bluuebunny/crossref_metadata_2025_split huggingface dataset:
SU‐C‐BRF‐06: Impact of Temporal Probability in 4D Dose Calculation for Lung Cancer Treatment Planning
Authors: Rouabhi O , Ma M , Bayouth J , Xia J 
Published: July 2014

Purpose:To evaluate dosimetric uncertainty in 4D dose calculation for lung cancer patients using three different temporal probabilities.Methods:The impact of temporal probability, defined as the fraction of time a patient spends in each respiratory amplitude, was evaluated in nine lung cancer patients. For each patient, 4D dose was computed using 4DCT and three temporal probability distributions: 1) uniform distribution, 2) sinusoidal distribution, and 3) patient‐specific distribution. To calculate 4D dose, the dose for each of 10 binned CTs was first computed using the same planning parameters as those used in the breath‐hold CT. Next, deformable image registration was used to deform the dose of each binned CT to the breathhold CT using the deformation map between each binned CT and the breathhold CT. Finally, 4D dose volume was computed by summing the 10 deformed doses using corresponding temporal probabilities. In this study, 4D dose calculated from patient‐specific temporal probabilities was used as the ground truth. Dosimetric comparison included: 1) 3D gamma (3% dose difference, 3mm distance to agreement tolerance), 2) mean tumor dose (MTD), 3) mean lung dose (MLD), and 4) lung V20.Results:For all patients, both uniform and sinusoidal dose distributions were found to have an average gamma passing rate >99% for both lung and PTV volume. Compared with 4D dose calculated using the patient respiratory trace, uniform distribution and sinusoidal distribution showed a percentage difference on average of ‐0.1±0.6% and ‐0.2±0.4% in MTD, ‐0.2±2.0% and ‐0.2±1.3% in MLD, 0.9±2.8% and ‐0.7±1.8% in lung V20, respectively.Conclusion:Both uniformly and sinusoidally‐distributed temporal probabilities can be used to approximate 4D dose calculation. The dosimetric difference among the three temporal probability distributions is not clinically significant.This research is supported by Siemens Medical Solutions USA, Inc
SU‐F‐BRF‐10: Deformable MRI to CT Validation Employing Same Day Planning MRI for Surrogate Analysis
Authors: Padgett K , Stoyanova R , Johnson P , Piper J , Javorek A , Dogan N , Pollack A 
Published: July 2014

Purpose:To compare rigid and deformable registrations of the prostate in the multi‐modality setting (diagnostic‐MRI to planning‐CT) by utilizing a planning‐MRI as a surrogate. The surrogate allows for the direct quantitative analysis which can be difficult in the multi‐modality domain where intensity mapping differs.Methods:For ten subjects, T2 fast‐spin‐echo images were acquired at two different time points, the first several weeks prior to planning (diagnostic‐MRI) and the second on the same day in which the planning CT was collected (planning‐MRI). Significant effort in patient positioning and bowel/bladder preparation was undertaken to minimize distortion of the prostate in all datasets. The diagnostic‐MRI was deformed to the planning‐CT utilizing a commercially available deformable registration algorithm synthesized from local registrations. The deformed MRI was then rigidly aligned to the planning MRI which was used as the surrogate for the planning‐CT. Agreement between the two MRI datasets was scored using intensity based metrics including Pearson correlation and normalized mutual information, NMI. A local analysis was performed by looking only within the prostate, proximal seminal vesicles, penile bulb and combined areas. A similar method was used to assess a rigid registration between the diagnostic‐MRI and planning‐CT.Results:Utilizing the NMI, the deformable registrations were superior to the rigid registrations in 9 of 10 cases demonstrating a 15.94% improvement (p‐value < 0.001) within the combined area. The Pearson correlation showed similar results with the deformable registration superior in the same number of cases and demonstrating a 6.97% improvement (p‐value <0.011).Conclusion:Validating deformable multi‐modality registrations using spatial intensity based metrics is difficult due to the inherent differences in intensity mapping. This population provides an ideal testing ground for MRI to CT deformable registrations by obviating the need for multi‐modality comparisons which are inherently more challenging. Deformable registrations generated in this work significantly outperformed rigid alignments.Research reported in this abstract was supported by the NIH National Cancer Institute R21CA153826 “MRI‐Guided Radiotherapy and Biomarkers for Prostate Cancer” and Bankhead‐Coley Cancer Research Program 10BT‐03 “MRI‐Guided Radiotherapy and Biomarkers for Prostate Cancer”.
SU‐F‐BRF‐11: Dose Rearrangement in High Dose Locally Advanced Lung Patients Based On Perfusion Imaging
Authors: Matrosic C , Jarema D , Kong F , McShan D , Stenmark M , Owen D , Ten Haken R , Matuszak M 
Published: July 2014

