bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detector dose response in megavoltage small photon beams. I. Theoretical concepts
Authors: Bouchard Hugo , Seuntjens Jan , Duane Simon , Kamio Yuji , Palmans Hugo 
Published: September 2015

Purpose:To explain the reasons for significant quality correction factors in megavoltage small photon fields and clarify the underlying concepts relevant to dosimetry under such conditions.Methods:The validity of cavity theory and the requirement of charged particle equilibrium (CPE) are addressed from a theoretical point of view in the context of nonstandard beams. Perturbation effects are described into four main subeffects, explaining their nature and pointing out their relative importance in small photon fields.Results:It is demonstrated that the failure to meet classical cavity theory requirements, such as CPE, is not the reason for significant quality correction factors. On the contrary, it is shown that the lack of CPE alone cannot explain these corrections and that what matters most, apart from volume averaging effects, is the relationship between the lack of CPE in the small field itself and the density of the detector cavity. The density perturbation effect is explained based on Fano's theorem, describing the compensating effect of two main contributions to cavity absorbed dose. Using the same approach, perturbation effects arising from the difference in atomic properties of the cavity medium and the presence of extracameral components are explained. Volume averaging effects are also discussed in detail.Conclusions:Quality correction factors of small megavoltage photon fields are mainly due to differences in electron density between water and the detector medium and to volume averaging over the detector cavity. Other effects, such as the presence of extracameral components and differences in atomic properties of the detection medium with respect to water, can also play an accentuated role in small photon fields compared to standard beams.
Detector dose response in megavoltage small photon beams. II. Pencil beam perturbation effects
Authors: Bouchard Hugo , Kamio Yuji , Palmans Hugo , Seuntjens Jan , Duane Simon 
Published: September 2015

Purpose:To quantify detector perturbation effects in megavoltage small photon fields and support the theoretical explanation on the nature of quality correction factors in these conditions.Methods:In this second paper, a modern approach to radiation dosimetry is defined for any detector and applied to small photon fields. Fano's theorem is adapted in the form of a cavity theory and applied in the context of nonstandard beams to express four main effects in the form of perturbation factors. The pencil‐beam decomposition method is detailed and adapted to the calculation of perturbation factors and quality correction factors. The approach defines a perturbation function which, for a given field size or beam modulation, entirely determines these dosimetric factors. Monte Carlo calculations are performed in different cavity sizes for different detection materials, electron densities, and extracameral components.Results:Perturbation effects are detailed with calculated perturbation functions, showing the relative magnitude of the effects as well as the geometrical extent to which collimating or modulating the beam impacts the dosimetric factors. The existence of a perturbation zone around the detector cavity is demonstrated and the approach is discussed and linked to previous approaches in the literature to determine critical field sizes.Conclusions:Monte Carlo simulations are valuable to describe pencil beam perturbation effects and detail the nature of dosimetric factors in megavoltage small photon fields. In practice, it is shown that dosimetric factors could be avoided if the field size remains larger than the detector perturbation zone. However, given a detector and beam quality, a full account for the detector geometry is necessary to determine critical field sizes.
Genome Sequence of Avirulent Riemerella anatipestifer Strain RA-JLLY
Authors: Zhang Tengfei , Zhang Rongrong , Luo Qingping , Wen Guoyuan , Ai Diyun , Wang Honglin , Luo Ling , Wang Hongcai , Shao Huabin 
Published: September 2015

ABSTRACT

Riemerella anatipestifer
is an important bacterial pathogen associated with epizootic infections in waterfowl and various other birds.
Riemerella anatipestifer
strain RA-JLLY is an avirulent strain, isolated from the brain of an old duck in Hubei province, China. Here, we report the genome sequence of this species.
Draft Genome Sequence of the Entomopathogenic Bacterium Bacillus pumilus 15.1, a Strain Highly Toxic to the Mediterranean Fruit Fly
Ceratitis capitata
Authors: García-Ramón Diana C. , Palma Leopoldo , Berry Colin , Osuna Antonio , Vílchez Susana 
Published: September 2015

ABSTRACT

We present the draft whole-genome sequence of the entomopathogenic
Bacillus pumilus
15.1 strain that consists of 3,795,691 bp and 3,776 predicted protein-coding genes. This genome sequence provides the basis for understanding the potential mechanism behind the toxicity and virulence of
B. pumilus
15.1 against the Mediterranean fruit fly.
Isolation of a Complete Circular Virus Genome Sequence from an Alaskan Black-Capped Chickadee (
Poecile atricapillus
) Gastrointestinal Tract Sample
Authors: Hanna Zachary R. , Runckel Charles , Fuchs Jérôme , DeRisi Joseph L. , Mindell David P. , Van Hemert Caroline , Handel Colleen M. , Dumbacher John P. 
Published: September 2015

