bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data for cancer comparative effectiveness research
Authors: Meyer Anne‐Marie , Carpenter William R. , Abernethy Amy P. , Stürmer Til , Kosorok Michael R. 
Published: April 2012

AbstractComparative effectiveness research (CER) can efficiently and rapidly generate new scientific evidence and address knowledge gaps, reduce clinical uncertainty, and guide health care choices. Much of the potential in CER is driven by the application of novel methods to analyze existing data. Despite its potential, several challenges must be identified and overcome so that CER may be improved, accelerated, and expeditiously implemented into the broad spectrum of cancer care and clinical practice. To identify and characterize the challenges to cancer CER, the authors reviewed the literature and conducted semistructured interviews with 41 cancer CER researchers at the Agency for Healthcare Research and Quality's Developing Evidence to Inform Decisions about Effectiveness (DEcIDE) Cancer CER Consortium. Several data sets for cancer CER were identified and differentiated into an ontology of 8 categories and were characterized in terms of strengths, weaknesses, and utility. Several themes emerged during the development of this ontology and discussions with CER researchers. Dominant among them was accelerating cancer CER and promoting the acceptance of findings, which will necessitate transcending disciplinary silos to incorporate diverse perspectives and expertise. Multidisciplinary collaboration is required, including those with expertise in nonexperimental data, statistics, outcomes research, clinical trials, epidemiology, generalist and specialty medicine, survivorship, informatics, data, and methods, among others. Recommendations highlight the systematic, collaborative identification of critical measures; application of more rigorous study design and sampling methods; policy‐level resolution of issues in data ownership, governance, access, and cost; and development and application of consistent standards for data security, privacy, and confidentiality. Cancer 2012. © 2012 American Cancer Society.
Incidence of soft tissue sarcoma and beyond
Authors: Mastrangelo Giuseppe , Coindre Jean‐Michel , Ducimetière Françoise , Dei Tos Angelo Paolo , Fadda Emanuela , Blay Jean‐Yves , Buja Alessandra , Fedeli Ugo , Cegolon Luca , Frasson Alvise , Ranchère‐Vince Dominique , Montesco Cristina , Ray‐Coquard Isabelle , Rossi Carlo Riccardo 
Published: April 2012

AbstractBACKGROUND:The objectives of this study were to measure the incidence of sarcomas, including viscerally sited tumors that are not reported in cancer statistics, and to draw explanatory clues from a large and reliable sarcoma incidence data set.METHODS:Cases of sarcomas regardless of primary site (except bone and joints) were collected during 2 years in 3 European regions totaling approximately 26,000,000 person‐years. The sources used were pathology reports and hospital discharges forms. Diagnoses were reviewed by expert sarcoma pathologists and were classified according to 2002 World Health Organization criteria. Soft tissue sarcomas (STS) were considered those located in arms, legs, trunk, head, neck, and retroperitoneum; visceral sarcomas (VS) were considered those that arose in internal organs. Rates were age standardized using the European (ASR‐E) and the USA standard population. The rate of coexistence of VS and STS was calculated by dividing the 2 corresponding ASRs.RESULTS:There were 1558 sarcomas, 968 STS, and 590 VS. The ASRs‐USA per 100,000 person‐years was 5.12 × 105 among males and 4.58 × 105 among females for all sarcomas. For males and females, respectively, the ASR‐E per 100,000 person‐years was 3.58 × 105 and 2.55 × 105, respectively, for STS; 1.47 × 105 and 1.97 × 105, respectively, for VS; and 0.55 × 105 and 0.10 × 105, respectively, for Kaposi sarcoma. The coexistence rate of VS and STS was 0.41 for males and 0.77 for females. For dermatofibrosarcoma (both sexes), uterine sarcoma, liposarcoma (females), and leiomyosarcoma, including or excluding the uterus (females), the age‐specific rates depicted a curve with a rapid increasing trend until ages 40 to 50 years and little variation thereafter.CONCLUSIONS:Compared with the incidence of STS, VS incidence made up an additional 41% in males and 77% in females. Because the shape of age‐specific curves for some histotypes was similar to that of breast cancer, the authors concluded that sex hormones (plus many chemicals that act as endocrine disruptors) may be involved in carcinogenesis. This evidence could pave the way to investigate alternative treatments and to explore etiology. Cancer 2012. © 2012 American Cancer Society.
Association between contralateral prophylactic mastectomy and breast cancer outcomes by hormone receptor status
Authors: Brewster Abenaa M. , Bedrosian Isabelle , Parker Patricia A. , Dong Wenli , Peterson Susan K. , Cantor Scott B. , Crosby Melissa , Shen Yu 
Published: April 2012

