bluuebunny/crossref_metadata_2025_split huggingface dataset:
A set of 4D pediatric XCAT reference phantoms for multimodality research
Authors: Norris Hannah , Zhang Yakun , Bond Jason , Sturgeon Gregory M. , Minhas Anum , Tward Daniel J. , Ratnanather J. T. , Miller M. I. , Frush D. , Samei E. , Segars W. P. 
Published: February 2014

Purpose:The authors previously developed an adult population of 4D extended cardiac‐torso (XCAT) phantoms for multimodality imaging research. In this work, the authors develop a reference set of 4D pediatric XCAT phantoms consisting of male and female anatomies at ages of newborn, 1, 5, 10, and 15 years. These models will serve as the foundation from which the authors will create a vast population of pediatric phantoms for optimizing pediatric CT imaging protocols.Methods:Each phantom was based on a unique set of CT data from a normal patient obtained from the Duke University database. The datasets were selected to best match the reference values for height and weight for the different ages and genders according to ICRP Publication 89. The major organs and structures were segmented from the CT data and used to create an initial pediatric model defined using nonuniform rational B‐spline surfaces. The CT data covered the entire torso and part of the head. To complete the body, the authors manually added on the top of the head and the arms and legs using scaled versions of the XCAT adult models or additional models created from cadaver data. A multichannel large deformation diffeomorphic metric mapping algorithm was then used to calculate the transform from a template XCAT phantom (male or female 50th percentile adult) to the target pediatric model. The transform was applied to the template XCAT to fill in any unsegmented structures within the target phantom and to implement the 4D cardiac and respiratory models in the new anatomy. The masses of the organs in each phantom were matched to the reference values given in ICRP Publication 89. The new reference models were checked for anatomical accuracy via visual inspection.Results:The authors created a set of ten pediatric reference phantoms that have the same level of detail and functionality as the original XCAT phantom adults. Each consists of thousands of anatomical structures and includes parameterized models for the cardiac and respiratory motions. Based on patient data, the phantoms capture the anatomic variations of childhood, such as the development of bone in the skull, pelvis, and long bones, and the growth of the vertebrae and organs. The phantoms can be combined with existing simulation packages to generate realistic pediatric imaging data from different modalities.Conclusions:The development of patient‐derived pediatric computational phantoms is useful in providing variable anatomies for simulation. Future work will expand this ten‐phantom base to a host of pediatric phantoms representative of the public at large. This can provide a means to evaluate and improve pediatric imaging devices and to optimize CT protocols in terms of image quality and radiation dose.
Geometric and dosimetric accuracy of dynamic tumor‐tracking conformal arc irradiation with a gimbaled x‐ray head
Authors: Ono Tomohiro , Miyabe Yuki , Yamada Masahiro , Shiinoki Takehiro , Sawada Akira , Kaneko Shuji , Monzen Hajime , Mizowaki Takashi , Kokubo Masaki , Hiraoka Masahiro 
Published: February 2014

Purpose:The Vero4DRT system has the capability for dynamic tumor‐tracking (DTT) stereotactic irradiation using a unique gimbaled x‐ray head. The purposes of this study were to develop DTT conformal arc irradiation and to estimate its geometric and dosimetric accuracy.Methods:The gimbaled x‐ray head, supported on an O‐ring gantry, was moved in the pan and tilt directions during O‐ring gantry rotation. To evaluate the mechanical accuracy, the gimbaled x‐ray head was moved during the gantry rotating according to input command signals without a target tracking, and a machine log analysis was performed. The difference between a command and a measured position was calculated as mechanical error. To evaluate beam‐positioning accuracy, a moving phantom, which had a steel ball fixed at the center, was driven based on a sinusoidal wave (amplitude [A]: 20 mm, time period [T]: 4 s), a patient breathing motion with a regular pattern (A: 16 mm, average T: 4.5 s), and an irregular pattern (A: 7.2–23.0 mm, T: 2.3–10.0 s), and irradiated with DTT during gantry rotation. The beam‐positioning error was evaluated as the difference between the centroid position of the irradiated field and the steel ball on images from an electronic portal imaging device. For dosimetric accuracy, dose distributions in static and moving targets were evaluated with DTT conformal arc irradiation.Results:The root mean squares (RMSs) of the mechanical error were up to 0.11 mm for pan motion and up to 0.14 mm for tilt motion. The RMSs of the beam‐positioning error were within 0.23 mm for each pattern. The dose distribution in a moving phantom with tracking arc irradiation was in good agreement with that in static conditions.Conclusions:The gimbal positional accuracy was not degraded by gantry motion. As in the case of a fixed port, the Vero4DRT system showed adequate accuracy of DTT conformal arc irradiation.
Generic method for automatic bladder segmentation on cone beam CT using a patient‐specific bladder shape model
Authors: van de Schoot A. J. A. J. , Schooneveldt G. , Wognum S. , Hoogeman M. S. , Chai X. , Stalpers L. J. A. , Rasch C. R. N. , Bel A. 
Published: February 2014