ABSTRACT

We report here the genome sequence of a circular virus isolated from samples of an Alaskan black-capped chickadee (
Poecile atricapillus
) gastrointestinal tract. The genome is 2,152 bp in length and is most similar (30 to 44.5% amino acid identity) to the genome sequences of other single-stranded DNA (ssDNA) circular viruses belonging to the gemycircularvirus group.
Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of
Negativicutes
in the
Firmicutes
Phylum
Authors: De León Kara B. , Utturkar Sagar M. , Camilleri Laura B. , Elias Dwayne A. , Arkin Adam P. , Fields Matthew W. , Brown Steven D. , Wall Judy D. 
Published: September 2015

ABSTRACT

The genome of
Pelosinus fermentans
JBW45, isolated from a chromium-contaminated site in Hanford, Washington, USA, has been completed with PacBio sequencing. Nine copies of the rRNA gene operon and multiple transposase genes with identical sequences resulted in breaks in the original draft genome and may suggest genomic instability of JBW45.
Molecular Signature of the Ebola Virus Associated with the Fishermen Community Outbreak in Aberdeen, Sierra Leone, in February 2015
Authors: Capobianchi Maria R. , Gruber Cesare E. M. , Carletti Fabrizio , Meschi Silvia , Castilletti Concetta , Vairo Francesco , Biava Mirella , Minosse Claudia , Strada Gino , Portella Gina , Miccio Rossella , Minardi Valeria , Rolla Luca , Kamara Abdul , Chillemi Giovanni , Desideri Alessandro , Di Caro Antonino , Ippolito Giuseppe 
Published: September 2015

ABSTRACT
We report the complete genome sequence of Ebola virus from a health worker linked to a cluster of cases occurring in the fishing community of Aberdeen, Sierra Leone (February 2015), which were characterized by unusually severe presentation. The sequence, clustering in the SL subclade 3.2.4, harbors mutations potentially relevant for pathogenesis.
Complete Genome Sequence of
Marinobacter
sp. CP1, Isolated from a Self-Regenerating Biocathode Biofilm
Authors: Wang Zheng , Eddie Brian J. , Malanoski Anthony P. , Hervey W. Judson , Lin Baochuan , Strycharz-Glaven Sarah M. 
Published: September 2015

ABSTRACT

Marinobacter
sp. CP1 was isolated from a self-regenerating and self-sustaining biocathode biofilm that can fix CO
2
and generate electric current. We present the complete genome sequence of this strain, which consists of a circular 4.8-Mbp chromosome, to understand the mechanism of extracellular electron transfer in a microbial consortium.
3D gravity, Chern–Simons and higher spins: A mini introduction
Authors: Kiran K. Surya , Krishnan Chethan , Raju Avinash 
Published: September 2015

We give a review on (a) elements of (2+1)-dimensional gravity, (b) some aspects of its relation to Chern–Simons theory, (c) its generalization to couple higher spins, and (d) cosmic singularity resolution as an application in the context of flat space higher spin theory. A knowledge of the Einstein–Hilbert action, classical non-Abelian gauge theory and some (negotiable amount of) maturity are the only pre-requisites.
The Association between Glyceraldehyde-Derived Advanced Glycation End-Products and Colorectal Cancer Risk
Authors: Kong So Yeon , Takeuchi Masayoshi , Hyogo Hideyuki , McKeown-Eyssen Gail , Yamagishi Sho-ichi , Chayama Kazuaki , O'Brien Peter J. , Ferrari Pietro , Overvad Kim , Olsen Anja , Tjønneland Anne , Boutron-Ruault Marie-Christine , Bastide Nadia , Carbonnel Franck , Kühn Tilman , Kaaks Rudolf , Boeing Heiner , Aleksandrova Krasimira , Trichopoulou Antonia , Lagiou Pagona , Vasilopoulou Effie , Masala Giovanna , Pala Valeria , Santucci De Magistris Maria , Tumino Rosario , Naccarati Alessio , Bueno-de-Mesquita H.B. , Peeters Petra H. , Weiderpass Elisabete , Quirós J. Ramón , Jakszyn Paula , Sánchez María-José , Dorronsoro Miren , Gavrila Diana , Ardanaz Eva , Rutegård Martin , Nyström Hanna , Wareham Nicholas J. , Khaw Kay-Tee , Bradbury Kathryn E. , Romieu Isabelle , Freisling Heinz , Stavropoulou Faidra , Gunter Marc J. , Cross Amanda J. , Riboli Elio , Jenab Mazda , Bruce W. Robert 
Published: September 2015

