bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technical Report: TG‐142 compliant and comprehensive quality assurance tests for respiratory gating
Authors: Woods Kyle , Rong Yi 
Published: October 2015

Purpose:To develop and establish a comprehensive gating commissioning and quality assurance procedure in compliance with TG‐142.Methods:Eight Varian TrueBeam Linacs were used for this study. Gating commissioning included an end‐to‐end test and baseline establishment. The end‐to‐end test was performed using a CIRS dynamic thoracic phantom with a moving cylinder inside the lung, which was used for carrying both optically simulated luminescence detectors (OSLDs) and Gafchromic EBT2 films while the target is moving, for a point dose check and 2D profile check. In addition, baselines were established for beam‐on temporal delay and calibration of the surrogate, for both megavoltage (MV) and kilovoltage (kV) beams. A motion simulation device (MotionSim) was used to provide periodic motion on a platform, in synchronizing with a surrogate motion. The overall accuracy and uncertainties were analyzed and compared.Results:The OSLD readings were within 5% compared to the planned dose (within measurement uncertainty) for both phase and amplitude gated deliveries. Film results showed less than 3% agreement to the predicted dose with a standard sinusoid motion. The gate‐on temporal accuracy was averaged at 139 ± 10 ms for MV beams and 92 ± 11 ms for kV beams. The temporal delay of the surrogate motion depends on the motion speed and was averaged at 54.6 ± 3.1 ms for slow, 24.9 ± 2.9 ms for intermediate, and 23.0 ± 20.1 ms for fast speed.Conclusions:A comprehensive gating commissioning procedure was introduced for verifying the output accuracy and establishing the temporal accuracy baselines with respiratory gating. The baselines are needed for routine quality assurance tests, as suggested by TG‐142.
Technical Note: Immunohistochemical evaluation of mouse brain irradiation targeting accuracy with 3D‐printed immobilization device
Authors: Zarghami Niloufar , Jensen Michael D. , Talluri Srikanth , Foster Paula J. , Chambers Ann F. , Dick Frederick A. , Wong Eugene 
Published: October 2015

Purpose:Small animal immobilization devices facilitate positioning of animals for reproducible imaging and accurate focal radiation therapy. In this study, the authors demonstrate the use of three‐dimensional (3D) printing technology to fabricate a custom‐designed mouse head restraint. The authors evaluate the accuracy of this device for the purpose of mouse brain irradiation.Methods:A mouse head holder was designed for a microCT couch using cad software and printed in an acrylic based material. Ten mice received half‐brain radiation while positioned in the 3D‐printed head holder. Animal placement was achieved using on‐board image guidance and computerized asymmetric collimators. To evaluate the precision of beam localization for half‐brain irradiation, mice were sacrificed approximately 30 min after treatment and brain sections were stained for γ‐H2AX, a marker for DNA breaks. The distance and angle of the γ‐H2AX radiation beam border to longitudinal fissure were measured on histological samples. Animals were monitored for any possible trauma from the device.Results:Visualization of the radiation beam on ex vivo brain sections with γ‐H2AX immunohistochemical staining showed a sharp radiation field within the tissue. Measurements showed a mean irradiation targeting error of 0.14 ± 0.09 mm (standard deviation). Rotation between the beam axis and mouse head was 1.2° ± 1.0° (standard deviation). The immobilization device was easily adjusted to accommodate different sizes of mice. No signs of trauma to the mice were observed from the use of tooth block and ear bars.Conclusions:The authors designed and built a novel 3D‐printed mouse head holder with many desired features for accurate and reproducible radiation targeting. The 3D printing technology was found to be practical and economical for producing a small animal imaging and radiation restraint device and allows for customization for study specific needs.
Complete Genome Sequences of Nine Phages Capable of Infecting Paenibacillus larvae, the Causative Agent of American Foulbrood Disease in Honeybees
Authors: Tsourkas Philippos K. , Yost Diane G. , Krohn Andrew , LeBlanc Lucy , Zhang Anna , Stamereilers Casey , Amy Penny S. 
Published: October 2015

