bluuebunny/crossref_metadata_2025_split huggingface dataset:
The feasibility of head motion tracking in helical CT: A step toward motion correction
Authors: Kim Jung‐Ha , Nuyts Johan , Kuncic Zdenka , Fulton Roger 
Published: March 2013

Purpose:To establish a practical and accurate motion tracking method for the development of rigid motion correction methods in helical x‐ray computed tomography (CT).Methods:A commercially available optical motion tracking system provided 6 degrees of freedom pose measurements at 60 Hz. A 4 × 4 calibration matrix was determined to convert raw pose data acquired in tracker coordinates to a fixed CT coordinate system with origin at the isocenter of the scanner. Two calibration methods, absolute orientation (AO), and a new method based on image registration (IR), were compared by means of landmark analysis and correlation coefficient in phantom images coregistered using the derived motion transformations.Results:Transformations calculated using the IR‐derived calibration matrix were found to be more accurate, with positional errors less than 0.5 mm (mean RMS), and highly correlated image voxel intensities. The AO‐derived calibration matrix yielded larger mean RMS positional errors (≃1.0 mm), and poorer correlation coefficients.Conclusions:The authors have demonstrated the feasibility of accurate motion tracking for retrospective motion correction in helical CT. Their new IR‐based calibration method based on image registration and function minimization was simpler to perform and delivered more accurate calibration matrices. This technique is a useful tool for future work on rigid motion correction in helical CT and potentially also other imaging modalities.
Optical photon transport in powdered‐phosphor scintillators. Part 1. Multiple‐scattering and validity of the Boltzmann transport equation
Authors: Poludniowski Gavin G. , Evans Philip M. 
Published: March 2013

Purpose:In Part 1 of this two‐part work, predictions for light transport in powdered‐phosphor screens are made, based on three distinct approaches. Predictions of geometrical optics‐based ray tracing through an explicit microscopic model (EMM) for screen structure are compared to a Monte Carlo program based on the Boltzmann transport equation (BTE) and Swank's diffusion equation solution. The purpose is to: (I) highlight the additional assumptions of the BTE Monte Carlo method and Swank's model (both previously used in the literature) with respect to the EMM approach; (II) demonstrate the equivalences of the approaches under well‐defined conditions and; (III) identify the onset and severity of any discrepancies between the models. A package of computer code (calledphsphr) is supplied which can be used to reproduce the BTE Monte Carlo results presented in this work.Methods:The EMM geometrical optics ray‐tracing model is implemented for hypothesized microstructures of phosphor grains in a binder. The BTE model is implemented as a Monte Carlo program with transport parameters, derived from geometrical optics, as inputs. The analytical solution of Swank to the diffusion equation is compared to the EMM and BTE predictions. Absorbed fractions and MTFs are calculated for a range of binder‐to‐phosphor relative refractive indices (n = 1.1–5.0), screen thicknesses (t = 50–200 μm), and packing fill factors (pf = 0.04–0.54).Results:Disagreement between the BTE and EMM approaches increased withn and pf. For the largest relative refractive index (n = 5) and highest packing fill (pf = 0.5), the BTE model underestimated the absorbed fraction and MTF50, by up to 40% and 20%, respectively. However, for relative refractive indices typical of real phosphor screens (n ≤ 2), such as Gd2O2S:Tb, the BTE and EMM predictions agreed well at all simulated packing densities. In addition, Swank's model agreed closely with the BTE predictions when the screen was thick enough to be considered turbid.Conclusions:Although some assumptions of the BTE are violated in realistic powdered‐phosphor screens, these appear to lead to negligible effects in the modeling of optical transport for typical phosphor and binder refractive indices. Therefore it is reasonable to use Monte Carlo codes based on the BTE to treat this problem. Furthermore, Swank's diffusion equation solution is an adequate approximation if a turbidity condition, presented here, is satisfied.
Genome Sequence of Vibrio cholerae G4222, a South African Clinical Isolate
Authors: le Roux Wouter J. , Chan Wai Yin , De Maayer Pieter , Venter Stephanus N. 
Published: March 2013

ABSTRACT

Vibrio cholerae
, a Gram-negative pathogen autochthonous to the aquatic environment, is the causative agent of cholera. Here, we report the complete genome sequence of
V. cholerae
G4222, a clinical isolate from South Africa.
Complete Genome Sequence of Pathogenic Guinea Pig Cytomegalovirus from Salivary Gland Homogenates of Infected Animals
Authors: Yang Dongmei , Tamburro Kristen , Dittmer Dirk , Cui Xiaohong , McVoy Michael A. , Hernandez-Alvarado Nelmary , Schleiss Mark R. 
Published: March 2013