Purpose:The aim of this study is to develop and validate a generic method for automatic bladder segmentation on cone beam computed tomography (CBCT), independent of gender and treatment position (prone or supine), using only pretreatment imaging data.Methods:Data of 20 patients, treated for tumors in the pelvic region with the entire bladder visible on CT and CBCT, were divided into four equally sized groups based on gender and treatment position. The full and empty bladder contour, that can be acquired with pretreatment CT imaging, were used to generate a patient‐specific bladder shape model. This model was used to guide the segmentation process on CBCT. To obtain the bladder segmentation, the reference bladder contour was deformed iteratively by maximizing the cross‐correlation between directional grey value gradients over the reference and CBCT bladder edge. To overcome incorrect segmentations caused by CBCT image artifacts, automatic adaptations were implemented. Moreover, locally incorrect segmentations could be adapted manually. After each adapted segmentation, the bladder shape model was expanded and new shape patterns were calculated for following segmentations. All available CBCTs were used to validate the segmentation algorithm. The bladder segmentations were validated by comparison with the manual delineations and the segmentation performance was quantified using the Dice similarity coefficient (DSC), surface distance error (SDE) and SD of contour‐to‐contour distances. Also, bladder volumes obtained by manual delineations and segmentations were compared using a Bland‐Altman error analysis.Results:The mean DSC, mean SDE, and mean SD of contour‐to‐contour distances between segmentations and manual delineations were 0.87, 0.27 cm and 0.22 cm (female, prone), 0.85, 0.28 cm and 0.22 cm (female, supine), 0.89, 0.21 cm and 0.17 cm (male, supine) and 0.88, 0.23 cm and 0.17 cm (male, prone), respectively. Manual local adaptations improved the segmentation results significantly (p < 0.01) based on DSC (6.72%) and SD of contour‐to‐contour distances (0.08 cm) and decreased the 95% confidence intervals of the bladder volume differences. Moreover, expanding the shape model improved the segmentation results significantly (p < 0.01) based on DSC and SD of contour‐to‐contour distances.Conclusions:This patient‐specific shape model based automatic bladder segmentation method on CBCT is accurate and generic. Our segmentation method only needs two pretreatment imaging data sets as prior knowledge, is independent of patient gender and patient treatment position and has the possibility to manually adapt the segmentation locally.
Antigenic and Genetic Evolution of Low-Pathogenicity Avian Influenza Viruses of Subtype H7N3 following Heterologous Vaccination
Authors: Beato Maria Serena , Xu Yifei , Long Li-Ping , Capua Ilaria , Wan Xiu-Feng 
Published: February 2014

ABSTRACTOutbreaks of low-pathogenicity avian influenza (LPAI) viruses of the H7N3 subtype were first detected in Italy in October 2002, and the virus continued to circulate between 2002 and 2004 in a densely populated poultry area in the northeast portion of that country. This virus circulated in unvaccinated and vaccinated poultry farms, and the infection was controlled in August 2003 by culling, control of movements, improved biosecurity, and heterologous vaccination. In 2004, H7N3 reoccurred in vaccinated poultry farms in which infection had been successfully controlled by the vaccination program. To shed light on this occurrence and the temporal pattern and genetic basis of antigenic drift for avian influenza viruses (AIVs) in the absence and presence of heterologous vaccination, a collection of H7N3 viruses isolated in 2002 and 2004 were characterized genetically and antigenically. Molecular analysis showed that viruses isolated in the 2004 outbreaks after the implementation of vaccination had acquired specific amino acid signatures, most of which were located at reported antibody binding sites of the hemagglutinin (HA) protein. Antigenic characterization of these 2004 isolates showed that they were antigenically different from those isolated prior to the implementation of vaccination. This is the first report on antigenic and genetic evolution of H7 LPAI viruses following the application of heterologous vaccination in poultry. These findings may have an impact on control strategies to combat AI infections in poultry based on vaccination.
Comparison of a Transplant Multiplex Viral Panel on the ICEPlex System with Real-Time PCR for Detection of Cytomegalovirus, Epstein-Barr Virus, and BK Virus in Clinical Specimens
Authors: Khare Reeti , Espy Mark J. , Mandrekar Jayawant N. , Binnicker Matthew J. 
Published: February 2014