ABSTRACT

We present here the complete genome sequences of nine phages that infect
Paenibacillus larvae
, the causative agent of American foulbrood disease in honeybees. The phages were isolated from soil, propolis, and infected bees from three U.S. states. This is the largest number of
P. larvae
phage genomes sequenced in a single publication to date.
Genome Sequence of a Multidrug-Resistant Strain of Stenotrophomonas maltophilia with Carbapenem Resistance, Isolated from King Abdullah Medical City, Makkah, Saudi Arabia
Authors: Abdel-Haleem Alyaa M. , Rchiad Zineb , Khan Babar K. , Abdallah Abdallah M. , Naeem Raeece , Nikhat Sheerin Shalam , Solovyev Victor , Ahmed Abdalla , Pain Arnab 
Published: October 2015

ABSTRACT

The emergence and spread of multidrug-resistant (MDR) bacteria have been regarded as major challenges among health care-associated infections worldwide. Here, we report the draft genome sequence of an MDR
Stenotrophomonas maltophilia
strain isolated in 2014 from King Abdulla Medical City, Makkah, Saudi Arabia.
Complete Genome Sequence of Type 1 Porcine Reproductive and Respiratory Syndrome Virus Strain E38, Isolated from South Korea with a Novel Deletion
Authors: Kim Jeong-Min , Kwon Young-Woo , Choi Eun-Jin , Ouh In-Ohk , Choe Se-Eun , Lee Jienny , Song Jae-Young , Cha Sang-Ho 
Published: October 2015

ABSTRACT
We report the complete genome sequence of the European type 1 porcine reproductive and respiratory syndrome virus E38 strain, isolated from South Korea with a novel deletion. It contains a 61-nucleotide discontinuous deletion of the Nsp2 and Nsp12 regions. This study will aid in understanding the genetic diversity of type 1 PRRSV and in manufacturing a construct based on Korean vaccine candidate development.
Draft Genome Sequence of the Pathogenic Bacterium Vibrio vulnificus V252 Biotype 1, Isolated in Israel
Authors: Efimov Vera , Danin-Poleg Yael , Green Stefan J. , Elgavish Sharona , Kashi Yechezkel 
Published: October 2015

ABSTRACT

We report the genome sequence of the pathogenic
Vibrio vulnificus
biotype 1 clade B, which is suggested to have a common ancestor with biotype 3. This draft genome of the clinical strain V252, isolated in Israel, represents the clonal clade B group that contains both clinical and environmental strains.
Complete Genome Sequence of Citrobacter freundii Myophage Mordin
Authors: Guan Jingwen , Snowden Jeffrey D. , Cahill Jesse L. , Rasche Eric S. , Kuty Everett Gabriel F. 
Published: October 2015

ABSTRACT

Citrobacter freundii
is a Gram-negative opportunistic pathogen that is associated with urinary tract infections. Bacteriophages infecting
C. freundii
can be used as an effective treatment to fight these infections. Here, we announce the complete genome sequence of the
C. freundii
Felix O1-like myophage Mordin and describe its features.
Draft Genome Sequence of Taylorella equigenitalis Strain ERC_G2224 Isolated from the Semen of a Lipizzaner Stallion in South Africa
Authors: May Catherine E. , Schulman Martin L. , Howell Peter G. , Lourens Carina W. , Gouws Johan , Joone Christopher , Monyai Mpho S. , le Grange Misha , Bezuidt Oliver K. I. , Harper Cindy K. , Guthrie Alan J. 
Published: October 2015

ABSTRACT

Taylorella equigenitalis
is the causative agent of contagious equine metritis (CEM), a sexually transmitted infection of horses. We report here the genome sequence of
T. equigenitalis
strain ERC_G2224, isolated in 2015 from a semen sample collected in 1996 from a Lipizzaner stallion in South Africa.
Draft Genome Sequence of Planomicrobium glaciei UCD-HAM (Phylum
Firmicutes
)
Authors: Betts Makayla N. , Jospin Guillaume , Eisen Jonathan A. , Coil David A. 
Published: October 2015

ABSTRACT

Here, we present the draft genome of
Planomicrobium glaciei
, a member of the phylum
Firmicutes
, found at the University of California Davis. Paired-end, 300-bp reads were generated on an Illumina MiSeq. The assembly consists of 3,925,122 bp, contained in 109 contigs, with a G+C content of 46.7%.
Draft Genome Sequence of
Streptomyces
sp. TP-A0890, a Producer of FR-900452 and A-74863a
Authors: Komaki Hisayuki , Ichikawa Natsuko , Hosoyama Akira , Fujita Nobuyuki , Igarashi Yasuhiro 
Published: October 2015

