bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding Green Occupations from a Task‐Based Approach
Authors: Peters David J. 
Published: October 2013

AbstractGreen occupations are identified using the diversity, use, and relevance of green tasks in the United States. Results find 176, of nearly 1,000, occupations use at least one green task, but only 70 intensively use green tasks. Green‐intensive jobs are quality jobs that are full‐time, pay above average wages, and have health insurance. The employment outlook for all green jobs is positive, but new job growth lags behind other sectors. Green jobs are accessible to disadvantaged workers with limited education and experience, but most are not well paid. The majority of green jobs are male dominated, yet are racially and ethnically diverse. Implications for green jobs policies are discussed.
Compound cis-regulatory elements with both boundary and enhancer sequences in the human genome
Authors: Jjingo Daudi , Wang Jianrong , Conley Andrew B. , Lunyak Victoria V. , Jordan I. King 
Published: October 2013

Abstract
Motivation: It has been suggested that presumably distinct classes of genomic regulatory elements may actually share common sets of features and mechanisms. However, there has been no genome-wide assessment of the prevalence of this phenomenon.
Results: To evaluate this possibility, we performed a bioinformatic screen for the existence of compound regulatory elements in the human genome. We identified numerous such colocated boundary and enhancer elements from human CD4+ T cells. We report evidence that such compound regulatory elements possess unique chromatin features and facilitate cell type-specific functions related to inflammation and immune response in CD4+ T cells.
Contact: king.jordan@biology.gatech.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Improving Electricity Market Price Forecasting with Factor Models for the Optimal Generation Bid
Authors: Muñoz M. Pilar , Corchero Cristina , Heredia F.‐Javier 
Published: October 2013

RésuméDans les marchés libéralisés de l'électricité, la façon dont les producteurs d'électricité gérent leur production est base sur une offre horaire qui est transmise vers le marché day‐ahead. Malgré l'objectif des producteurs d'électricité est de maximiser leurs profits, le spot price auquel l'énergie sera payée n'est pas connu au cours du processus d'appel d'offres. Cette situation rend la prévision du spot price un point essentiel dans les stratégies de gestion économique de l'électricité. Dans ce travail, nous appliquons des modéles de prévision des facteurs pour l'estimation du spot price en étudiant sa pertinence. Les résultats obtenus en termes de qualité de l'ajustement sont équivalents á ceux obtenus avec les modéles ARIMA, mais leur application est plus facile. Ce modèle de prévision du spot price est utilisé pour générer les scénarios des prix d'un modèle de programmation stochastique qui trouve l'offre optimale de génération dans le marché Espagnol de l'électricité day‐ahead Les courbes d'offres optimales de génération sont présentées et analysées.
A Review on Dimension Reduction
Authors: Ma Yanyuan , Zhu Liping 
Published: October 2013

RésuméRésumer l'impact d'un nombre élevé de variables explicatives à celui d'un nombre réduit de combinaisons linéaires bien choisies constitue une façon efficace de réduire la dimension d'un problème. Cette réduction à un petit nombre de combinaisons linéaires est réalisée à partir d'hypothèses minimales sur la forme de la dépendance et jouit, par rapport à une approche fondée sur la sélection de variables, de propriétés particulièrement attractives. Nous passons en revue la littérature existante sur ce sujet, en mettant l'accent sur les modèles les plus courants, dans lesquels la réduction de dimension affecte l'espérance conditionnelle de la réponse ou sa loi conditionnelle tout entière. Nous discutons plusieurs méthodes d'estimation et d'inférence, en insistant sur les idées sous‐jacentes plutôt que sur les aspects techniques. Nous présentons également quelques problèmes non résolus et thèmes de recherches futures dans ce domaine.
A Special Gen(d)re of Statistics: Roots, Development and Methodological Prospects of Gender Statistics
Authors: Mecatti Fulvia , Crippa Franca , Farina Patrizia 
Published: October 2013