Purpose:The use of mean lung dose (MLD) limits allows individualization of lung patient tumor doses at safe levels. However, MLD does not account for local lung function differences between patients, leading to toxicity variability at the same MLD. We investigated dose rearrangement to minimize dose to functional lung, as measured by perfusion SPECT, while maintaining target coverage and conventional MLD limits.Methods:Retrospective plans were optimized for 15 locally advanced NSCLC patients enrolled in a prospective imaging trial. A priority‐based optimization system was used. The baseline priorities were (1) meet OAR dose constraints, (2) maximize target gEUD, and (3) minimize physical MLD. As a final step, normal tissue doses were minimized. To determine the benefit of rearranging dose using perfusion SPECT, plans were reoptimized to minimize functional lung gEUD as the 4th priority.Results:When only minimizing physical MLD, the functional lung gEUD was 10.8+/−5.0 Gy (4.3–19.8 Gy). Only 3/15 cases showed a decrease in functional lung gEUD of ≥4% when rearranging dose to minimize functional gEUD in the cost function (10.5+/−5.0 Gy range 4.3−19.7). Although OAR constraints were respected, the dose rearrangement resulted in ≥10% increases in gEUD to an OAR in 4/15 cases. Only slight reductions in functional lung gEUD were noted when omitting the minimization of physical MLD, suggesting that constraining the target gEUD minimizes the potential to redistribute dose.Conclusion:Prioritydriven optimization permits the generation of plans that respect traditional OAR limits and target coverage, but with the ability to rearrange dose based on functional imaging. The latter appears to be limited due to the decreased solution space when constraining target coverage. Since dose rearrangement may increase dose to other OARs, it is also worthwhile to investigate global biomarkers of lung toxicity to further individualize treatment in this population.Partially supported by R01‐CA142840 and P01‐CA59827
Complete Genome Sequence of Vibrio anguillarum Phage CHOED Successfully Used for Phage Therapy in Aquaculture
Authors: Romero Jaime , Higuera Gastón , Gajardo Felipe , Castillo Daniel , Middleboe Mathias , García Katherine , Ramírez Carolina , Espejo Romilio T. 
Published: July 2014

ABSTRACT

Vibrio anguillarum
phage CHOED was isolated from Chilean mussels. It is a virulent phage showing effective inhibition of
V. anguillarum
. CHOED has potential in phage therapy, because it can protect fish from vibriosis in fish farms. Here, we announce the completely sequenced genome of
V. anguillarum
phage CHOED.
Complete Genome Sequences of Four Novel Lactococcus lactis Phages Distantly Related to the Rare 1706 Phage Species
Authors: Kot Witold , Neve Horst , Vogensen Finn K. , Heller Knut J. , Sørensen Søren J. , Hansen Lars H. 
Published: July 2014

ABSTRACT

Lactoccocus lactis
is a Gram-positive bacterium widely used in the dairy industry in the production of an array of cheeses and other fermented milk products. Here, we describe the sequencing and genome annotations of a set of four phages virulent to
L. lactis
and exhibiting similarities to phage 1706.
Draft Genome Sequence of
Rhodosporidium toruloides
CECT1137, an Oleaginous Yeast of Biotechnological Interest
Authors: Morin Nicolas , Calcas Xavier , Devillers Hugo , Durrens Pascal , Sherman David James , Nicaud Jean-Marc , Neuvéglise Cécile 
Published: July 2014