ABSTRACT

The sequence of guinea pig cytomegalovirus (GPCMV) was determined by direct sequencing of salivary gland homogenates obtained following sustained, serial
in vivo
passage of pathogenic virus in guinea pigs. The 233,501-nucleotide salivary gland (SG) genome was noted to have 11 differences compared to the tissue culture-passaged virus, although no variations were noted in putative protein coding sequences.
Draft Genome Sequence of Vibrio mimicus Strain CAIM 602
T
Authors: Guardiola-Avila Iliana , Acedo-Felix Evelia , Noriega-Orozco Lorena , Yepiz-Plascencia Gloria , Sifuentes-Romero Itzel , Gomez-Gil Bruno 
Published: March 2013

ABSTRACT

Vibrio mimicus
is a Gram-negative bacterium associated with gastrointestinal diseases in humans around the world. We report the complete genome sequence of the
Vibrio mimicus
strain CAIM 602
T
(CDC1721-77, LMG 7896
T
, ATCC 33653
T
).
Complete Genomic Sequence of a Novel Reassortant H4N2 Avian Influenza Virus Isolated from Domestic Ducks in Jiangsu, China
Authors: Zhao Qingqing , Li Qunhui , Zhong Lei , Gu Min , Zhu Jie , Zhao Guo , Chen Chaoyang , Wang Xiaoquan , Liu Xiaowen , Liu Xiufan 
Published: March 2013

ABSTRACT
Here, we report the complete genomic sequence of a novel reassortant H4N2 influenza virus isolated from domestic ducks in the Jiangsu province of China in 2011. Phylogenetic analysis showed that all the viral genes except for hemagglutinin (HA) were highly homologous to the clade 2.3.4 H5N2 viruses. The data suggest that genetic reassortment occurred between H4 and H5N2 avian influenza viruses, which highlights the role of domestic poultry as a reassortment vessel in China.
Emergency care staff experiences of lay presence during adult cardiopulmonary resuscitation: a phenomenological study
Authors: Walker Wendy Marina 
Published: March 2013

BackgroundPublic support in favour of family presence during an adult cardiopulmonary resuscitation (CPR) attempt is a contentious issue among providers of emergency care. Researchers have mostly relied on attitudinal surveys to elicit staff views, leaving the life-world of those who have experienced this phenomenon, largely unexplored.ObjectiveTo explore the lived experience of lay presence during an adult CPR attempt in primary (out-of-hospital) and secondary (inhospital) environments of care.DesignHermeneutical phenomenological study.MethodsSemistructured, face-to-face interviews with 8 ambulance staff and 12 registered nurses. The interviews were audio-recorded and subjected to thematic analysis.ResultsParticipants provided insight into situations where lay presence during adult CPR came about either spontaneously or as a planned event. Their accounts portrayed a mixture of benefits and concerns. Familiarity of working in the presence of lay people, practical experience in emergency care and personal confidence were important antecedents. Divergent practices within and across the contexts of care were revealed. The concept of exposure emerged as the essence of this phenomenon. Overall, the study findings serve to challenge some of the previously reported attitudes and opinions of emergency care staff.ConclusionsImproved intraprofessional and interprofessional collaboration is essential to overcoming the barriers associated with lay presence during adult CPR. The future of this practice is dependent on initiatives that seek to bring about attitudinal change. Priority should be given to further exploring this phenomenon in the context of patient and family centred end-of-life care.
Novel HSP90 Inhibitor NVP-HSP990 Targets Cell-Cycle Regulators to Ablate Olig2-Positive Glioma Tumor–Initiating Cells
Authors: Fu Jun , Koul Dimpy , Yao Jun , Wang Shuzhen , Yuan Ying , Colman Howard , Sulman Erik. P. , Lang Frederick. F. , Alfred Yung W.K. 
Published: March 2013

