bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of a free‐running synchronization artifact correction for MV‐imaging with aSi:H flat panels
Authors: Mooslechner Michaela , Mitterlechner Bernhard , Weichenberger Harald , Huber Stefan , Sedlmayer Felix , Deutschmann Heinz 
Published: February 2013

Purpose:Solid state flat panel electronic portal imaging devices (EPIDs) are widely used for megavolt (MV) photon imaging applications in radiotherapy. In addition to their original purpose in patient position verification, they are convenient to use in quality assurance and dosimetry to verify beam geometry and dose deposition or to perform linear accelerator (linac) calibration procedures. However, native image frames from amorphous silicon (aSi:H) detectors show a range of artifacts which have to be eliminated by proper correction algorithms. When a panel is operated in free‐running frame acquisition mode, moving vertical stripes (periodic synchronization artifacts) are a disturbing feature in image frames. Especially for applications in volumetric intensity modulated arc therapy (VMAT) or motion tracking, the synchronization (sync) artifacts are the limiting factor for potential and accuracy since they become even worse at higher frame rates and at lower dose rates, i.e., linac pulse repetition frequencies (PRFs).Methods:The authors introduced a synchronization correction method which is based on a theoretical model describing the interferences of the panel's readout clocking with the linac's dose pulsing. Depending on the applied PRF, a certain number of dose pulses is captured per frame which is readout columnwise, sequentially. The interference of the PRF with the panel readout is responsible for the period and the different gray value levels of the sync stripes, which can be calculated analytically. Sync artifacts can then be eliminated multiplicatively in precorrected frames without additional information about radiation pulse timing.Results:For the analysis, three aSi:H EPIDs of various types were investigated with 6 and 15 MV photon beams at varying PRFs of 25, 50, 100, 200, and 400 pulses per second. Applying the sync correction at panels with gadolinium oxysulfide scintillators improved single frame flood field image quality drastically [improvement of the signal‐to‐noise ratio (SNR) up to 66.1 dB for 6 MV and 66.0 dB for 15 MV]. Also for the EPID with a caesium iodide scintillator, the noise for the lower PRFs could be reduced (SNR at 6 MV of up to 56.3 dB and at 15 MV up to 46.7 dB). However, the simplistic readout interference model fails at higher PRFs, where image lag and ghosting effects due to trapped charges in the thin film transistor and scintillator postglowing require additional corrections.Conclusions:The presented free‐running sync correction method improves SNR of single frames and enables imaging applications, like low‐dose rate imaging at increased image frame rates (e.g., to track moving gold fiducials in the lung). Adaptive image guided radiotherapy protocols become even feasible in VMAT plans. Also simultaneous kilovolt and MV imaging applications can benefit from new possibilities of MV scatter removal in x‐ray images.
Evaluation of a Mycobacterium avium subsp. paratuberculosisleuDMutant as a Vaccine Candidate against Challenge in a Caprine Model
Authors: Faisal Syed M. , Chen Jenn-Wei , Yan Falong , Chen Tsai-Tzu , Useh Nicodemus M. , Yan Weiwei , Guo Shanguang , Wang Shih-Jon , Glaser Amy L. , McDonough Sean P. , Singh Bhupinder , Davis William C. , Akey Bruce L. , Chang Yung-Fu 
Published: February 2013

ABSTRACTJohne's disease (JD) is prevalent worldwide and has a significant impact on the global agricultural economy. In the present study, we evaluated the protective efficacy of aleuD(Δleud) mutant and gained insight into differential immune responses after challenge with virulentM. aviumsubsp.paratuberculosisin a caprine colonization model. The immune response and protective efficacy were compared with those of the killed vaccine Mycopar.In vitrostimulation of peripheral blood mononuclear cells with johnin purified protein derivative showed that Mycopar and ΔleuDgenerated similar levels of gamma interferon (IFN-γ) but significantly higher levels than unvaccinated and challenged phosphate-buffered saline controls. However, only with ΔleuDwas the IFN-γ response maintained. Flow cytometric analysis showed that the increase in IFN-γ correlated with proliferation and activation (increased expression of CD25) of CD4, CD8, and γδT cells, but this response was significantly higher in ΔleuD-vaccinated animals at some time points after challenge. Both Mycopar and ΔleuDvaccines upregulated Th1/proinflammatory and Th17 cytokines and downregulated Th2/anti-inflammatory and regulatory cytokines at similar levels at almost all time points. However, significantly higher levels of IFN-γ (at weeks 26 and 30), interleukin-2 (IL-2; week 18), IL-1b (weeks 14 and 22), IL-17 (weeks 18 and 22), and IL-23 (week 18) and a significantly lower level of IL-10 (weeks 14 and 18) and transforming growth factor β (week 18) were detected in theΔleuD-vaccinated group. Most importantly, ΔleuDelicited an immune response that significantly limited colonization of tissues compared to Mycopar upon challenge with wild-typeM. aviumsubsp.paratuberculosis. In conclusion, the ΔleuDmutant is a promising vaccine candidate for development of a live attenuated vaccine for JD in ruminants.
Genomic Sequencing Reveals Mutations Potentially Related to the Overattenuation of a Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus
Authors: Yu Xiuling , Chen Nanhua , Deng Xiaoyu , Cao Zhen , Han Wei , Hu Dongmei , Wu Jiajun , Zhang Shuo , Wang Baoyue , Gu Xiaoxue , Tian Kegong 
Published: February 2013