AbstractBackground: A large proportion of colorectal cancers are thought to be associated with unhealthy dietary and lifestyle exposures, particularly energy excess, obesity, hyperinsulinemia, and hyperglycemia. It has been suggested that these processes stimulate the production of toxic reactive carbonyls from sugars such as glyceraldehyde. Glyceraldehyde contributes to the production of a group of compounds known as glyceraldehyde-derived advanced glycation end-products (glycer-AGEs), which may promote colorectal cancer through their proinflammatory and pro-oxidative properties. The objective of this study nested within a prospective cohort was to explore the association of circulating glycer-AGEs with risk of colorectal cancer.Methods: A total of 1,055 colorectal cancer cases (colon n = 659; rectal n = 396) were matchced (1:1) to control subjects. Circulating glycer-AGEs were measured by a competitive ELISA. Multivariable conditional logistic regression models were used to calculate ORs and 95% confidence intervals (95% CI), adjusting for potential confounding factors, including smoking, alcohol, physical activity, body mass index, and diabetes status.Results: Elevated glycer-AGEs levels were not associated with colorectal cancer risk (highest vs. lowest quartile, 1.10; 95% CI, 0.82–1.49). Subgroup analyses showed possible divergence by anatomical subsites (OR for colon cancer, 0.83; 95% CI, 0.57–1.22; OR for rectal cancer, 1.90; 95% CI, 1.14–3.19; Pheterogeneity = 0.14).Conclusions: In this prospective study, circulating glycer-AGEs were not associated with risk of colon cancer, but showed a positive association with the risk of rectal cancer.Impact: Further research is needed to clarify the role of toxic products of carbohydrate metabolism and energy excess in colorectal cancer development. Cancer Epidemiol Biomarkers Prev; 24(12); 1855–63. ©2015 AACR.
A Novel Risk Locus at 6p21.3 for Epstein–Barr Virus-Positive Hodgkin Lymphoma
Authors: Delahaye-Sourdeix Manon , Urayama Kevin Y. , Gaborieau Valérie , Veenstra Rianne , Foll Matthieu , Chabrier Amelie , Benavente Yolanda , Nieters Alexandra , Becker Nikolaus , Foretova Lenka , Maynadié Marc , Staines Anthony , Smedby Karin Ekstrom , Glimelius Ingrid , Lightfoot Tracy , Cocco Pierluigi , Galan Pilar , Vatten Lars J. , Duell Eric J. , Kiemeney Lambertus , Roman Eve , de Sanjosé Silvia , Lathrop Mark , Melbye Mads , Brennan Paul , Diepstra Arjan , van den Berg Anke , Hjalgrim Henrik , Jarrett Ruth F. , McKay James D. 
Published: September 2015

Abstract
Background: A proportion of the genetic variants involved in susceptibility to Hodgkin lymphoma differ by the tumor's Epstein–Barr virus (EBV) status, particularly within the MHC region.
Methods: We have conducted an SNP imputation study of the MHC region, considering tumor EBV status in 1,200 classical Hodgkin lymphoma (cHL) cases and 5,726 control subjects of European origin. Notable findings were genotyped in an independent study population of 468 cHL cases and 551 controls.
Results: We identified and subsequently replicated a novel association between a common genetic variant rs6457715 and cHL. Although strongly associated with EBV-positive cHL [OR, 2.33; 95% confidence interval (CI), 1.83–2.97; P = 7 × 10–12], there was little evidence for association between rs6457715 and the EBV-negative subgroup of cHL (OR, 1.06; 95% CI, 0.92–1.21), indicating that this association was specific to the EBV-positive subgroup (Phet &lt; P = 10−8). Furthermore, the association was limited to EBV-positive cHL subgroups within mixed cell (MCHL) and nodular sclerosis subtypes (NSHL), suggesting that the association is independent of histologic subtype of cHL.
Conclusions: rs6457715, located near the HLA-DPB1 gene, is associated with EBV-positive cHL and suggests this region as a novel susceptibility locus for cHL.
Impact: This expands the number of genetic variants that are associated with cHL and provides additional evidence for a critical and specific role of EBV in the etiology of this disease. Cancer Epidemiol Biomarkers Prev; 24(12); 1838–43. ©2015 AACR.
Physical Activity and Risk of Male Breast Cancer
Authors: Arem Hannah , Brinton Louise A. , Moore Steven C. , Gapstur Susan M. , Habel Laurel A. , Johnson Kenneth , Kolonel Laurence N. , McCormack Valerie A. , Michels Karin B. , Sesso Howard D. , Ursin Giske , Van Den Eeden Stephen K. , Weiderpass Elisabete , Cook Michael B. , Matthews Charles E. 
Published: September 2015