ABSTRACT

We report the sequencing of the basidiomycetous yeast
Rhodosporidium toruloides
CECT1137. The current assembly comprises 62 scaffolds, for a total size of ca. 20.45 Mbp and a G+C content of ca. 61.9%. The genome annotation predicts 8,206 putative protein-coding genes.
Draft Genome Sequence of Marine-Derived Actinomycete
Nocardiopsis
sp. Strain TP-A0876, a Producer of Polyketide Pyrones
Authors: Komaki Hisayuki , Ichikawa Natsuko , Hosoyama Akira , Fujita Nobuyuki , Igarashi Yasuhiro 
Published: July 2014

ABSTRACT

Here we report the draft genome sequence of
Nocardiopsis
sp. strain TP-A0876, isolated from marine sediment, which produces polyketide-derived pyrones called nocapyrones. The genome contains three polyketide synthase (PKS) gene clusters, one of which was proposed to be responsible for nocapyrone biosynthesis. This genome sequence will facilitate the study of the potential for secondary metabolism in
Nocardiopsis
strains.
Complete Genome Sequence of Mycoplasma californicum Strain HAZ160_1 from Bovine Mastitic Milk in Japan
Authors: Hata Eiji , Murakami Kenji 
Published: July 2014

ABSTRACT

Bovine mycoplasmal mastitis is spreading quickly among cows. It often leads to clinical mastitis outbreaks and often results in huge economic losses.
Mycoplasma californicum
is an important causal species of bovine mastitis. Presented here is the 799,088-bp complete genome sequence of
M. californicum
strain HAZ160_1, which was isolated in Japan.
Complete Genome Sequences of Two Central European Brucella suis bv. 2 Haplotype 2c Strains Isolated from Wild Boars
Authors: Ferreira Ana Cristina , Tenreiro Rogério , Corrêa de Sá Maria Inácia , Dias Ricardo 
Published: July 2014

ABSTRACT

The
Brucella suis
haplotype 2c is commonly isolated from wild boars and domestic pigs across Central Europe, though it is rarely described in the Iberian Peninsula. We report here the complete and annotated genome sequences of two haplotype 2c strains isolated from wild boars in the northeast region of Spain, above the Ebro River.
Draft Genomes of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Strain MM66 and MM66 Derivatives with Altered Vancomycin Resistance Levels
Authors: Matyi Stephanie A. , Ramaraj Thiruvarangan , Sundararajan Anitha , Lindquist Ingrid E. , Devitt Nicolas P. , Schilkey Faye D. , Lamichhane-Khadka Reena , Hoyt Peter R. , Mudge Joann , Gustafson John E. 
Published: July 2014

ABSTRACT

The draft genomes of heterogeneous vancomycin-intermediate
Staphylococcus aureus
(hVISA) strain MM66 and MM66 isolates demonstrating altered vancomycin resistance levels were produced in an effort to provide information on mutations contributing to the vancomycin resistance levels observed in these strains
.
Draft Genome Sequence of Polaromonas glacialis Strain R3-9, a Psychrotolerant Bacterium Isolated from Arctic Glacial Foreland
Authors: Wang Zhiyong , Chang Xulu , Yang Xu , Pan Li , Dai Jun 
Published: July 2014

ABSTRACT

Here we report the draft genome sequence of the psychrotolerant
Polaromonas glacialis
strain R3-9, isolated from Midtre Lovénbreen glacial foreland near Ny-Alesund, Svalbard Archipelago, Norway.
Successful removal of strangulating metal penile ring using a dental handpiece
Authors: Etetafia Mabel Okiemute , Nwajei Charles Onochie 
Published: July 2014