ABSTRACT

Here, we report the draft genome sequence of
Streptomyces
sp. TP-A0890, a producer of FR-900452 and A-74863a. The genome was found to contain at least eight polyketide synthase and nonribosomal peptide synthetase gene clusters. A prediction of gene functions based on the sequence similarity allowed us to assign the biosynthetic gene clusters for FR-900452 and A-74863a.
Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Comamonas testosteroni KF712 (NBRC 110673)
Authors: Hirose Jun , Yamazoe Atsushi , Hosoyama Akira , Kimura Nobutada , Suenaga Hikaru , Watanabe Takahito , Fujihara Hidehiko , Futagami Taiki , Goto Masatoshi , Furukawa Kensuke 
Published: October 2015

ABSTRACT

We present a 5.89-Mb draft genome sequence of
Comamonas testosteroni
KF712 (NBRC 110673), a polychlorinated biphenyl degrader. The genome sequence clarified that KF712 harbors the gene clusters coding for the catabolism of biphenyl and at least seven other aromatic compounds.
Contributions of Subtypes of Non-Hodgkin Lymphoma to Mortality Trends
Authors: Howlader Nadia , Morton Lindsay M. , Feuer Eric J. , Besson Caroline , Engels Eric A. 
Published: October 2015

Abstract
Background: Non-Hodgkin lymphoma (NHL) comprises distinct tumor subtypes. Although mortality from NHL overall has changed dramatically in the United States over time, little is known about trends for subtypes, because death certificates do not record this information.
Methods: Using data from U.S. Surveillance, Epidemiology, and End Results (SEER) areas, we assessed NHL mortality rates and mapped NHL deaths to incident NHL cases in SEER cancer registries. This allowed us to evaluate population-level mortality trends attributed to specific NHL subtypes (incidence-based mortality; IBM). We also describe NHL incidence and survival after NHL diagnosis by calendar year. We used Joinpoint to identify years when IBM and incidence rate trends changed slope.
Results: Overall NHL mortality rates increased during 1975–1997, peaking at 10.9 per 100,000 person-years, then decreased subsequently in 1997–2011. Overall IBM rates mirror this trend during 1990–2011. For B-cell NHL subtypes, IBM rates decreased beginning in the mid-1990s, with yearly declines of −3.0% for diffuse large B-cell lymphoma (DLBCL), −2.7% for chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), and −5.3% for follicular lymphoma. Incidence rates for these subtypes did not decrease until after 2003. Corresponding 5-year cancer-specific survival increased dramatically over time for DLBCL (from 37%–66%), CLL/SLL (69%–84%), and follicular lymphoma (69%–82%). IBM for peripheral T-cell lymphoma was flat during 2006–2011, although incidence increased.
Conclusions: Mortality due to three common B-cell NHL subtypes has fallen over time in the United States.
Impact: This decline reflects better survival after NHL diagnosis, likely from improved therapies, because the decline in NHL incidence occurred later. Cancer Epidemiol Biomarkers Prev; 25(1); 174–9. ©2015 AACR.
Abstract A02: The art of omission: Low fucose antibodies enhance tumor cell clearance in vivo
Authors: Braster Rens , Visser Remco , Vidarsson Gestur , Egmond Marjolein van 
Published: October 2015