Abstract
The association between leisure-time physical activity (LTPA) and male breast cancer risk is unclear. In the Male Breast Cancer Pooling Project, with 449 cases and 13,855 matched controls, we used logistic regression with study stratification to generate adjusted ORs and 95% confidence intervals (CI) for LTPA tertiles and male breast cancer risk. Compared with low LTPA, medium and high LTPA were not associated with male breast cancer risk (OR, 1.01; 95% CI, 0.79–1.29; 0.90, 0.69–1.18, respectively). In joint-effects analyses, compared with the referent of high body mass index (BMI; ≥25 kg/m2)/low LTPA, neither medium nor high PA was associated with risk among high BMI men, but normal BMI men (&lt;25 kg/m2) with low or medium LTPA were at a nonsignificant ∼16% reduced risk and those with high LTPA were at a 27% reduced risk (OR, 0.73; 95% CI, 0.50–1.07). Physical activity alone may not confer protection against male breast cancer risk. Cancer Epidemiol Biomarkers Prev; 24(12); 1898–901. ©2015 AACR.
Molecular Pathogenesis and Targeted Therapies for Intrahepatic Cholangiocarcinoma
Authors: Moeini Agrin , Sia Daniela , Bardeesy Nabeel , Mazzaferro Vincenzo , Llovet Josep M. 
Published: September 2015

Abstract
Intrahepatic cholangiocarcinoma (iCCA) is a molecularly heterogeneous hepatobiliary neoplasm with poor prognosis and limited therapeutic options. The incidence of this neoplasm is growing globally. One third of iCCA tumors are amenable to surgical resection, but most cases are diagnosed at advanced stages with chemotherapy as the only established standard of practice. No molecular therapies are currently available for the treatment of this neoplasm. The poor understanding of the biology of iCCA and the lack of known oncogenic addiction loops has hindered the development of effective targeted therapies. Studies with sophisticated animal models defined IDH mutation as the first gatekeeper in the carcinogenic process and led to the discovery of striking alternative cellular origins. RNA- and exome-sequencing technologies revealed the presence of recurrent novel fusion events (FGFR2 and ROS1 fusions) and somatic mutations in metabolic (IDH1/2) and chromatin-remodeling genes (ARID1A, BAP1). These latest advancements along with known mutations in KRAS/BRAF/EGFR and 11q13 high-level amplification have contributed to a better understanding of the landscape of molecular alterations in iCCA. More than 100 clinical trials testing molecular therapies alone or in combination with chemotherapy including iCCA patients have not reported conclusive clinical benefits. Recent discoveries have shown that up to 70% of iCCA patients harbor potential actionable alterations that are amenable to therapeutic targeting in early clinical trials. Thus, the first biomarker-driven trials are currently underway. Clin Cancer Res; 22(2); 291–300. ©2015 AACR.
Impaired Synthesis of Stromal Components in Response to Minnelide Improves Vascular Function, Drug Delivery, and Survival in Pancreatic Cancer
Authors: Banerjee Sulagna , Modi Shrey , McGinn Olivia , Zhao Xianda , Dudeja Vikas , Ramakrishnan Sundaram , Saluja Ashok K. 
Published: September 2015