ABSTRACT
We compared a multiplex viral transplant panel on the ICEPlex system to real-time PCR for the detection of cytomegalovirus (CMV), Epstein-Barr virus (EBV), and BK virus (BKV). The sensitivities of the ICEPlex were 83.3%, 95.5%, and 65.5% for the detection of CMV, EBV, and BKV, respectively. Interestingly, the multiplex assay detected dual infections in 16/280 (5.7%) samples tested.
Azole-Resistant Aspergillus fumigatus Isolate with the TR34/L98H Mutation in Both a Fungicide-Sprayed Field and the Lung of a Hematopoietic Stem Cell Transplant Recipient with Invasive Aspergillosis
Authors: Rocchi Steffi , Daguindau Etienne , Grenouillet Frédéric , Deconinck Eric , Bellanger Anne-Pauline , Garcia-Hermoso Dea , Bretagne Stéphane , Reboux Gabriel , Millon Laurence 
Published: February 2014

ABSTRACT

A French farmer developed invasive aspergillosis with azole-resistant
Aspergillus fumigatus
with the TR34/L98H mutation following a hematopoietic stem cell transplantation. He had worked in fungicide-sprayed fields where a non-genetically related
A. fumigatus
TR34/L98H isolate was collected. If azole resistance detection increases, voriconazole as first-line therapy might be questioned in agricultural areas.
Recombinant Protein- and Synthetic Peptide-Based Immunoblot Test for Diagnosis of Neurocysticercosis
Authors: Noh John , Rodriguez Silvia , Lee Yeuk-Mui , Handali Sukwan , Gonzalez Armando E. , Gilman Robert H. , Tsang Victor C. W. , Garcia Hector H. , Wilkins Patricia P. 
Published: February 2014

ABSTRACT

One of the most well-characterized tests for diagnosing neurocysticercosis (NCC) is the enzyme-linked immunoelectrotransfer blot (EITB) assay developed at the CDC, which uses lentil lectin-bound glycoproteins (LLGP) extracted from
Taenia solium
cysticerci. Although the test is very reliable, the purification process for the LLGP antigens has been difficult to transfer to other laboratories because of the need for expensive equipment and technical expertise. To develop a simpler assay, we previously purified and cloned the diagnostic glycoproteins in the LLGP fraction. In this study, we evaluated three representative recombinant or synthetic antigens from the LLGP fraction, individually and in different combinations, using an immunoblot assay (recombinant EITB). Using a panel of 249 confirmed NCC-positive and 401 negative blood serum samples, the sensitivity of the recombinant EITB assay was determined to be 99% and the specificity was 99% for diagnosing NCC. We also tested a panel of 239 confirmed NCC-positive serum samples in Lima, Peru, and found similar results. Overall, our data show that the performance characteristics of the recombinant EITB assay are comparable to those of the LLGP-EITB assay. This new recombinant- and synthetic antigen-based assay is sustainable and can be easily transferred to other laboratories in the United States and throughout the world.
Spread of CTX-M-15 Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates through Household Contact and Plasmid Transfer
Authors: Kojima Yasuko , Harada Sohei , Aoki Kotaro , Ishii Yoshikazu , Sawa Tomoka , Hasegawa Kei , Saji Tsutomu , Yamaguchi Keizo , Tateda Kazuhiro 
Published: February 2014

ABSTRACT

We document the household spread of extended-spectrum β-lactamase-producing
Escherichia coli
. One isolate belonged to sequence type 1193 and caused urinary tract infection in a 4-month-old female, and the other isolate belonged to sequence type 131 and colonized three family members, including the index patient. These isolates carried similar Inc-I1-Iγ plasmids, harboring
bla
CTX-M-15
.
Development and Validation of an In-House Database for Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry-Based Yeast Identification Using a Fast Protein Extraction Procedure
Authors: De Carolis Elena , Vella Antonietta , Vaccaro Luisa , Torelli Riccardo , Posteraro Patrizia , Ricciardi Walter , Sanguinetti Maurizio , Posteraro Brunella 
Published: February 2014

