monitored using GFP fusions, was present in young, mature conidia. The protein level decreased during saprophytic growth, but increased and was located primarily in fungal nuclei during pathogenesis. Levels of the proteins and transcripts sharply decreased following colonization of host tissues beyond the initial infection site. When expression of the transcription factor was induced in the wild‐type during early pathogenesis, 106 fungal genes were also induced in the wild‐type but not in the ∆abpf2 mutants. Notably, 33 of the 106 genes encoded secreted proteins, including eight putative effector proteins. Plants inoculated with ∆abpf2 mutants expressed higher levels of genes associated with photosynthesis, the pentose phosphate pathway and primary metabolism, but lower levels of defense‐related genes. Our results suggest that AbPf2 is an important regulator of pathogenesis, but does not affect other cellular processes in A. brassicicola.
Independence of -adic Galois representations over function fields
Authors: Gajda Wojciech , Petersen Sebastian 
Published: April 2013

AbstractLet$K$be a finitely generated extension of$\mathbb {Q}$. We consider the family of$\ell $-adic representations ($\ell $varies through the set of all prime numbers) of the absolute Galois group of$K$, attached to$\ell $-adic cohomology of a separated scheme of finite type over$K$. We prove that the fields cut out from the algebraic closure of$K$by the kernels of the representations of the family are linearly disjoint over a finite extension of K. This gives a positive answer to a question of Serre.
Automatic assessment of regional and global wall motion abnormalities in echocardiography images by nonlinear dimensionality reduction
Authors: Shalbaf Ahmad , Behnam Hamid , Alizade‐Sani Zahra , Shojaifard Maryam 
Published: April 2013

Purpose:Identification and assessment of left ventricular (LV) global and regional wall motion (RWM) abnormalities are essential for clinical evaluation of various cardiovascular diseases. Currently, this evaluation is performed visually which is highly dependent on the training and experience of echocardiographers and thus is prone to considerable interobserver and intraobserver variability. This paper presents a new automatic method, based on nonlinear dimensionality reduction (NLDR) for global wall motion evaluation and also detection and classification of RWM abnormalities of LV wall in a three‐point scale as follows: (1) normokinesia, (2) hypokinesia, and (3) akinesia.Methods:Isometric feature mapping (Isomap) is one of the most popular NLDR algorithms. In this paper, a modified version of Isomap algorithm, where image to image distance metric is computed using nonrigid registration, is applied on two‐dimensional (2D) echocardiography images of one cycle of heart. By this approach, nonlinear information in these images is embedded in a 2D manifold and each image is characterized by a point on the constructed manifold. This new representation visualizes the relationship between these images based on LV volume changes. Then, a new global and regional quantitative index from the resultant manifold is proposed for global wall motion estimation and also classification of RWM of LV wall in a three‐point scale. Obtained results by our method are quantitatively evaluated to those obtained visually by two experienced echocardiographers as the reference (gold standard) on 10 healthy volunteers and 14 patients.Results:Linear regression analysis between the proposed global quantitative index and the global wall motion score index and also with LV ejection fraction obtained by reference experienced echocardiographers resulted in the correlation coefficients of 0.85 and 0.90, respectively. Comparison between the proposed automatic RWM scoring and the reference visual scoring resulted in an absolute agreement of 82% and a relative agreement of 97%.Conclusions:The proposed diagnostic method can be used as a useful tool as well as a reference visual assessment by experienced echocardiographers for global wall motion estimation and also classification of RWM abnormalities of LV wall in a three‐point scale in clinical evaluations.
Proteomics Meets Cellular Signaling: Exploring Post-translational Modifications by Mass Spectrometry
Authors: Suri Vipin , Paweletz Cloud , Choudhary Chunaram 
Published: April 2013

Post-translational modifications (PTMs)—including phosphorylation, acetylation, and ubiquitination—are specific modifications that can alter the activity of an individual protein target. The cumulative effect of these small modifications is the regulation of large signaling pathways and networks within cells.
Mass spectrometry is a powerful tool for the identification of individual PTMs during the investigation of signaling networks. A new approach using antibody-based peptide enrichment for a class of PTMs combined with tandem mass spectrometry has been successfully used for global identification of hundreds to thousands of PTMs within a sample. In this webinar, examples of how the technology was applied to each of these PTM classes will be described.
Cross-Protective Efficacy of Recombinant Transferrin-Binding Protein A of Haemophilus parasuis in Guinea Pigs
Authors: Huang Xiaohui , Li Yu , Fu Yuguang , Ji Yanhong , Lian Kaiqi , Zheng Haixue , Wei Jianzhong , Cai Xuepeng , Zhu Qiyun 
Published: April 2013