SummaryThe very expression Gender Statistics calls for a double interpretation. It accounts for the popular mix‐up of statistical methodology with its typical products such as indexes, tables and graphs. At the same time it implies a broader and forward‐looking perspective, which is inspired by the increasing demand of gender sensitive statistical information coming from society, official agencies, economy. Gender statistics stands as a proper independent field of statistics with its own objectives and a variety of applications in social, human and life science. Concurrently an emerging necessity of appropriate equipment of methods and dissemination tools is noticeable. The paper tracks the roots and the historical development of gender statistics, reviews critically the existing indexes and practice and outlines methodological needs and research prospects.
Proton radiography in three dimensions: A proof of principle of a new technique
Authors: Raytchev Milen , Seco Joao 
Published: October 2013

Purpose:Monte Carlo simulations were used to investigate a range of phantom configurations to establish enabling three‐dimensional proton radiographic techniques.Methods:A large parameter space of stacked phantom geometries composed of tissue inhomogeneity materials such as lung, bone, and cartilage inserted within water background were simulated using a purposefully modified version ofTOPAS, an application running on top of the GEANT4 Monte Carlo code. The phantoms were grouped in two classes, one with the inhomogeneity inserted only half‐way in the lateral direction and another with complete inhomogeneity insertion. The former class was used to calculate the track count and the energy fluence of the protons as they exit the phantoms either having traversed the inhomogeneity or not. The latter class was used to calculate one yield value accounting for loss of protons due to physical processes only and another yield value accounting for deliberately discarded protons due to large scattering angles. A graphical fingerprinting method was developed to determine the inhomogeneity thickness and location within the phantom based on track count and energy fluence information. Two additional yield values extended this method to the general case which also determines the inhomogeneity material and the phantom thickness.Results:The graphical fingerprinting method was manually validated for two, and automatically tested for all, tissue materials using an exhaustive set of inhomogeneity geometries for 16 cm thick phantoms. Unique recognition of test phantom configurations was achieved in the large majority of cases. The method in the general case was further tested using an exhaustive set of inhomogeneity and phantom tissues and geometries where the phantom thicknesses ranged between 8 and 24 cm. Unique recognition of the test phantom configurations was achieved only for part of the phantom parameter space. The correlations between the remaining false positive recognitions were analyzed.Conclusions:The concept of 3D proton radiography for tissue inhomogeneities of simple geometries was established with the current work. In contrast to conventional 2D proton radiography, the main objective of the demonstrated 3D technique is not proton range. Rather, it is to measure the depth and thickness of an inhomogeneity located in an imaged geometry. Further work is needed to extend and apply the method to more complex geometries.
A virtual phantom library for the quantification of deformable image registration uncertainties in patients with cancers of the head and neck
Authors: Pukala Jason , Meeks Sanford L. , Staton Robert J. , Bova Frank J. , Mañon Rafael R. , Langen Katja M. 
Published: October 2013

Purpose:Deformable image registration (DIR) is being used increasingly in various clinical applications. However, the underlying uncertainties of DIR are not well‐understood and a comprehensive methodology has not been developed for assessing a range of interfraction anatomic changes during head and neck cancer radiotherapy. This study describes the development of a library of clinically relevant virtual phantoms for the purpose of aiding clinicians in the QA of DIR software. These phantoms will also be available to the community for the independent study and comparison of other DIR algorithms and processes.Methods:Each phantom was derived from a pair of kVCT volumetric image sets. The first images were acquired of head and neck cancer patients prior to the start‐of‐treatment and the second were acquired near the end‐of‐treatment. A research algorithm was used to autosegment and deform the start‐of‐treatment (SOT) images according to a biomechanical model. This algorithm allowed the user to adjust the head position, mandible position, and weight loss in the neck region of the SOT images to resemble the end‐of‐treatment (EOT) images. A human‐guided thin‐plate splines algorithm was then used to iteratively apply further deformations to the images with the objective of matching the EOT anatomy as closely as possible. The deformations from each algorithm were combined into a single deformation vector field (DVF) and a simulated end‐of‐treatment (SEOT) image dataset was generated from that DVF. Artificial noise was added to the SEOT images and these images, along with the original SOT images, created a virtual phantom where the underlying “ground‐truth” DVF is known. Images from ten patients were deformed in this fashion to create ten clinically relevant virtual phantoms. The virtual phantoms were evaluated to identify unrealistic DVFs using the normalized cross correlation (NCC) and the determinant of the Jacobian matrix. A commercial deformation algorithm was applied to the virtual phantoms to show how they may be used to generate estimates of DIR uncertainty.Results:The NCC showed that the simulated phantom images had greater similarity to the actual EOT images than the images from which they were derived, supporting the clinical relevance of the synthetic deformation maps. Calculation of the Jacobian of the “ground‐truth” DVFs resulted in only positive values. As an example, mean error statistics are presented for all phantoms for the brainstem, cord, mandible, left parotid, and right parotid.Conclusions:It is essential that DIR algorithms be evaluated using a range of possible clinical scenarios for each treatment site. This work introduces a library of virtual phantoms intended to resemble real cases for interfraction head and neck DIR that may be used to estimate and compare the uncertainty of any DIR algorithm.
Promoter Sequence of Shiga Toxin 2 (Stx2) Is Recognized
In Vivo
, Leading to Production of Biologically Active Stx2
Authors: Bentancor Leticia V. , Mejías Maria P. , Pinto Alípio , Bilen Marcos F. , Meiss Roberto , Rodriguez-Galán Maria C. , Baez Natalia , Pedrotti Luciano P. , Goldstein Jorge , Ghiringhelli Pablo D. , Palermo Marina S. 
Published: October 2013