AbstractBACKGROUND:The effect of contralateral prophylactic mastectomy (CPM) on the survival of patients with early‐stage breast cancer remains controversial. The objective of this study was to evaluate the benefits of CPM using a propensity scoring approach that reduces selection bias from the nonrandom assignment of patients in observational studies.METHODS:A total of 3889 female patients with stage I to III breast cancer were identified who were treated at The University of Texas MD Anderson Cancer Center from 1997 to 2009. We assessed the association between CPM and disease‐free (DFS) and overall survival (OS), by using Cox proportional hazards models to estimate hazard ratios (HRs), and by matching patients in the CPM and no‐CPM groups using propensity scores (n = 497 pairs).RESULTS:With a median follow‐up time of 4.5 years, CPM was associated with improved DFS (HR, 0.75; 95% confidence interval [CI], 0.59‐0.97) and OS (HR, 0.74; 95% CI, 0.56‐0.99), adjusted for prognostic factors. The improved DFS was seen predominantly among hormone receptor–negative (HR, 0.60; 95% CI, 0.38‐0.95) compared with hormone receptor–positive patients (HR, 0.80; 95% CI, 0.58‐1.10). For the matched patient cohort, stratified survival analysis also showed an improvement in DFS with CPM (HR, 0.48; 95% CI, 0.22‐1.01) in hormone receptor–negative patients that was nearly statistically significant.CONCLUSIONS:CPM was associated with improved DFS for some patients with hormone receptor–negative breast cancer, after reducing selection bias. Identifying subsets of patients most likely to benefit from CPM may have important implications for a more personalized approach to treatment decisions about CPM. Cancer 2012. © 2012 American Cancer Society.
Standardized uptake value by positron emission tomography/computed tomography as a prognostic variable in metastatic breast cancer
Authors: Morris Patrick G. , Ulaner Gary A. , Eaton Anne , Fazio Maurizio , Jhaveri Komal , Patil Sujata , Evangelista Laura , Park Joseph Y. , Serna‐Tamayo Cristian , Howard Jane , Larson Steven , Hudis Clifford A. , McArthur Heather L. , Jochelson Maxine S. 
Published: April 2012