ABSTRACTThe causative agent of Glasser's disease in swine isHaemophilus parasuis. Commercial bacterins are widely used for protection of the swine population. However, cross protection is limited becauseH. parasuishas more than 15 serovars. Transferrin-binding protein A has shown potential as a broad-spectrum vaccine candidate against homologous and heterologous strains. Here we amplified the full-lengthtbpAgene from anH. parasuisserovar 13 isolate and cloned it into a pET-SUMO expression vector. We then expressed and purified the TbpA protein by Ni affinity chromatography. First, the immunogenicity and protective efficacy of the protein were evaluated in guinea pigs by two subcutaneous immunizations with different doses of Montanide IMS 206 VG adjuvant. The immunized guinea pigs were, respectively, challenged on week 3 after a booster immunization with homologous strain LJ3 (serovar 13) and heterologous strain FX1 (serovar 4), and vaccine-inoculated groups were compared with nonvaccinated controls. All immunized groups showed serum antibody titers higher than those of negative-control groups. Furthermore, the cytokine and chemokine levels were evaluated at the transcriptional level by the real-time PCR analysis of six cytokines and chemokines. Gamma interferon and interleukin-5 in groups immunized with 100 μg were elevated more than 15-fold over those in negative-control groups. The protection rates were 80 and 60% after a challenge with strains LJ3 and FX1, respectively, in the groups vaccinated with 100 μg of recombinant TbpA protein. Subsequently, the data showed that guinea pigs immunized with a single dose (100 μg) were protected at levels of 80, 80, and 60% against LJ3, FX1, and another heterologous strain, SZ (serovar 14), respectively. The results indicate for the first time that TbpA protein cross protects guinea pigs against serovars 13, 4, and 14 ofH. parasuis. Taken together, these results suggest that the recombinant TbpA protein is a promising vaccine candidate that needs to be confirmed in a swine population.
Interaction between Endogenous Bacterial Flora and Latent HIV Infection
Authors: Victoriano Ann Florence B. , Imai Kenichi , Okamoto Takashi 
Published: April 2013

ABSTRACT
Human commensal bacteria do not normally cause any diseases. However, in certain pathological conditions, they exhibit a number of curious behaviors. In HIV infection, these bacteria exhibit bidirectional relationships: whereas they cause opportunistic infections based on immunological deterioration, they also augment HIV replication, in particular, viral replication from latently infected cells, which is attributable to the effect of butyric acid produced by certain anaerobic bacteria by modifying the state of chromatin. Here, we review recent evidence supporting the contributory role of such endogenous microbes in disrupting HIV latency and its potential link to the clinical progression of AIDS.
Fully Automated Quantification of Cytomegalovirus (CMV) in Whole Blood with the New Sensitive Abbott RealTi
m
e CMV Assay in the Era of the CMV International Standard
Authors: Schnepf Nathalie , Scieux Catherine , Resche-Riggon Matthieu , Feghoul Linda , Xhaard Alienor , Gallien Sébastien , Molina Jean-Michel , Socié Gérard , Viglietti Denis , Simon François , Mazeron Marie-Christine , LeGoff Jérôme 
Published: April 2013

ABSTRACT

Fully standardized reproducible and sensitive quantification assays for cytomegalovirus (CMV) are needed to better define thresholds for antiviral therapy initiation and interruption. We evaluated the newly released Abbott RealTi
m
e CMV assay for CMV quantification in whole blood (WB) that includes automated extraction and amplification (
m
2000 RealTi
m
e system). Sensitivity, accuracy, linearity, and intra- and interassay variability were validated in a WB matrix using Quality Control for Molecular Diagnostics (QCMD) panels and the WHO international standard (IS). The intra- and interassay coefficients of variation were 1.37% and 2.09% at 5 log
10
copies/ml and 2.41% and 3.80% at 3 log
10
copies/ml, respectively. According to expected values for the QCMD and Abbott RealTi
m
e CMV methods, the lower limits of quantification were 104 and <50 copies/ml, respectively. The conversion factor between international units and copies (2.18), determined from serial dilutions of the WHO IS in WB, was significantly different from the factor provided by the manufacturer (1.56) (
P
= 0.001). Results from 302 clinical samples were compared with those from the Qiagen artus CMV assay on the same
m
2000 RealTi
m
e system. The two assays provided highly concordant results (concordance correlation coefficient, 0.92), but the Abbott RealTi
m
e CMV assay detected and quantified, respectively, 20.6% and 47.8% more samples than the Qiagen/artus CMV assay. The sensitivity and reproducibility of the results, along with the automation, fulfilled the quality requirements for implementation of the Abbott RealTi
m
e CMV assay in clinical settings. Our results highlight the need for careful validation of conversion factors provided by the manufacturers for the WHO IS in WB to allow future comparison of results obtained with different assays.
Evaluation of Cobas TaqMan MTB for Direct Detection of the Mycobacterium tuberculosis Complex in Comparison with Cobas Amplicor MTB
Authors: Bloemberg Guido V. , Voit Antje , Ritter Claudia , Deggim Vanessa , Böttger Erik C. 
Published: April 2013