Abstract
Genetic heterogeneity and signaling alterations diminish the effectiveness of single-agent therapies in glioblastoma multiforme (GBM). HSP90 is a molecular chaperone for several signaling proteins that are deregulated in glioma cells. Thus, HSP90 inhibition may offer an approach to coordinately correct multiple signaling pathways as a strategy for GBM therapy. In this study, we evaluated the effects of a novel HSP90 inhibitor, NVP-HSP990, in glioma tumor–initiating cell (GIC) populations, which are strongly implicated in the root pathobiology of GBM. In GIC cultures, NVP-HSP990 elicited a dose-dependent growth inhibition with IC50 values in the low nanomolar range. Two GIC subgroups with different responses were observed with an Olig2-expressing subset relatively more sensitive to treatment. We also showed that Olig2 is a functional marker associated with cell proliferation and response to NVP-HSP990, as NVP-HSP990 attenuated cell proliferation in Olig2-high GIC lines. In addition, NVP-HSP990 disrupted cell-cycle control mechanism by decreasing CDK2 and CDK4 and elevating apoptosis-related molecules. Mechanistic investigations revealed molecular interactions between CDK2/CDK4 and Olig2. Inhibition of CDK2/CDK4 activity disrupted Olig2–CDK2/CDK4 interactions and attenuated Olig2 protein stability. In vivo evaluation showed a relative prolongation of median survival in an intracranial model of GIC growth. Our results suggest that GBM characterized by high-expressing Olig2 GIC may exhibit greater sensitivity to NVP-HSP990 treatment, establishing a foundation for further investigation of the role of HSP90 signaling in GBM. Cancer Res; 73(10); 3062–74. ©2013 AACR.
Hsp27 Regulates Epithelial Mesenchymal Transition, Metastasis, and Circulating Tumor Cells in Prostate Cancer
Authors: Shiota Masaki , Bishop Jennifer L. , Nip Ka Mun , Zardan Anousheh , Takeuchi Ario , Cordonnier Thomas , Beraldi Eliana , Bazov Jenny , Fazli Ladan , Chi Kim , Gleave Martin , Zoubeidi Amina 
Published: March 2013

Abstract
Defining the mechanisms underlying metastatic progression of prostate cancer may lead to insights into how to decrease morbidity and mortality in this disease. An important determinant of metastasis is epithelial-to-mesenchymal transition (EMT), and the mechanisms that control the process of EMT in cancer cells are still emerging. Here, we report that the molecular chaperone Hsp27 (HSPB1) drives EMT in prostate cancer, whereas its attenuation reverses EMT and decreases cell migration, invasion, and matrix metalloproteinase activity. Mechanistically, silencing Hsp27 decreased IL-6–dependent STAT3 phosphorylation, nuclear translocation, and STAT3 binding to the Twist promoter, suggesting that Hsp27 is required for IL-6–mediated EMT via modulation of STAT3/Twist signaling. We observed a correlation between Hsp27 and Twist in patients with prostate cancer, with Hsp27 and Twist expression each elevated in high-grade prostate cancer tumors. Hsp27 inhibition by OGX-427, an antisense therapy currently in phase II trials, reduced tumor metastasis in a murine model of prostate cancer. More importantly, OGX-427 treatment decreased the number of circulating tumor cells in patients with metastatic castration-resistant prostate cancer in a phase I clinical trial. Overall, this study defines Hsp27 as a critical regulator of IL-6–dependent and IL-6–independent EMT, validating this chaperone as a therapeutic target to treat metastatic prostate cancer. Cancer Res; 73(10); 3109–19. ©2013 AACR.
The Prognostic Significance and Therapeutic Potential of Hedgehog Signaling in Intrahepatic Cholangiocellular Carcinoma
Authors: Tang Liang , Tan Ye-Xiong , Jiang Bei-Ge , Pan Yu-Fei , Li Shuang-Xi , Yang Guang-Zhen , Wang Min , Wang Qing , Zhang Jian , Zhou Wei-Ping , Dong Li-Wei , Wang Hong-Yang 
Published: March 2013

Abstract
Purpose: The correlation of the hedgehog signaling pathway with the progression, prognosis, and therapeutics of intrahepatic cholangiocellular carcinoma (ICC) has not been well documented. The study aimed to investigate the expression, prognostic significance, and therapeutic value of hedgehog components in ICC.
Experimental Design: Two independent cohorts of 200 patients with ICC were enrolled. By real-time PCR and immunohistochemistry assay, hedgehog components expression was evaluated. The prognostic values of hedgehog proteins were identified and verified. Cyclopamine or siRNA-targeting Gli was used to block the hedgehog signaling. Cell proliferation and apoptosis were observed by CCK8, cell cycle, and annexin V staining assays. In vivo murine tumor model was used to evaluate the role of hedgehog in ICC.
Results: In ICC tissues, the Gli1 nuclear immune-intensity was associated with intrahepatic metastasis and the expression of Gli2 was associated with intrahepatic metastasis, venous invasion, and Unio Internationale Contra Cancrum (UICC) pT characteristics. In survival analysis, high Gli1 or Gli2 expressers had an unfavorable overall survival (OS) prognosis and a shorter disease-free survival (DFS) than those with low expression. In multivariate analysis, Gli1 expression was found to be an independent prognostic factor of OS, which was validated by another independent cohort. Furthermore, blocking the hedgehog signaling by cyclopamine or siRNA-targeting Gli1 resulted in apoptosis and growth inhibition in ICC cells.
Conclusions: This study shows, for the first time, activation of hedgehog pathway associated with the progression and metastasis in ICC, which may provide prognostic and therapeutic values for this tumor. Clin Cancer Res; 19(8); 2014–24. ©2013 AACR.
Antiviral and Antitumor T-cell Immunity in Patients Treated with GM-CSF–Coding Oncolytic Adenovirus
Authors: Kanerva Anna , Nokisalmi Petri , Diaconu Iulia , Koski Anniina , Cerullo Vincenzo , Liikanen Ilkka , Tähtinen Siri , Oksanen Minna , Heiskanen Raita , Pesonen Saila , Joensuu Timo , Alanko Tuomo , Partanen Kaarina , Laasonen Leena , Kairemo Kalevi , Pesonen Sari , Kangasniemi Lotta , Hemminki Akseli 
Published: March 2013