ABSTRACT
In recent studies evaluating the usefulness of the matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS)-based identification of yeasts for the routine diagnosis of fungal infections, preanalytical sample processing has emerged as a critical step for reliable MALDI-TOF MS outcomes, especially when the Bruker Daltonics Biotyper software was used. In addition, inadequate results often occurred due to discrepancies between the methods used for clinical testing and database construction. Therefore, we created an in-house MALDI-TOF MS library using the spectra from 156 reference and clinical yeast isolates (48 species in 11 genera), which were generated with a fast sample preparation procedure. After a retrospective validation study, our database was evaluated on 4,232 yeasts routinely isolated during a 6-month period and fast prepared for MALDI-TOF MS analysis. Thus, 4,209 (99.5%) of the isolates were successfully identified to the species level (with scores of ≥2.0), with 1,676 (39.6%) having scores of >2.3. For the remaining 23 (0.5%) isolates, no reliable identification (with scores of <1.7) was obtained. Interestingly, these isolates were almost always from species uniquely represented or not included in the database. As the MALDI-TOF MS results were, except for 23 isolates, validated without additional phenotypic or molecular tests, our proposed strategy can enhance the rapidity and accuracy of MALDI-TOF MS in identifying medically important yeast species. However, while continuous updating of our database will be necessary to enrich it with more strains/species of new and emerging yeasts, the present in-house MALDI-TOF MS library can be made publicly available for future multicenter studies.
Effect of Preanalytical Processing of ThinPrep Specimens on Detection of High-Risk Human Papillomavirus by the Aptima HPV Assay
Authors: Munson Erik , Schroeder Elizabeth R. , Ross Kevin C. , Yauck Connie , Bieganski Theresa , Amrhein Robert D. , Napierala Maureen , Harkins April L. 
Published: February 2014

ABSTRACT

Two important preanalytical protocols performed on liquid-based cytological specimens, namely, automated cytology processing and glacial acetic acid (GAA) treatment, may occur prior to the arrival of specimens in a molecular diagnostics laboratory. Ninety-two ThinPrep vials previously positive for high-risk human papillomavirus (HPV) via the Cervista HPV HR test were preselected and alternated with 92 previously negative ThinPrep vials. The specimen set was processed in a consecutive fashion by an automated cytology processor without fastidious decontamination precautions. Carryover potential was subsequently assessed by performance of the Aptima HPV assay on aliquots from reprocessed ThinPrep vials. All previously negative ThinPrep vials yielded a negative result following routine automated cytology processing, despite close proximity to known-positive ThinPrep vials. In separate experiments, aliquots from 236 ThinPrep vials were forwarded for tandem analysis with and without GAA treatment. Data from GAA- and mock-treated specimens generated by Aptima HPV were compared to correlate data generated by Cervista. A 99.2% concordance of Aptima HPV results from GAA-treated and mock-treated specimens was noted. This result differed from the concordance result derived from Cervista (91.5%;
P
< 0.0002). Of the initially positive Cervista results, 21.9% reverted to negative following GAA treatment; the correlate value was 2.7% for Aptima HPV (
P
= 0.01). While deleterious effects of GAA treatment on genomic DNA were noted with Cervista (
P
= 0.0015), GAA treatment had no significant effects on Aptima HPV specimen signal/cutoff ratios or amplification of internal control RNA (
P
≥ 0.07). The validity of an Aptima HPV result is independent of GAA treatment and routine automated cytology processing.
Epstein-Barr Virus BALF3 Has Nuclease Activity and Mediates Mature Virion Production during the Lytic Cycle
Authors: Chiu Shih-Hsin , Wu Meng-Chuan , Wu Chung-Chun , Chen Yu-Ching , Lin Su-Fang , Hsu John T.-A. , Yang Chung-Shi , Tsai Ching-Hwa , Takada Kenzo , Chen Mei-Ru , Chen Jen-Yang 
Published: February 2014