BackgroundUnder emergency conditions, the dental handpiece can be a useful tool for removing a strangulating penile ring.ObjectiveTo report the successful use of a dental handpiece (dental drill) to remove a strangulating penile ring in an emergency.MethodA case report of a strangulating metal penile ring in a psychiatric patient who presented at the accident and emergency unit of Delta State University Teaching Hospital.ResultThe metal ring was removed using a diamond bur in a dental handpiece.ConclusionsIn case of emergency, the dental handpiece is a useful tool for removing a strangulating penile ring.
Palliative care development in the Asia-Pacific region: an international survey from the Asia Pacific Hospice Palliative Care Network (APHN)
Authors: Yamaguchi Takashi , Kuriya Meiko , Morita Tatsuya , Agar Meera , Choi Youn Seon , Goh Cynthia , Lingegowda K B , Lim Richard , Liu Rico K Y , MacLeod Roderick , Ocampo Rhodora , Cheng Shao-Yi , Phungrassami Temsak , Nguyen Yen-Phi , Tsuneto Satoru 
Published: July 2014

BackgroundAlthough palliative care is an important public healthcare issue worldwide, the current situation in the Asia-Pacific region has not been systematically evaluated.ObjectivesThis survey aimed to clarify the current status of palliative care in the Asia-Pacific region.MethodsQuestionnaires were sent to a representative physician of each member country/region of the Asia Pacific Hospice Palliative Care Network (APHN). The questionnaire examined palliative care service provision, information regarding physician certification in palliative care, the availability of essential drugs for palliative care listed by the International Association for Hospice and Palliative Care (IAHPC) and the regulation of opioid-prescribing practice.ResultsOf the 14 member countries/regions of the APHN, 12 (86%) responded. Some form of specialist palliative care services had developed in all the responding countries/regions. Eight member countries/regions had physician certifications for palliative care. Most essential drugs for palliative care listed by the IAHPC were available, whereas hydromorphone, oxycodone and transmucosal fentanyl were unavailable in most countries/regions. Six member countries/regions required permission to prescribe and receive opioids.ConclusionsThe development of palliative care is in different stages across the surveyed countries/regions in the Asia-Pacific region. Data from this survey can be used as baseline data for monitoring the development of palliative care in this region.
Direct oral anticoagulants: integration into clinical practice
Authors: Cowell Richard P W 
Published: July 2014

Abstract
The introduction of direct oral anticoagulants (OACs) for the treatment and prevention of thromboembolic disease represents a shift from the traditional vitamin K antagonist-based therapies, which have been the mainstay of treatment for almost 60 years. A challenge for hospital formularies will be to manage the use of direct OACs from hospital to outpatient settings. Three direct OACs—apixaban, dabigatran and rivaroxaban—are widely approved across different indications, with rivaroxaban approved across the widest breadth of indications. A fourth direct OAC, edoxaban, has also completed phase III trials. Implementation of these agents by physicians will require an understanding of the efficacy and safety profile of these drugs, as well as an awareness of renal function, comedication use, patient adherence and compliance. Optimal implementation of direct OACs in the hospital setting will provide improved patient outcomes when compared with traditional anticoagulants and will simplify the treatment and prevention of thromboembolic diseases.
Androgen Receptor Polymorphism-Dependent Variation in Prostate-Specific Antigen Concentrations of European Men
Authors: Bentmar Holgersson Magdalena , Giwercman Aleksander ,   for the EMAS group, Bjartell Anders , Wu Frederick C.W. , Huhtaniemi Ilpo T. , O'Neill Terence W. , Pendleton Neil , Vanderschueren Dirk , Lean Michael E.J. , Han Thang S. , Finn Joseph D. , Kula Krzysztof , Forti Gianni , Casanueva Felipe F. , Bartfai György , Punab Margus ,   for the EMAS group, Lundberg Giwercman Yvonne 
Published: July 2014