Abstract
Purpose: Multiple injections of oncolytic adenovirus could enhance immunologic response. In the first part of this article, the focus was on immunologic aspects. Sixty patients previously naïve to oncolytic virus and who had white blood cells available were treated. Thirty-nine of 60 were assessed after a single virus administration, whereas 21 of 60 received a “serial treatment” consisting of three injections within 10 weeks. In the second part, we focused on 115 patients treated with a granulocyte macrophage colony-stimulating factor (GM–CSF)–coding capsid chimeric adenovirus, CGTG-102.
Results: Following serial treatment, both increase and decrease in antitumor T cells in blood were seen more frequently, findings which are compatible with induction of T-cell immunity and trafficking of T cells to tumors, respectively. Safety was good in both groups. In 115 patients treated with CGTG-102 (Ad5/3-D24-GMCSF), median overall survival was 111 days following single and 277 days after serial treatment in nonrandomized comparison. Switching the virus capsid for avoiding neutralizing antibodies in a serial treatment featuring three different viruses did not impact safety or efficacy. A correlation between antiviral and antitumor T cells was seen (P = 0.001), suggesting that viral oncolysis can result in epitope spreading and breaking of tumor-associated immunologic tolerance. Alternatively, some patients may be more susceptible to induction of T-cell immunity and/or trafficking.
Conclusions: These results provide the first human data linking antiviral immunity with antitumor immunity, implying that oncolytic viruses could have an important role in cancer immunotherapy. Clin Cancer Res; 19(10); 2734–44. ©2013 AACR.
Epstein-Barr Virus DNA Load in Nasopharyngeal Brushings and Whole Blood in Nasopharyngeal Carcinoma Patients before and after Treatment
Authors: Adham Marlinda , Greijer Astrid E. , Verkuijlen Sandra A.W.M. , Juwana Hedy , Fleig Sabine , Rachmadi Lisnawati , Malik Octavia , Kurniawan A.N. , Roezin Averdi , Gondhowiardjo Soehartati , Atmakusumah Djumhana , Stevens Servi J.C. , Hermani Bambang , Tan I. Bing , Middeldorp Jaap M. 
Published: March 2013

Abstract
Purpose: Nasopharyngeal carcinoma (NPC) is consistently associated with Epstein-Barr virus (EBV) and highly prevalent in Indonesia. EBV-DNA load can be used for early diagnosis and may have prognostic value. In this study, EBV-DNA load was evaluated in minimal invasive nasopharyngeal (NP) brushings and whole blood for initial diagnosis and therapy assessment against the standard-of-care diagnosis by biopsy with EBV-RISH and standard EBV-IgA serology.
Experimental Design: NP brushings and blood samples were collected from 289 consecutive ENT patients suspected of NPCs and 53 local healthy controls. EBV-DNA load was quantified by real-time PCR and serology by peptide-based EBV-IgA ELISA. Tissue biopsies were examined by routine histochemistry and by EBER RNA in situ hybridization.
Results: Repeated NP brushing was well tolerated by patients and revealed high viral load in the 228 NPC cases at diagnosis than 61 non-NPC cancer cases and healthy controls (P &lt; 0.001). The diagnostic value of EBV-DNA load in blood and EBV-IgA serology was inferior to the NP brush results. The level of EBV-DNA load in brushes of patients with NPC was not related to T, N, or M stage, whereas elevated EBV-DNA load in blood correlated with N and M stage. EBV-DNA levels in brushings and whole blood showed a significant reduction at 2 months after treatment (P = 0.001 and P = 0.005, respectively), which was not reflected in EBV-IgA serology.
Conclusions: NP brush sampling combined with EBV-DNA load analysis is a minimal invasive and well-tolerated diagnostic procedure, suited for initial diagnosis and follow-up monitoring of NPCs. Clin Cancer Res; 19(8); 2175–86. ©2013 AACR.
Aberrant BAF57 Signaling Facilitates Prometastatic Phenotypes
Authors: Balasubramaniam Sucharitha , Comstock Clay E.S. , Ertel Adam , Jeong Kwang Won , Stallcup Michael R. , Addya Sankar , McCue Peter A. , Ostrander William F. , Augello Michael A. , Knudsen Karen E. 
Published: March 2013