ABSTRACT

Shiga toxins (Stx) are the main agent responsible for the development of hemolytic-uremic syndrome (HUS), the most severe and life-threatening systemic complication of infection with enterohemorrhagic
Escherichia coli
(EHEC) strains. We previously described Stx2 expression by eukaryotic cells after they were transfected
in vitro
with the
stx
2
gene cloned into a prokaryotic plasmid (pStx2). The aim of this study was to evaluate whether mammalian cells were also able to express Stx2
in vivo
after pStx2 injection. Mice were inoculated by hydrodynamics-based transfection (HBT) with pStx2. We studied the survival, percentage of polymorphonuclear leukocytes in plasma, plasma urea levels, and histology of the kidneys and the brains of mice. Mice displayed a lethal dose-related response to pStx2. Stx2 mRNA was recovered from the liver, and Stx2 cytotoxic activity was observed in plasma of mice injected with pStx2. Stx2 was detected by immunofluorescence in the brains of mice inoculated with pStx2, and markers of central nervous system (CNS) damage were observed, including increased expression of glial fibrillary acidic protein (GFAP) and fragmentation of NeuN in neurons. Moreover, anti-Stx2B-immunized mice were protected against pStx2 inoculation. Our results show that Stx2 is expressed
in vivo
from the wild
stx
2
gene, reproducing pathogenic damage induced by purified Stx2 or secondary to EHEC infection.

IMPORTANCE
Enterohemorrhagic Shiga toxin (Stx)-producing
Escherichia coli
(EHEC) infections are a serious public health problem, and Stx is the main pathogenic agent associated with typical hemolytic-uremic syndrome (HUS). In contrast to the detailed information describing the molecular basis for EHEC adherence to epithelial cells, very little is known about how Stx is released from bacteria in the gut, reaching its target tissues, mainly the kidney and central nervous system (CNS). In order to develop an efficient treatment for EHEC infections, it is necessary to understand the mechanisms involved in Stx expression. In this regard, the present study demonstrates that mammals can synthesize biologically active Stx using the natural promoter associated with the Stx-converting bacteriophage genome. These results could impact the comprehension of EHEC HUS, since local eukaryotic cells transduced and/or infected by bacteriophage encoding Stx2 could be an alternative source of Stx production.
Crizotinib Inhibits Metabolic Inactivation of Gemcitabine in c-Met–driven Pancreatic Carcinoma
Authors: Avan Amir , Caretti Viola , Funel Niccola , Galvani Elena , Maftouh Mina , Honeywell Richard J. , Lagerweij Tonny , Van Tellingen Olaf , Campani Daniela , Fuchs Dieter , Verheul Henk M. , Schuurhuis Gerrit-Jan , Boggi Ugo , Peters Godefridus J. , Würdinger Thomas , Giovannetti Elisa 
Published: October 2013

Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains a major unsolved health problem. Most drugs that pass preclinical tests fail in these patients, emphasizing the need of improved preclinical models to test novel anticancer strategies. Here, we developed four orthotopic mouse models using primary human PDAC cells genetically engineered to express firefly- and Gaussia luciferase, simplifying the ability to monitor tumor growth and metastasis longitudinally in individual animals with MRI and high-frequency ultrasound. In these models, we conducted detailed histopathologic and immunohistochemical analyses on paraffin-embedded pancreatic tissues and metastatic lesions in liver, lungs, and lymph nodes. Genetic characteristics were compared with the originator tumor and primary tumor cells using array-based comparative genomic hybridization, using frozen specimens obtained by laser microdissection. Notably, the orthotopic human xenografts in these models recapitulated the phenotype of human PDACs, including hypovascular and hypoxic areas. Pursuing genomic and immunohistochemical evidence revealed an increased copy number and overexpression of c-Met in one of the models; we examined the preclinical efficacy of c-Met inhibitors in vitro and in vivo. In particular, we found that crizotinib decreased tumor dimension, prolonged survival, and increased blood and tissue concentrations of gemcitabine, synergizing with a cytidine deaminase–mediated mechanism of action. Together, these more readily imaged orthotopic PDAC models displayed genetic, histopathologic, and metastatic features similar to their human tumors of origin. Moreover, their use pointed to c-Met as a candidate therapeutic target in PDAC and highlighted crizotinib and gemcitabine as a synergistic combination of drugs warranting clinical evaluation for PDAC treatment. Cancer Res; 73(22); 6745–56. ©2013 AACR.
Enhancement of Antitumor Immunity in Lung Cancer by Targeting Myeloid-Derived Suppressor Cell Pathways
Authors: Sawant Anandi , Schafer Cara C. , Jin Tong Huan , Zmijewski Jaroslaw , Tse Hubert M. , Roth Justin , Sun Zhihuan , Siegal Gene P. , Thannickal Victor J. , Grant Stefan C. , Ponnazhagan Selvarangan , Deshane Jessy S. 
Published: October 2013

Abstract
Chemoresistance due to heterogeneity of the tumor microenvironment (TME) hampers the long-term efficacy of first-line therapies for lung cancer. Current combination therapies for lung cancer provide only modest improvement in survival, implicating necessity for novel approaches that suppress malignant growth and stimulate long-term antitumor immunity. Oxidative stress in the TME promotes immunosuppression by tumor-infiltrating myeloid-derived suppressor cells (MDSC), which inhibit host protective antitumor immunity. Using a murine model of lung cancer, we demonstrate that a combination treatment with gemcitabine and a superoxide dismutase mimetic targets immunosuppressive MDSC in the TME and enhances the quantity and quality of both effector and memory CD8+ T-cell responses. At the effector cell function level, the unique combination therapy targeting MDSC and redox signaling greatly enhanced cytolytic CD8+ T-cell response and further decreased regulatory T cell infiltration. For long-term antitumor effects, this therapy altered the metabolism of memory cells with self-renewing phenotype and provided a preferential advantage for survival of memory subsets with long-term efficacy and persistence. Adoptive transfer of memory cells from this combination therapy prolonged survival of tumor-bearing recipients. Furthermore, the adoptively transferred memory cells responded to tumor rechallenge exerting long-term persistence. This approach offers a new paradigm to inhibit immunosuppression by direct targeting of MDSC function, to generate effector and persistent memory cells for tumor eradication, and to prevent lung cancer relapse. Cancer Res; 73(22); 6609–20. ©2013 AACR.
Loss of PTEN Is Associated with Aggressive Behavior in ERG-Positive Prostate Cancer
Authors: Leinonen Katri A. , Saramäki Outi R. , Furusato Bungo , Kimura Takahiro , Takahashi Hiroyuki , Egawa Shin , Suzuki Hiroyoshi , Keiger Kerri , Ho Hahm Sung , Isaacs William B. , Tolonen Teemu T. , Stenman Ulf-Håkan , Tammela Teuvo L.J. , Nykter Matti , Bova G. Steven , Visakorpi Tapio 
Published: October 2013