Abstract
The use of monoclonal antibodies (mAbs) in treating cancer patients has become an important addition to chemo- and radiotherapy. Depending on the type of antibody, these mAbs induce a variety of different effector functions, including induction of apoptosis and growth inhibition that can lead to eradication of the tumor. Additionally, tumor targeting mAbs can activate the immune system resulting in induction of complement dependent cytotoxicity (CDC), antibody dependent cellular cytotoxicity (ADCC) or phagocytosis (ADCP) of tumor cells by natural killer cells or myeloid cells (monocyte/macrophages and neutrophils). Currently most clinically used mAbs are primarily chimeric or humanized Immunoglobulin G1 (IgG1) mAbs, which bind to IgG Fc receptors (FcγRs).
Efficient binding to FcγRs requires the IgG-Fc-glycan moieties at position 297. In humans, core-fucosylation of IgG is particularly important for binding to human FcγRIIIa and FcγRIIIb, resulting in enhanced uptake of opsonized particles and enhanced ADCC. These properties are increasingly exploited in the next generation of therapeutic anti-tumor IgG.
In this study we investigated whether removal of the core fucose also enhanced killing of tumor cells by mouse effector cells, and whether this prevented tumor outgrowth in vivo. Therefore a chimeric IgG1 (TA99), targeting gp75 on B16F10 mouse melanoma cells, was generated with- and without core-fucose, and their effect was assessed in both in vitro and in vivo models.
In vitro mouse immune cells were incubated with B16F10-gp75 cells in the presence or absence of wildtype or low fucose TA99 and tumor killing was analyzed. In vivo the effect of the TA99 IgG1 low fucose on tumor outgrowth was assessed by injecting both B16F10-gp75 cells and either TA99 IgG1 wt or low fucose in the peritoneal cavity of mice.
Fourteen days post injection tumor outgrowth was analyzed. Mice treated with TA99 low fucose had significantly less tumors in comparison to the wildtype TA99 IgG1, showing that changing the fucosylation of the Fc domain has a remarkable effect on the effectiveness of an antibody therapy.
These results emphasize that when the core fucose of therapeutic IgG antibodies is removed, efficacy of monoclonal antibody therapies will be enhanced significantly. Additionally, the effect works cross species, suggesting mouse models are also suitable to study this phenomenon and to screen antibodies in vivo for enhanced effector functions. Ultimately, this may lead to improved clinical outcome of cancer patients.
Citation Format: Rens Braster, Remco Visser, Gestur Vidarsson, Marjolein van Egmond. The art of omission: Low fucose antibodies enhance tumor cell clearance in vivo. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A02.
Abstract A25: Immunotherapy using LOAd700 armed with CD40 ligand controls experimental pancreatic cancer and activates immune responses
Authors: Svensson Emma , Moreno Rafael , Milenova Ioanna , Christiansson Lisa , Alemany Ramon , Loskog Angelica 
Published: October 2015

Abstract
The aim of this study was to evaluate the efficacy of LOAd immunotherapy to treat pancreatic cancer in a xenograft model as well as to determine the capacity of LOAds to stimulate the immune system in in vitro models. LOAd viruses are oncolytic adenoviruses (5/35) armed with immunostimulatory genes in order to shift the tumor milieu towards immune activation at the same time providing release and spread of tumor antigens due to oncolysis. In this manner, LOAd virus is an antigen-independent immunotherapy for various solid tumors.
LOAd armed with CD40 ligand (LOAd700) was constructed from the ICOVIR system by changing the virus shaft and knob to that of serotype 35 to broaden virus binding and entry into cells (pending patent EP14163704). Oncolysis in OCOVIRs is restricted to cells with a disrupted Rb pathway. Viruses were produced using A549 cells. The pancreatic cancer cell lines BxPC3, Panc01, MiaPaCa2 and PaCa3 were used for in vitro evaluation and Panc01 was used in the xenograft model in Nu/Nu mice. Human dendritic cells (DCs) were obtained by differentiation of CD14+ monocytes with GM-CSF and IL4 for 7 days.
LOAd viruses infected both the panel of pancreatic tumor cell lines and human DCs with high efficacy and both the cell lines and the DCs expressed the CMV driven transgene/s post transduction. The oncolytic LOAd virus did not kill DCs nor healthy pancreatic cells present in donor islet cell isolation surplus material. In contrast, oncolysis was restricted to the tumor cell lines. The LOAd-transduced DCs increased markers of maturation such as MHC II, CD86, CD70 and CD83 and produced high levels of IL12. LOAd stimulated DCs were able to activate and expand antigen-specific T cells and NK cells as demonstrated in a CMV in vitro system. LOAd viruses could control tumor growth in a xenograft immunodeficient model due to oncolysis alone.
In conclusion, LOAd700 can kill pancreatic tumor cells in vitro and control growing tumor in mice due to oncolysis alone. Further, upon DC transduction, LOAd viruses mature DCs to efficient antigen presenters and stimulators of Th1 effector cells such as T cells and NK cells. LOAd is an interesting new immunotherapy for solid malignancies including pancreatic cancer.
Citation Format: Emma Svensson, Rafael Moreno, Ioanna Milenova, Lisa Christiansson, Ramon Alemany, Angelica Loskog. Immunotherapy using LOAd700 armed with CD40 ligand controls experimental pancreatic cancer and activates immune responses. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A25.
Abstract A35: Genomic characterization of immune escape pathways in gastric cancer
Authors: Wang Kai , Leung Suet Yi 
Published: October 2015