AbstractBackground: Androgens acting via the androgen receptor (AR) stimulate production of PSA, which is a clinical marker of prostate cancer. Because genetic variants in the AR may have a significant impact on the risk of being diagnosed with prostate cancer, the aim was to investigate whether AR variants were associated with the risk of having PSA above clinically used cutoff thresholds of 3 or 4 ng/mL in men without prostate cancer.Methods: Men without prostate cancer history (n = 1,744) were selected from the European Male Ageing Study cohort of 40 to 79-year-old men from eight different European centers. Using linear and logistic regression models, with age and center as covariates, we investigated whether AR variants (CAG repeat-length and/or SNP genotype) were associated with having serum PSA concentrations above 3 or 4 ng/mL, which often are set as cutoff concentrations for further investigation of prostate cancer.Results: Carriers of the SNP rs1204038 A-allele (16% of the men) were more likely to have PSA&gt;3 and 4 ng/mL (OR; 95% confidence intervals, 1.65; 1.13–2.40 and 1.87; 1.18–2.96, respectively) than G-allele carriers. They also had shorter CAG repeats (median 20 vs. 23, P &lt; 0.0005), but CAG repeat length per se did not affect the PSA concentrations.Conclusion: The A-allele of the SNP rs1204038 gives a 65% higher risk of having PSA above 3 ng/mL than the G-allele in men without prostate cancer, and thereby an increased risk of being referred for further examination on suspicion of prostate cancer.Impact: Serum PSA as a clinical marker could be improved by adjustment for AR-genotype. Cancer Epidemiol Biomarkers Prev; 23(10); 2048–56. ©2014 AACR.
Noninvasive Diagnosis of Actionable Mutations by Deep Sequencing of Circulating Free DNA in Lung Cancer from Never-Smokers: A Proof-of-Concept Study from BioCAST/IFCT-1002
Authors: Couraud Sébastien , Vaca-Paniagua Felipe , Villar Stéphanie , Oliver Javier , Schuster Tibor , Blanché Hélène , Girard Nicolas , Trédaniel Jean , Guilleminault Laurent , Gervais Radj , Prim Nathalie , Vincent Michel , Margery Jacques , Larivé Sébastien , Foucher Pascal , Duvert Bernard , Vallee Maxime , Le Calvez-Kelm Florence , McKay James , Missy Pascale , Morin Franck , Zalcman Gérard , Olivier Magali , Souquet Pierre-Jean 
Published: July 2014

AbstractPurpose: Tumor somatic mutation analysis is part of the standard management of metastatic lung cancer. However, physicians often have to deal with small biopsies and consequently with challenging mutation testing. Circulating free DNA (cfDNA) is a promising tool for accessing the tumor genome as a liquid biopsy. Here, we evaluated next-generation sequencing (NGS) on cfDNA samples obtained from a consecutive series of patients for the screening of a range of clinically relevant mutations.Experimental Design: A total of 107 plasma samples were collected from the BioCAST/IFCT-1002 lung cancer study (never-smokers cohort). Matched tumor DNA (tDNA) was obtained for 68 cases. Multiplex PCR-based assays were designed to target specific coding regions in EGFR, KRAS, BRAF, ERBB2, and PI3KCA genes, and amplicon sequencing was performed at deep coverage on the cfDNA/tDNA pairs using the NGS IonTorrent Personal Genome Machine Platform.Results: CfDNA concentration in plasma was significantly associated with both stage and number of metastatic sites. In tDNA, 50 mutations (36 EGFR, 5 ERBB2, 4 KRAS, 3 BRAF, and 2 PIK3CA) were identified, of which 26 were detected in cfDNA. Sensitivity of the test was 58% (95% confidence interval, 43%–71%) and the estimated specificity was 87% (62%–96%).Conclusion: These data demonstrate the feasibility and potential utility of mutation screening in cfDNA using IonTorrent NGS for the detection of a range of tumor biomarkers in patients with metastatic lung cancer. Clin Cancer Res; 20(17); 4613–24. ©2014 AACR.
Cell and Molecular Determinants ofIn VivoEfficacy of the BH3 Mimetic ABT-263 against Pediatric Acute Lymphoblastic Leukemia Xenografts
Authors: Suryani Santi , Carol Hernan , Chonghaile Triona Ni , Frismantas Viktoras , Sarmah Chintanu , High Laura , Bornhauser Beat , Cowley Mark J. , Szymanska Barbara , Evans Kathryn , Boehm Ingrid , Tonna Elise , Jones Luke , Manesh Donya Moradi , Kurmasheva Raushan T. , Billups Catherine , Kaplan Warren , Letai Anthony , Bourquin Jean-Pierre , Houghton Peter J. , Smith Malcolm A. , Lock Richard B. 
Published: July 2014