Abstract
Purpose: Pancreatic cancer stromal microenvironment is considered to be the major reason for failure of conventional and targeted therapy for this disease. The desmoplastic stroma, comprising mainly collagen and glycosaminoglycans like hyaluronan (HA), is responsible for compression of vasculature in the tumor resulting in impaired drug delivery and poor prognosis. Minnelide, a water-soluble prodrug of triptolide currently in phase I clinical trial, has been very effective in multiple animal models of pancreatic cancer. However, whether Minnelide will have efficacious delivery into the tumor despite the desmoplastic stroma has not been evaluated before.
Experiment Design: Patient tumor-derived xenografts (PDX) and spontaneous pancreatic cancer mice were treated with 0.42 and 0.21 mg/kg body weight for 30 days. Stromal components were determined by IHC and ELISA-based assays. Vascular functionality and drug delivery to the tumor were assessed following treatment with Minnelide.
Result: Our current study shows that treatment with Minnelide resulted in reduction of ECM components like HA and collagen in the pancreatic cancer stroma of both the spontaneous KPC mice as well as in patient tumor xenografts. Furthermore, treatment with Minnelide improved functional vasculature in the tumors resulting in four times more functional vessels in the treated animals compared with untreated animals. Consistent with this observation, Minnelide also resulted in increased drug delivery into the tumor compared with untreated animals. Along with this, Minnelide also decreased viability of the stromal cells along with the tumor cells in pancreatic adenocarcinoma.
Conclusions: In conclusion, these results are extremely promising as they indicate that Minnelide, along with having anticancer effects is also able to deplete stroma in pancreatic tumors, which makes it an effective therapy for pancreatic cancer. Clin Cancer Res; 22(2); 415–25. ©2015 AACR.
Bleeding events with dabigatran or warfarin in patients with venous thromboembolism
Authors: Goldhaber Samuel Z. , Kakkar Ajay , Kearon Clive , Eriksson Henry , Kreuzer Jörg , Feuring Martin , Hantel Stephan , Friedman Jeffrey , Schellong Sebastian , Schulman Sam , Majeed Ammar 
Published: September 2015

SummaryDabigatran was as effective as warfarin for the acute treatment of venous thromboembolism in the RE-COVER and RE-COVER II trials. We compared the incidence of bleeding with dabigatran versus warfarin in pooled data from these studies. The localisation, bleeding severity, and the impact of key factors on the incidence of bleeding, were compared between the dabigatran and warfarin treatment group. Altogether, 2553 patients received dabigatran and 2554 warfarin, each for a mean of 164 days. The incidence of any bleeding event was significantly lower with dabigatran (hazard ratio [HR] 0.70; 95 % confidence interval [CI], 0.61–0.79), as was the incidence of the composite of MBEs and clinically relevant non-major bleeding events (HR 0.62; 95 % CI, 0.50–0.76). The incidence of major bleeding events (MBEs) was also significantly lower with dabigatran in the double-dummy phase (HR, 0.60; 95 % CI, 0.36–0.99) but not statistically different between the two treatment arms when the entire treatment period is considered (HR 0.73 95 % CI, 0.48–1.11). Increasing age, reduced renal function, Asian ethnicity, and concomitant antiplatelet therapy were associated with higher bleeding rates in both treatment groups. The reduction in bleeding with dabigatran compared to warfarin was consistent among the subgroups and with a similar pattern for intracranial, and urogenital major bleeding. In conclusion, treatment of venous thromboembolism with dabigatran is associated with a lower risk of bleeding compared to warfarin. This reduction did not differ with respect to the location of bleeding or among predefined subgroups.
Hyperoxia Exacerbates Myocardial Ischemia in the Presence of Acute Coronary Artery Stenosis in Swine
Authors: Guensch Dominik P. , Fischer Kady , Shie Nancy , Lebel Julie , Friedrich Matthias G. 
Published: September 2015

Background—
Current guidelines limit the use of high oxygen tension after return of spontaneous circulation after cardiac arrest, focusing on neurological outcome and mortality. Little is known about the impact of hyperoxia on the ischemic heart. Oxygen is frequently administered and is generally expected to be beneficial. This study seeks to assess the effects of hyperoxia on myocardia oxygenation in the presence of severe coronary artery stenosis in swine.

Methods and Results—

In 22 healthy pigs, we surgically attached a magnetic resonance compatible flow probe to the left anterior descending coronary artery (LAD). In 11 pigs, a hydraulic occluder was inflated distal to the flow probe. After increasing Pa
O
2
to >300 mm Hg, LAD flow decreased in all animals. In 8 stenosed animals with a mean fractional flow reserve of 0.64±0.02, hyperoxia resulted in a significant decrease of myocardial signal intensity in oxygenation-sensitive cardiovascular magnetic resonance images of the midapical segments of the LAD territory. This was not seen in remote myocardium or in the other 8 healthy animals. The decreased signal intensity was accompanied by a decrease in circumferential strain in the same segments. Furthermore, ejection fraction, cardiac output, and oxygen extraction ratio declined in these animals. Changing PaCO
2
levels did not have a significant effect on any of the parameters; however, hypercapnia seemed to nonsignificantly attenuate the hyperoxia-induced changes.

Conclusions—
Ventilation-induced hyperoxia may decrease myocardial oxygenation and lead to ischemia in myocardium subject to severe coronary artery stenosis.