ABSTRACT

Highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) continues to evolve when serially passaged in Marc-145 cells. In this study, we analyzed the genomic and antigenic variants of HP-PRRSV strain JXA1 during
in vitro
passage. Protective efficacies of JXA1 from passages 100, 110, 120, 140, and 170 against the high-virulence parental virus were evaluated by inoculating pigs with each of these viruses and then challenging with JXA1 from passage 5 at 28 days postimmunization. We found that the antigenicities of JXA1 from passages after 110 were significantly reduced. Inoculation with JXA1 from passages after 110 provided only insufficient protection against the parental strain challenge, indicating that the immunogenicity of JXA1 is significantly decreased when it is
in vitro
passaged for 110 times and more. To identify the genomic variants that emerged during the overattenuation, eight complete genomes of highly passaged JXA1 were sequenced. One guanine deletion in the 5′ untranslated region (UTR), two nucleotide substitutions in the 3′ UTR, and 65 amino acid mutations in nonstructural and structural proteins that accompanied with the attenuation and overattenuation were determined. Genomic sequencing of
in vitro
serially passaged HP-PRRSV first identified the mutations potentially correlated with the overattenuation of a HP-PRRSV strain. These results facilitate the research aimed at elucidating the mechanisms for PRRSV genomic and antigenic changes and may also contribute to developing a safe and effective PRRSV vaccine.
Value of a Quality Assessment Program in Optimizing Cryopreservation of Peripheral Blood Mononuclear Cells in a Multicenter Study
Authors: Aziz Najib , Margolick Joseph B. , Detels Roger , Rinaldo Charles R. , Phair John , Jamieson Beth D. , Butch Anthony W. 
Published: February 2013

ABSTRACTCryopreservation of peripheral blood mononuclear cells (PBMC) allows assays of cellular function and phenotype to be performed in batches at a later time on PBMC at a central laboratory to minimize assay variability. The Multicenter AIDS Cohort Study (MACS) is an ongoing prospective study of the natural and treated history of human immunodeficiency virus (HIV) infection that stores cryopreserved PBMC from participants two times a year at four study sites. In order to ensure consistent recovery of viable PBMC after cryopreservation, a quality assessment program was implemented and conducted in the MACS over a 6-year period. Every 4 months, recently cryopreserved PBMC from HIV-1-infected and HIV-1-uninfected participants at each MACS site were thawed and evaluated. The median recoveries of viable PBMC for HIV-1-infected and -uninfected participants were 80% and 83%, respectively. Thawed PBMC from both HIV-1-infected and -uninfected participants mounted a strong proliferative response to phytohemagglutinin, with median stimulation indices of 84 and 120, respectively. Expression of the lymphocyte surface markers CD3, CD4, and CD8 by thawed PBMC was virtually identical to what was observed on cells measured in real time using whole blood from the same participants. Furthermore, despite overall excellent performance of the four participating laboratories, problems were identified that intermittently compromised the quality of cryopreserved PBMC, which could be corrected and monitored for improvement over time. Ongoing quality assessment helps laboratories improve protocols and performance on a real-time basis to ensure optimal cryopreservation of PBMC for future studies.
Regional Immune Response to Immunization with Escherichia coli O157:H7-Derived Intimin in Cattle
Authors: Boland Kathryn G. , Hayles Andrea N. , Miller Claire B. , Kerr Tovah , Brown Wendy C. , Lahmers Kevin K. 
Published: February 2013