ABSTRACT

The Roche Cobas Amplicor MTB assay, recently replaced by the Roche Cobas TaqMan MTB assay, was one of the first commercially available assays for detection of the
Mycobacterium tuberculosis
complex based on nucleic acid amplification. We reported previously on the limited specificity of the Cobas Amplicor MTB assay, in particular for positive samples with an optical density at 660 nm (OD
660
) of <2.0. Using a selected set of respiratory samples, which were scored as false positive by the Cobas Amplicor test, we demonstrate here that the specificity of the Cobas TaqMan assay is significantly improved. In addition, our study of a set of 133 clinical samples revealed that the Cobas TaqMan MTB assay showed significantly less PCR inhibition than the Cobas Amplicor test. An overall concordance of 98.2% was observed between the two assays. In a subsequent prospective study, we evaluated the performance of the Roche Cobas TaqMan MTB assay on 1,143 clinical specimens, including respiratory (
n
= 838) and nonrespiratory (
n
= 305) specimens. Using culture as the gold standard, we found a sensitivity of 88.4% and a specificity of 98.8% for the 838 respiratory specimens, compared to a sensitivity of 63.6% and a specificity of 94.6% for the 305 nonrespiratory specimens. We conclude that the Cobas TaqMan MTB assay is a significantly improved tool for the direct detection of
M. tuberculosis
DNA in clinical specimens.
Toxoplasma Seroconversion with Negative or Transient Immunoglobulin M in Pregnant Women: Myth or Reality? A French Multicenter Retrospective Study
Authors: Fricker-Hidalgo H. , Cimon B. , Chemla C. , Darde M. L. , Delhaes L. , L'Ollivier C. , Godineau N. , Houze S. , Paris L. , Quinio D. , Robert-Gangneux F. , Villard O. , Villena I. , Candolfi E. , Pelloux H. 
Published: April 2013

ABSTRACT

Classically,
Toxoplasma
infection is associated with high levels of specific IgM antibody and a rise in specific IgG levels 1 to 3 weeks later. Atypical IgG seroconversion, without IgM detection or with transient IgM levels, has been described during serologic follow-up of seronegative pregnant women and raises difficulties in interpreting the results. To evaluate the frequency and the characteristics of these atypical cases of seroconversion, an investigation was conducted within the French National Reference Center for Toxoplasmosis, from which 26 cases collected from 12 laboratories belonging to the network were identified. The aim of this work was to retrospectively analyze the results of serologic testing, the treatments administered, and the results of prenatal and postnatal follow-up for these women. In each case, IgG antibodies were detected using both screening and confirmatory tests. IgM antibodies were not detected in 15 cases, and the levels were equivocal or low-positive in 11 cases. The IgG avidity results were low in 16 cases and high in one case. Most of the pregnant women (22/26) were treated with spiramycin from the time that IgG antibodies appeared until delivery. Amniotic fluid was analyzed for
Toxoplasma gondii
DNA by PCR in 11/26 cases, and the results were negative in all cases. Congenital toxoplasmosis was ruled out in 12/26 newborns. There was no abnormality observed at birth for 10 newborns and no information available for 4 newborns. In conclusion, when the interpretation of serological results is so difficult, it seems cautious to initiate treatment by spiramycin and to follow the pregnant women and their newborns.
Development and Evaluation of a Calibrator Material for Nucleic Acid-Based Assays for Diagnosing Aspergillosis
Authors: Lyon G. Marshall , Abdul-Ali Deborah , Loeffler Juergen , White P. Lewis , Wickes Brian , Herrera Monica L. , Alexander Barbara D. , Baden Lindsey R. , Clancy Cornelius , Denning David , Nguyen M. Hong , Sugrue Michele , Wheat L. Joseph , Wingard John R. , Donnelly J. Peter , Barnes Rosemary , Patterson Thomas F. , Caliendo Angela M. 
Published: April 2013