Abstract
Purpose: BAF57, a component of the switching-defective and sucrose nonfermenting (SWI/SNF) chromatin-remodeling complex conglomerate, modulates androgen receptor activity to promote prostate cancer. However, the molecular consequences of tumor-associated BAF57 expression have remained undefined in advanced disease such as castration-resistant prostate cancer and/or metastasis.
Experimental Design: Clinical human specimens of primary and metastatic prostate cancer were immunohistochemically examined for tumor-grade association of BAF57 expression. Global gene expression analyses were conducted in models mimicking tumor-associated BAF57 expression. Aberrant BAF57-dependent gene expression changes, bypass of androgen-mediated signaling, and chromatin-specific SWI/SNF complex alterations with respect to cytoskeletal remodelers such as integrins were validated. Cell migration assays were used to profile the biologic phenotypes conferred under conditions simulating tumor-derived BAF57 expression.
Results: Immunohistochemical quantitation of primary human specimens revealed that BAF57 was significantly and aberrantly elevated as a function of tumor grade. Critically, gene expression analyses showed that BAF57 deregulation circumvented androgen-mediated signaling, elicited α2 integrin upregulation, and altered other SWI/SNF complex components at the α2 integrin locus. BAF57-dependent α2 integrin induction conferred a prometastatic migratory advantage, which was attenuated by anti-α2 integrin antibody blockade. Furthermore, BAF57 was found to be markedly upregulated in human prostate cancer metastases of the lung, lymph node, and dura.
Conclusion: The findings herein, identifying tumor-associated BAF57 perturbation as a means to bypass androgen-signaling events that facilitate novel prometastatic phenotypes, link BAF57 upregulation to tumor dissemination. These data thereby establish BAF57 as a putative marker of metastatic potential that could be leveraged for therapeutic intervention. Clin Cancer Res; 19(10); 2657–67. ©2013 AACR.
Elevated TNFR1 and Serotonin in Bone Metastasis Are Correlated with Poor Survival following Bone Metastasis Diagnosis for Both Carcinoma and Sarcoma Primary Tumors
Authors: Chiechi Antonella , Novello Chiara , Magagnoli Giovanna , Petricoin Emanuel F. , Deng Jianghong , Benassi Maria S. , Picci Piero , Vaisman Iosif , Espina Virginia , Liotta Lance A. 
Published: March 2013

Abstract
Purpose: There is an urgent need for therapies that will reduce the mortality of patients with bone metastasis. In this study, we profiled the protein signal pathway networks of the human bone metastasis microenvironment. The goal was to identify sets of interacting proteins that correlate with survival time following the first diagnosis of bone metastasis.
Experimental Design: Using Reverse Phase Protein Microarray technology, we measured the expression of 88 end points in the bone microenvironment of 159 bone metastasis tissue samples derived from patients with primary carcinomas and sarcomas.
Results: Metastases originating from different primary tumors showed similar levels of cell signaling across tissue types for the majority of proteins analyzed, suggesting that the bone microenvironment strongly influences the metastatic tumor signaling profiles. In a training set (72 samples), TNF receptor 1, alone (P = 0.0013) or combined with serotonin (P = 0.0004), TNFα (P = 0.0214), and RANK (P = 0.0226), was associated with poor survival, regardless of the primary tumor of origin. Results were confirmed by (i) analysis of an independent validation set (71 samples) and (ii) independent bioinformatic analysis using a support vector machine learning model. Spearman rho analysis revealed a highly significant number of interactions intersecting with ERα S118, serotonin, TNFα, RANKL, and matrix metalloproteinase in the bone metastasis signaling network, regardless of the primary tumor. The interaction network pattern was significantly different in the short versus long survivors.
Conclusions: TNF receptor 1 and neuroendocrine-regulated protein signal pathways seem to play an important role in bone metastasis and may constitute a novel drug-targetable mechanism of seed-soil cross talk in bone metastasis. Clin Cancer Res; 19(9); 2473–85. ©2013 AACR.