Abstract
Background: The associations of ERG overexpression with clinical behavior and molecular pathways of prostate cancer are incompletely known. We assessed the association of ERG expression with AR, PTEN, SPINK1, Ki-67, and EZH2 expression levels, deletion, and mutations of chromosomal region 3p14 and TP53, and clinicopathologic variables.
Methods: The material consisted of 326 prostatectomies, 166 needle biopsies from men treated primarily with endocrine therapy, 177 transurethral resections of castration-resistant prostate cancers (CRPC), and 114 CRPC metastases obtained from 32 men. Immunohistochemistry, FISH, and sequencing was used for the measurements.
Results: ERG expression was found in about 45% of all patient cohorts. In a multivariate analysis, ERG expression showed independent value of favorable prognosis (P = 0.019). ERG positivity was significantly associated with loss of PTEN expression in prostatectomy (P = 0.0348), and locally recurrent CRPCs (P = 0.0042). Loss of PTEN expression was associated (P = 0.0085) with shorter progression-free survival in ERG-positive, but not in negative cases. When metastases in each subject were compared, consistent ERG, PTEN, and AR expression as well as TP53 mutations were found in a majority of subjects.
Conclusions: A similar frequency of ERG positivity from early to late stage of the disease suggests lack of selection of ERG expression during disease progression. The prognostic significance of PTEN loss solely in ERG-positive cases indicates interaction of these pathways. The finding of consistent genetic alterations in different metastases suggests that the major genetic alterations take place in the primary tumor.
Impact: Interaction of PTEN and ERG pathways warrants further studies. Cancer Epidemiol Biomarkers Prev; 22(12); 2333–44. ©2013 AACR.
Germline Variants and Advanced Colorectal Adenomas: Adenoma Prevention with Celecoxib Trial Genome-wide Association Study
Authors: Wang Jiping , Carvajal-Carmona Luis G. , Chu Jen-Hwa , Zauber Ann G. ,   APC Trial Collaborators, Kubo Michikai , Matsuda Koichi , Dunlop Malcolm , Houlston Richard S. , Sieber Oliver , Lipton Lara , Gibbs Peter , Martin Nicholas G. , Montgomery Grant W. , Young Joanne , Baird Paul N. , Ratain Mark J. , Nakamura Yusuke , Weiss Scott T. , Tomlinson Ian , Bertagnolli Monica M. 
Published: October 2013

AbstractPurpose: Identification of single-nucleotide polymorphisms (SNP) associated with development of advanced colorectal adenomas.Experimental Design: Discovery phase: 1,406 Caucasian patients (139 advanced adenoma cases and 1,267 controls) from the Adenoma Prevention with Celecoxib (APC) trial were included in a genome-wide association study (GWAS) to identify variants associated with postpolypectomy disease recurrence. Genome-wide significance was defined as false discovery rate less than 0.05, unadjusted P = 7.4 × 10−7. Validation phase: results were further evaluated using 4,175 familial colorectal adenoma cases and 5,036 controls from patients of European ancestry [COloRectal Gene Identification consortium (CORGI), Scotland, Australia, and VQ58].Results: Our study identified eight SNPs associated with advanced-adenoma risk in the APC trial (rs2837156, rs7278863, rs2837237, rs2837241, rs2837254, rs741864 at 21q22.2, and rs1381392 and rs17651822 at 3p24.1, at P &lt; 10−7 level with OR &gt; 2). Five variants in strong pairwise linkage disequilibrium (rs7278863, rs2837237, rs741864, rs741864, and rs2837241; r2 = 0.8–1) are in or near the coding region for the tight junction adhesion protein, IGSF5. An additional variant associated with advanced adenomas, rs1535989 [minor allele frequency, 0.11; OR, 2.09; 95% confidence interval (CI), 1.50–2.91], also predicted colorectal cancer development in a validation analysis (P = 0.019) using a series of adenoma cases or colorectal cancer (CORGI study) and 3 sets of colorectal cancer cases and controls (Scotland, VQ58, and Australia; N = 9,211).Conclusions: Our results suggest that common polymorphisms contribute to the risk of developing advanced adenomas and might also contribute to the risk of developing colorectal cancer. The variant at rs1535989 may identify patients whose risk for neoplasia warrants increased colonoscopic surveillance. Clin Cancer Res; 19(23); 6430–7. ©2013 AACR.