ABSTRACTEscherichia coliO157:H7 is an enteric pathogen of animals and humans that can result in deadly sequelae. Cattle are asymptomatic carriers and shedders of the bacteria and serve as an important reservoir of human infection.E. coliO157:H7 colonizes the gastrointestinal tract, most frequently at the rectoanal junction mucosa in cattle. Vaccination is a potentially highly effective means of decreasing cattle colonization and shedding and thereby decreasing human infections. Currently available vaccines are administered subcutaneously or intramuscularly, and immune responses have been evaluated solely by systemic immunoglobulin responses. This study evaluated local and systemic lymphoproliferative responses in addition to immunoglobulin responses following subcutaneous or mucosal (rectal) immunization withE. coliO157:H7 outer membrane protein intimin over three trials. In all three trials, significant local and systemic lymphoproliferative responses (P< 0.05) occurred following immunization in the majority of animals, as well as significant immunoglobulin responses (P< 0.001) in all animals. Surprisingly, local responses in the mesorectal lymph nodes were very similar between the subcutaneous and mucosal immunization groups. Moreover, the responses in mesorectal lymph nodes appeared targeted rather than generalized, as minimal or no significant responses were observed in the associated prescapular lymph nodes of subcutaneously immunized animals. The results indicate that both subcutaneous and mucosal immunizations are effective methods of inducing immune responses againstE. coliO157:H7 in cattle.
Development of an Immunochromatographic Assay Based on Dense Granule Protein 7 for Serological Detection of Toxoplasma gondii Infection
Authors: Terkawi Mohamad Alaa , Kameyama Kyohko , Rasul Nazim Hamza , Xuan Xuean , Nishikawa Yoshifumi 
Published: February 2013

ABSTRACTDense granule antigen proteins derived fromToxoplasma gondii(TgGRAs) are potential antigens for the development of diagnostic tools. TgGRA7 and TgGRA14 were detected in the peritoneal fluid ofT. gondii-infected mice, suggesting that TgGRAs may be highly antigenic proteins. Here, TgGRA7 and TgGRA14 were evaluated as candidates for the development of a marker for a rapid diagnostic test. The specificity and sensitivity of purified recombinant proteins of TgGRA7 and TgGRA14 were compared in an indirect enzyme-linked immunosorbent assay (iELISA) using a series of serum samples fromT. gondii-experimentally infected mice and using recombinantT. gondiimajor surface antigen 2 (TgSAG2) as a reference control. The iELISA with TgGRA7 showed the greatest diagnostic accuracy and could detect anti-TgGRA7 antibody in acute and chronic infections. A total of 59 field samples from pigs were also examined by the iELISAs, and the results compared with those of the latex agglutination test (LAT). Among the three recombinant antigens, TgGRA7 had the highest rates of positivity, with significant concordance (88.14) and kappa value (0.76) in comparison with the results using LAT. Furthermore, an immunochromatographic test (ICT) based on recombinant TgGRA7 was developed for rapid detection of antibodies to the infection. The ICT differentiated clearly between sera fromT. gondii-infected mice and uninfected orNeospora caninum-infected mice. Pig sera were examined with the ICT, and the results compared favorably with those of LAT and iELISA for TgGRA7, with kappa values of 0.66 and 0.70 to 0.79, respectively. These data suggest that the ICT based on TgGRA7 is a promising diagnostic tool for routine testing in the clinic and mass screening of samples in the field.
Region of Difference 4 in Alpine Mycobacterium caprae Isolates Indicates Three Variants
Authors: Domogalla Janina , Prodinger Wolfgang M. , Blum Helmut , Krebs Stefan , Gellert Susanne , Müller Matthias , Neuendorf Erdmute , Sedlmaier Florian , Büttner Mathias 
Published: February 2013

ABSTRACT

The lack of complete genome sequence information for
Mycobacterium caprae
complicates a robust differentiation of
M. caprae
and
Mycobacterium bovis
. In this study, the presence or absence of
M. caprae
-specific single nucleotide polymorphisms in
lepA
and
gyrB
genes was assessed. The region of difference 4 (RD4) was analyzed for the identification and characterization of
M. caprae
. Molecular characteristics were evaluated in 12 recent
M. caprae
isolates from livestock and wildlife collected over a 3-year period in Bavaria, Germany. Conventional PCR strategies, sequence analysis of PCR fragments, and data from a next-generation sequencing approach together with variable-number tandem-repeat genotyping were utilized. Single nucleotide polymorphisms in the
lepA
and
gyrB
genes indicating the presence of
M. caprae
were detected in all the isolates. At least three different RD4 variants were found for Alpine
M. caprae
isolates. The results demonstrate that the RD4 region is rather heterogeneous in
M. caprae
genomes. As assumed by others, the presence of RD4 is critical for PCR-based differentiation of
M. caprae
from
M. bovis
, but in addition, the observed variability of RD4 allows the identification of
M. caprae
genotypes and may be indicative of a geographical-type appearance.
CHD6, a Cellular Repressor of Influenza Virus Replication, Is Degraded in Human Alveolar Epithelial Cells and Mice Lungs during Infection
Authors: Alfonso Roberto , Rodriguez Ariel , Rodriguez Paloma , Lutz Thomas , Nieto Amelia 
Published: February 2013