ABSTRACTEpstein-Barr virus (EBV) lytic replication involves complex processes, including DNA synthesis, DNA cleavage and packaging, and virion egress. These processes require many different lytic gene products, but the mechanisms of their actions remain unclear, especially for DNA cleavage and packaging. According to sequence homology analysis, EBV BALF3, encoded by the third leftward open reading frame of the BamHI-A fragment in the viral genome, is a homologue of herpes simplex virus type 1 UL28. This gene product is believed to possess the properties of a terminase, such as nucleolytic activity on newly synthesized viral DNA and translocation of unit length viral genomes into procapsids. In order to characterize EBV BALF3, the protein was produced by and purified from recombinant baculoviruses and examined in an enzymatic reactionin vitro, which determined that EBV BALF3 acts as an endonuclease and its activity is modulated by Mg2+, Mn2+, and ATP. Moreover, in EBV-positive epithelial cells, BALF3 was expressed and transported from the cytoplasm into the nucleus following induction of the lytic cycle, and gene silencing of BALF3 caused a reduction of DNA packaging and virion release. Interestingly, suppression of BALF3 expression also decreased the efficiency of DNA synthesis. On the basis of these results, we suggest that EBV BALF3 is involved simultaneously in DNA synthesis and packaging and is required for the production of mature virions.IMPORTANCEVirus lytic replication is essential to produce infectious virions, which is responsible for virus survival and spread. This work shows that an uncharacterized gene product of the human herpesvirus Epstein-Barr virus (EBV), BALF3, is expressed during the lytic cycle. In addition, BALF3 mediates an endonucleolytic reaction and is involved in viral DNA synthesis and packaging, leading to influence on the production of mature virions. According to sequence homology and physical properties, the lytic gene product BALF3 is considered a terminase in EBV. These findings identify a novel viral gene with an important role in contributing to a better understanding of the EBV life cycle.
VSV-GP: a Potent Viral Vaccine Vector That Boosts the Immune Response upon Repeated Applications
Authors: Tober Reinhard , Banki Zoltan , Egerer Lisa , Muik Alexander , Behmüller Sandra , Kreppel Florian , Greczmiel Ute , Oxenius Annette , von Laer Dorothee , Kimpel Janine 
Published: February 2014

ABSTRACT

Antivector immunity limits the response to homologous boosting for viral vector vaccines. Here, we describe a new, potent vaccine vector based on replication-competent vesicular stomatitis virus pseudotyped with the glycoprotein of the lymphocytic choriomeningitis virus (VSV-GP), which we previously showed to be safe in mice. In mice, VSV and VSV-GP encoding ovalbumin (OVA) as a model antigen (VSV-OVA and VSV-GP-OVA) induced equal levels of OVA-specific humoral and cellular immune responses upon a single immunization. However, boosting with the same vector was possible only for VSV-GP-OVA as neutralizing antibodies to VSV limited the immunogenicity of the VSV-OVA boost. OVA-specific cytotoxic T-lymphocyte (CTL) responses induced by VSV-GP-OVA were at least as potent as those induced by an adenoviral state-of-the-art vaccine vector and completely protected mice in a
Listeria monocytogenes
challenge model. VSV-GP is so far the only replication-competent vaccine vector that does not lose efficacy upon repeated application.

IMPORTANCE
Although there has been great progress in treatment and prevention of infectious diseases in the past several years, effective vaccines against some of the most serious infections, e.g., AIDS, malaria, hepatitis C, or tuberculosis, are urgently needed. Here, several approaches based on viral vector vaccines are under development. However, for all viral vaccine vectors currently in clinical testing, repeated application is limited by neutralizing antibodies to the vector itself. Here, we have exploited the potential of vesicular stomatitis virus pseudotyped with the glycoprotein of the lymphocytic choriomeningitis virus (VSV-GP) as a vaccine platform. VSV-GP is the first replication-competent viral vector vaccine that does not induce vector-specific humoral immunity, i.e., neutralizing antibodies, and therefore can boost immune responses against a foreign antigen by repeated applications. The vector allows introduction of various antigens and therefore can serve as a platform technology for the development of novel vaccines against a broad spectrum of diseases.
Role of the Immunoreceptor Tyrosine-Based Activation Motif of Latent Membrane Protein 2A (LMP2A) in Epstein-Barr Virus LMP2A-Induced Cell Transformation
Authors: Fukuda Makoto , Kawaguchi Yasushi 
Published: February 2014

ABSTRACT
Latent membrane protein 2A (LMP2A) of Epstein-Barr virus (EBV) is widely expressed in EBV-associated malignancies. We demonstrate that LMP2A has a transformation ability. This study shows that LMP2A-induced transformation in several human nonhematopoietic cell lines was blocked in those cells expressing an immunoreceptor tyrosine-based activation motif (ITAM) LMP2A mutant. The Syk inhibitor or Syk-specific small interfering RNA (siRNA) inhibited LMP2A-induced transformation. These results indicate that the interaction of the LMP2A ITAM with Syk is a key step for LMP2A-mediated transformation.