ABSTRACT

Twelve laboratories evaluated candidate material for an
Aspergillus
DNA calibrator. The DNA material was quantified using limiting-dilution analysis; the mean concentration was determined to be 1.73 × 10
10
units/ml. The calibrator can be used to standardize aspergillosis diagnostic assays which detect and/or quantify nucleic acid.
A Single Early Introduction of HIV-1 Subtype B into Central America Accounts for Most Current Cases
Authors: Murillo Wendy , Veras Nazle , Prosperi Mattia , de Rivera Ivette Lorenzana , Paz-Bailey Gabriela , Morales-Miranda Sonia , Juarez Sandra I. , Yang Chunfu , DeVos Joshua , Marín José Pablo , Mild Mattias , Albert Jan , Salemi Marco 
Published: April 2013

ABSTRACTHuman immunodeficiency virus type 1 (HIV-1) variants show considerable geographical separation across the world, but there is limited information from Central America. We provide the first detailed investigation of the genetic diversity and molecular epidemiology of HIV-1 in six Central American countries. Phylogenetic analysis was performed on 625 HIV-1polgene sequences collected between 2002 and 2010 in Honduras, El Salvador, Nicaragua, Costa Rica, Panama, and Belize. Published sequences from neighboring countries (n= 57) and the rest of the world (n= 740) were included as controls. Maximum likelihood methods were used to explore phylogenetic relationships. Bayesian coalescence-based methods were used to time HIV-1 introductions. Nearly all (98.9%) Central American sequences were of subtype B. Phylogenetic analysis revealed that 437 (70%) sequences clustered within five significantly supported monophyletic clades formed essentially by Central American sequences. One clade contained 386 (62%) sequences from all six countries; the other four clades were smaller and more country specific, suggesting discrete subepidemics. The existence of one large well-supported Central American clade provides evidence that a single introduction of HIV-1 subtype B in Central America accounts for most current cases. An introduction during the early phase of the HIV-1 pandemic may explain its epidemiological success. Moreover, the smaller clades suggest a subsequent regional spread related to specific transmission networks within each country.
Human Cytomegalovirus pUL97 Regulates the Viral Major Immediate Early Promoter by Phosphorylation-Mediated Disruption of Histone Deacetylase 1 Binding
Authors: Bigley Tarin M. , Reitsma Justin M. , Mirza Shama P. , Terhune Scott S. 
Published: April 2013

ABSTRACT
Human cytomegalovirus (HCMV) is a common agent of congenital infection and causes severe disease in immunocompromised patients. Current approved therapies focus on inhibiting viral DNA replication. The HCMV kinase pUL97 contributes to multiple stages of viral infection including DNA replication, controlling the cell cycle, and virion maturation. Our studies demonstrate that pUL97 also functions by influencing immediate early (IE) gene expression during the initial stages of infection. Inhibition of kinase activity using the antiviral compound maribavir or deletion of the UL97 gene resulted in decreased expression of viral immediate early genes during infection. Expression of pUL97 was sufficient to transactivate IE1 gene expression from the viral genome, which was dependent on viral kinase activity. We observed that pUL97 associates with histone deacetylase 1 (HDAC1). HDAC1 is a transcriptional corepressor that acts to silence expression of viral genes. We observed that inhibition or deletion of pUL97 kinase resulted in increased HDAC1 and decreased histone H3 lysine 9 acetylation associating with the viral major immediate early (MIE) promoter. IE expression during pUL97 inhibition or deletion was rescued following inhibition of deacetylase activity. HDAC1 associates with chromatin by protein-protein interactions. Expression of active but not inactive pUL97 kinase decreased HDAC1 interaction with the transcriptional repressor protein DAXX. Finally, using mass spectrometry, we found that HDAC1 is uniquely phosphorylated upon expression of pUL97. Our results support the conclusion that HCMV pUL97 kinase regulates viral immediate early gene expression by phosphorylation-mediated disruption of HDAC1 binding to the MIE promoter.