ABSTRACT

The influenza virus polymerase associates to an important number of transcription-related proteins, including the largest subunit of the RNA polymerase II complex (RNAP II). Despite this association, degradation of the RNAP II takes place in the infected cells once viral transcription is completed. We have previously shown that the chromatin remodeler CHD6 protein interacts with the influenza virus polymerase complex, represses viral replication, and relocalizes to inactive chromatin during influenza virus infection. In this paper, we report that CHD6 acts as a negative modulator of the influenza virus polymerase activity and is also subjected to degradation through a process that includes the following characteristics: (i) the cellular proteasome is not implicated, (ii) the sole expression of the three viral polymerase subunits from its cloned cDNAs is sufficient to induce proteolysis, and (iii) degradation is also observed
in vivo
in lungs of infected mice and correlates with the increase of viral titers in the lungs. Collectively, the data indicate that CHD6 degradation is a general effect exerted by influenza A viruses and suggest that this viral repressor may play an important inhibitory role since degradation and accumulation into inactive chromatin occur during the infection.
Galectin-9 Functionally Impairs Natural Killer Cells in Humans and Mice
Authors: Golden-Mason Lucy , McMahan Rachel H. , Strong Michael , Reisdorph Richard , Mahaffey Spencer , Palmer Brent E. , Cheng Linling , Kulesza Caroline , Hirashima Mitsuomi , Niki Toshiro , Rosen Hugo R. 
Published: February 2013

ABSTRACT
Galectin-9 is a pleiotropic immune modulator affecting numerous cell types of innate and adaptive immunity. Patients with chronic infection with either hepatitis C virus (HCV) or HIV have elevated circulating levels. Limited data exist on the regulation of natural killer (NK) cell function through interaction with galectin-9. We found that galectin-9 ligation downregulates multiple immune-activating genes, including eight involved in the NK cell-mediated cytotoxicity pathway, impairs lymphokine-activated killing, and decreases the proportion of gamma interferon (IFN-γ)-producing NK cells that had been stimulated with interleukin-12 (IL-12)/IL-15. We demonstrate that the transcriptional and functional changes induced by galectin-9 are independent of Tim-3. Consistent with these results for humans, we find that the genetic absence of galectin-9 in mice is associated with greater IFN-γ production by NK cells and enhanced degranulation. We also show that in the setting of a short-term (4-day) murine cytomegalovirus infection, terminally differentiated NKs accumulate in the livers of galectin-9 knockout mice, and that hepatic NKs spontaneously produce significantly more IFN-γ in this setting. Taken together, our results indicate that galectin-9 engagement impairs the function of NK cells, including cytotoxicity and cytokine production.
Synergistic Effect of the PDZ and p85β-Binding Domains of the NS1 Protein on Virulence of an Avian H5N1 Influenza A Virus
Authors: Fan Shufang , Macken Catherine A. , Li Chengjun , Ozawa Makoto , Goto Hideo , Iswahyudi N. F. N. , Nidom Chairul A. , Chen Hualan , Neumann Gabriele , Kawaoka Yoshihiro 
Published: February 2013

ABSTRACT
The influenza A virus NS1 protein affects virulence through several mechanisms, including the host's innate immune response and various signaling pathways. Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype continue to evolve through reassortment and mutations. Our recent phylogenetic analysis identified a group of HPAI H5N1 viruses with two characteristic mutations in NS1: the avian virus-type PDZ domain-binding motif ESEV (which affects virulence) was replaced with ESKV, and NS1-138F (which is highly conserved among all influenza A viruses and may affect the activation of the phosphatidylinositol 3-kinase [PI3K]/Akt signaling pathway) was replaced with NS1-138Y. Here, we show that an HPAI H5N1 virus (A/duck/Hunan/69/2004) encoding NS1-ESKV and NS1-138Y was confined to the respiratory tract of infected mice, whereas a mutant encoding NS1-ESEV and NS1-138F caused systemic infection and killed mice more efficiently. Mutation of either one of these sites had small effects on virulence. In addition, we found that the amino acid at NS1-138 affected not only the induction of the PI3K/Akt pathway but also the interaction of NS1 with cellular PDZ domain proteins. Similarly, the mutation in the PDZ domain-binding motif of NS1 altered its binding to cellular PDZ domain proteins and affected Akt phosphorylation. These findings suggest a functional interplay between the mutations at NS1-138 and NS1-229 that results in a synergistic effect on influenza virulence.
Congruent Evolution of Fitness and Genetic Robustness in Vesicular Stomatitis Virus
Authors: Novella Isabel S. , Presloid John B. , Beech Cameron , Wilke Claus O. 
Published: February 2013