AbstractPurpose: Predictive biomarkers are required to identify patients who may benefit from the use of BH3 mimetics such as ABT-263. This study investigated the efficacy of ABT-263 against a panel of patient-derived pediatric acute lymphoblastic leukemia (ALL) xenografts and utilized cell and molecular approaches to identify biomarkers that predict in vivo ABT-263 sensitivity.Experimental Design: The in vivo efficacy of ABT-263 was tested against a panel of 31 patient-derived ALL xenografts composed of MLL-, BCP-, and T-ALL subtypes. Basal gene expression profiles of ALL xenografts were analyzed and confirmed by quantitative RT-PCR, protein expression and BH3 profiling. An in vitro coculture assay with immortalized human mesenchymal cells was utilized to build a predictive model of in vivo ABT-263 sensitivity.Results: ABT-263 demonstrated impressive activity against pediatric ALL xenografts, with 19 of 31 achieving objective responses. Among BCL2 family members, in vivo ABT-263 sensitivity correlated best with low MCL1 mRNA expression levels. BH3 profiling revealed that resistance to ABT-263 correlated with mitochondrial priming by NOXA peptide, suggesting a functional role for MCL1 protein. Using an in vitro coculture assay, a predictive model of in vivo ABT-263 sensitivity was built. Testing this model against 11 xenografts predicted in vivo ABT-263 responses with high sensitivity (50%) and specificity (100%).Conclusion: These results highlight the in vivo efficacy of ABT-263 against a broad range of pediatric ALL subtypes and shows that a combination of in vitro functional assays can be used to predict its in vivo efficacy. Clin Cancer Res; 20(17); 4520–31. ©2014 AACR.
Cross Talk Between Vascular Smooth Muscle Cells and Monocytes Through Interleukin-1β/Interleukin-18 Signaling Promotes Vein Graft Thickening
Authors: Li Ping , Li Yu-lin , Li Zhen-ya , Wu Yi-na , Zhang Cong-cong , A Xi , Wang Chun-xiao , Shi Hong-tao , Hui Mi-zhou , Xie Bo , Ahmed Mohammed , Du Jie 
Published: July 2014

Objective—
Interleukin (IL)-1β and IL-18 are key proinflammatory cytokines that play important roles in the pathophysiology of vein graft remodeling. However, the mechanism of IL-1β/IL-18 production and its role in the development of graft remodeling remain unclear.

Approach and Results—
IL-1β/IL-18 were rapidly expressed in venous interposition grafts. Vascular smooth muscle cell (VSMC) death and monocytic inflammasome activation occurred in grafted veins. Necrotic VSMCs induced the expression of IL-1β, IL-18, and other inflammasome-associated proteins in monocytes, which was partially inhibited by their antagonist, recombinant IL-1ra-Fc-IL-18bp. Activated monocytes stimulated proliferation of VSMCs by activating cell growth–related signaling molecules (AKT, STAT3, ERK1/2, and mTOR [AKT/protein kinase B, signal transducer and activator of transcription 3, extracellular signal-regulated kinase 1/2, mammalian target of rapamycin]) and increasing production of platelet-derived growth factor-bb; these effects were suppressed by IL-1ra-Fc-IL-18bp. Activated monocytes also promoted migration of VSMCs, which was independent of IL-1β/IL-18 signaling. Importantly, administration of IL-1ra-Fc-IL-18bp inhibited activation of cell growth–related signaling molecules, VSMC proliferation, and vein graft thickening in vivo.

Conclusions—
Our work identified an interaction among necrotic VSMCs, monocytes, and viable VSMCs through IL-1β/IL-18 signaling, which might be exploited as a therapeutic target in vein graft remodeling.