Abstract
This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR06) of the Conference Proceedings.
Citation Format: Kai Wang, Suet Yi Leung. Genomic characterization of immune escape pathways in gastric cancer. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A35.
Abstract A36: Novel therapeutic approaches for human malignant mesothelioma
Authors: Yang Haining , Jube Sandro , Carbone Michele 
Published: October 2015

Abstract
Human malignant mesothelioma (MM) is an aggressive and highly lethal cancer that has been linked to asbestos and erionite exposure. MM causes about 3,200 deaths per year in the US and more than 100,000 deaths per year worldwide. We previously found that high-mobility group box-1 protein (HMGB1), a prototypic damage-associated molecular pattern (DAMP), plays a critical role in the early events of HM malignant transformation and MM development. More recently we showed that MM cells are “addicted” to HMGB1 that supports the malignant phenotype by promoting proliferation and invasiveness of MM cells. We demonstrated that MM growth is inhibited by targeting HMGB1 using HMGB1 neutralizing antibody or BoxA, a HMGB1 antagonist. Ethyl pyruvate (EP) is the ethyl ester of pyruvic acid, known to suppress oxygen radical formation and HMGB1 secretion. Here we show that EP impaired motility, survival and proliferation of MM cells in vitro. Both BoxA and EP inhibited the activity of the pro-inflammatory transcription factor NF-kappaB, as well as reduced HMGB1 serum levels and the growth of MM xenografts in SCID mice. Taken together, our results provide a preclinical proof-of-principle that inhibition of HMGB1 activity using either HMGB1 antibody, BoxA or EP offers novel therapeutic approaches for MM treatment.
Citation Format: Haining Yang, Sandro Jube, Michele Carbone. Novel therapeutic approaches for human malignant mesothelioma. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A36.
Abstract A42: MK-1775, a WEE1 inhibitor alleviates resistance to immune attack of tumor cells undergoing an epithelial-mesenchymal transition
Authors: Hamilton Duane H. , Fernando Romaine I. , Tsang Kwong-Yok , Palena Claudia 
Published: October 2015

Abstract
The phenomenon of epithelial-mesenchymal transition (EMT) is a phenotypic switch that allows epithelial tumor cells to acquire features of mesenchymal cells, including the ability to migrate and invade and, therefore, to disseminate from the primary site. In addition to promoting tumor dissemination, various reports have demonstrated that acquisition of features of EMT associates with tumor resistance to the cytotoxic effects of chemotherapy, radiation, and some targeted therapies. It is not well understood, however, the contribution of EMT to the escape of tumors from host immune-surveillance and immune-mediated rejection. Our laboratory has characterized the T-box transcription factor brachyury as a tumor-associated antigen and a regulator of EMT in human carcinomas. By generating isogenic cancer cell lines with various levels of brachyury expression, we demonstrated that high levels of brachyury significantly reduce the susceptibility of cancer cells to lysis by both antigen-specific T cells and natural killer cells, and render tumor cells less responsive to a cancer vaccine in syngeneic murine tumor models. This resistance was due to inefficient caspase-dependent apoptosis, manifested as inefficient nuclear lamin degradation in the presence of activated effector caspases. We correlated this phenomenon to loss of cell cycle kinase CDK1, which mediates lamin phosphorylation. In support of a causal connection, pre-treatment of tumor cells with MK-1775, a specific inhibitor of WEE1, which is known to be a negative regulator kinase of CDK1 activity, could counter the defective apoptosis of tumor cells expressing high levels of brachyury. Thus, our findings suggest reconstituting CDK1 activity to threshold levels might be sufficient to elevate immune-mediated lysis of mesenchymal-like cancer cells, and improve the efficacy of anti-tumor vaccines.
Citation Format: Duane H. Hamilton, Romaine I. Fernando, Kwong-Yok Tsang, Claudia Palena. MK-1775, a WEE1 inhibitor alleviates resistance to immune attack of tumor cells undergoing an epithelial-mesenchymal transition. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A42.