ABSTRACT

Quasispecies theory is a case of mutation-selection balance for evolution at high mutation rates, such as those observed in RNA viruses. One of the main predictions of this model is the selection for robustness, defined as the ability of an organism to remain phenotypically unchanged in the face of mutation. We have used a collection of vesicular stomatitis virus strains that had been evolving either under positive selection or under random drift. We had previously shown that the former increase in fitness while the latter have overall fitness decreases (I. S. Novella, J. B. Presloid, T. Zhou, S. D. Smith-Tsurkan, B. E. Ebendick-Corpus, R. N. Dutta, K. L. Lust, and C. O. Wilke, J. Virol.
84:
4960–4968, 2010). Here, we determined the robustness of these strains and demonstrated that strains under positive selection not only increase in fitness but also increase in robustness. In contrast, strains under drift not only decreased in fitness but also decreased in robustness. There was a good overall correlation between fitness and robustness. We also tested whether there was a correlation between fitness and thermostability, and we observed that the correlation was imperfect, indicating that the fitness effects of mutations are exerted in part at a level other than changing the resistance of the protein to temperature.
Multiple Independent Emergences of Type 2 Vaccine-Derived Polioviruses during a Large Outbreak in Northern Nigeria
Authors: Burns Cara C. , Shaw Jing , Jorba Jaume , Bukbuk David , Adu Festus , Gumede Nicksy , Pate Muhammed Ali , Abanida Emmanuel Ade , Gasasira Alex , Iber Jane , Chen Qi , Vincent Annelet , Chenoweth Paul , Henderson Elizabeth , Wannemuehler Kathleen , Naeem Asif , Umami Rifqiyah Nur , Nishimura Yorihiro , Shimizu Hiroyuki , Baba Marycelin , Adeniji Adekunle , Williams A. J. , Kilpatrick David R. , Oberste M. Steven , Wassilak Steven G. , Tomori Oyewale , Pallansch Mark A. , Kew Olen 
Published: February 2013

ABSTRACT

Since 2005, a large poliomyelitis outbreak associated with type 2 circulating vaccine-derived poliovirus (cVDPV2) has occurred in northern Nigeria, where immunization coverage with trivalent oral poliovirus vaccine (tOPV) has been low. Phylogenetic analysis of P1/capsid region sequences of isolates from each of the 403 cases reported in 2005 to 2011 resolved the outbreak into 23 independent type 2 vaccine-derived poliovirus (VDPV2) emergences, at least 7 of which established circulating lineage groups. Virus from one emergence (lineage group 2005-8; 361 isolates) was estimated to have circulated for over 6 years. The population of the major cVDPV2 lineage group expanded rapidly in early 2009, fell sharply after two tOPV rounds in mid-2009, and gradually expanded again through 2011. The two major determinants of attenuation of the Sabin 2 oral poliovirus vaccine strain (A
481
in the 5′-untranslated region [5′-UTR] and VP1-Ile
143
) had been replaced in all VDPV2 isolates; most A
481
5′-UTR replacements occurred by recombination with other enteroviruses. cVDPV2 isolates representing different lineage groups had biological properties indistinguishable from those of wild polioviruses, including efficient growth in neuron-derived HEK293 cells, the capacity to cause paralytic disease in both humans and PVR-Tg21 transgenic mice, loss of the temperature-sensitive phenotype, and the capacity for sustained person-to-person transmission. We estimate from the poliomyelitis case count and the paralytic case-to-infection ratio for type 2 wild poliovirus infections that ∼700,000 cVDPV2 infections have occurred during the outbreak. The detection of multiple concurrent cVDPV2 outbreaks in northern Nigeria highlights the risks of cVDPV emergence accompanying tOPV use at low rates of coverage in developing countries.