AbstractBACKGROUND:In this retrospective, single‐institution study, the authors examine the maximum standardized uptake value (SUVmax) on positron emission tomography/computed tomography (PET/CT) images as a prognostic variable in patients with newly diagnosed metastatic breast cancer (MBC).METHODS:Patients with ≥1 metastatic lesion on PET/CT images that were obtained within 60 days of their MBC diagnosis between January 1, 2001 and December 31, 2008 were included. Patients were excluded if they had received chemotherapy ≤30 days before the PET/CT images were obtained. Electronic medical reports were reviewed to determine the SUVmax and overall survival. Because of intraindividual variation in the SUV by body site, separate analyses were conducted by metastatic site. Relationships between site‐specific PET/CT variable tertiles and overall survival were assessed using Cox regression; hazard ratios for the highest tertile versus the lowest tertile were reported.RESULTS:In total, 253 patients were identified, and their median age was 57 years (range, 27‐90 years). Of these, 152 patients (60%) died, and the median follow‐up was 40 months. On univariate analysis, SUVmax tertile was strongly associated with overall survival in patients who had bone metastases (N = 141; hazard ratio, 3.13; 95% confidence interval, 1.79‐5.48; P < .001). This effect was maintained on multivariate analysis (HR = 3.19; 95% confidence interval, 1.64‐6.20, P = .002) after correcting for known prognostic variables. A greater risk of death was associated with SUVmax tertile in patients who had metastases to the liver (N = 46; hazard ratio, 2.07; 95% confidence interval, 0.90‐4.76), lymph nodes (N = 149; hazard ratio, 1.1; 95% confidence interval, 0.69‐1.88), and lung (N = 62; hazard ratio, 2.2; 95% confidence interval, 0.97‐4.95), although these results were not significant (P = .18, P = .31, and P = .095, respectively).CONCLUSIONS:The current results indicate that PET/CT has value as a prognostic tool in patients with newly diagnosed MBC to bone. Cancer 2012. © 2012 American Cancer Society.
Proteasome inhibitor interacts synergistically with autophagy inhibitor to suppress proliferation and induce apoptosis in hepatocellular carcinoma
Authors: Hui Bo , Shi Ying‐Hong , Ding Zhen‐Bin , Zhou Jian , Gu Cheng‐Yu , Peng Yuan‐Fei , Yang Hua , Liu Wei‐Ren , Shi Guo‐Ming , Fan Jia 
Published: April 2012

AbstractBACKGROUND:The ubiquitin‐proteasome system and autophagy‐lysosome system are 2 major protein degradation pathways in eukaryotic cells, which are tightly linked to cancer. Proteasome inhibitors have been approved in clinical use against hematologic malignancies, but their application in solid tumors is uncertain. Moreover, the role of autophagy after proteasome inhibition is controversial.METHODS:Two proteasome inhibitors, 2 autophagy inhibitors, and 3 hepatocellular carcinoma (HCC) cell lines were investigated in the current study. In vitro, cell proliferation was evaluated by 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) assay, cell apoptosis was evaluated by flow cytometry analysis of annexin‐V/propidium iodide staining, and autophagy was evaluated by green fluorescent protein‐light chain 3 (GFP‐LC3) redistribution and LC3 Western blot analysis. In vivo, Ki‐67 staining was used to detect cell proliferation, terminal deoxynucleotidyl transferase‐mediated deoxyuridine triphosphate nick‐end labeling (TUNEL) staining was used to detect apoptosis, and electron microscopy and p62 immunohistochemical staining were used to detect autophagy.RESULTS:Proteasome inhibitors suppressed proliferation, induced apoptosis, and activated autophagy in HCC cell lines in vitro, and autophagy exerted a protective role after proteasome inhibition. In vivo, anticancer effects of bortezomib on the MHCC‐97H orthotopic model (human HCC cells) were different from the effects observed on the Huh‐7 subcutaneous model (human HCC cells). The autophagy inhibitor chloroquine interacted synergistically with bortezomib to suppress proliferation and induce apoptosis in both tumor models.CONCLUSIONS:The current results indicated that simultaneous targeting of the proteasome and autophagy pathways may represent a promising method for HCC treatment. Cancer 2012. © 2012 American Cancer Society.
Nanomaterial‐Based Treatments for Medical Device‐Associated Infections
Authors: Tran Nhiem , Tran Phong A. 
Published: April 2012

AbstractBacterial infections remain one of the biggest concerns to our society. Conventional antibiotic treatments showed little effect on the increasing number of antibiotic‐resistant bacteria. Advances in synthetic chemistry and nanotechnology have resulted in a new class of nanometer‐scale materials with distinguished properties and great potential to be an alternative for antibiotics. In this Minireview, we address the current situation of medical‐device‐associated infections and the emerging opportunities for antibacterial nanomaterials in preventing these complications. Several important antimicrobial nanomaterials emergent from advances in synthesis chemistry are introduced and their bactericidal mechanisms are analyzed. In addition, concerns regarding the biocompatibility of such materials are also addressed.
Essential Data and Techniques for Conducting Microbial Fuel Cell and other Types of Bioelectrochemical System Experiments
Authors: Logan Bruce E. 
Published: April 2012

AbstractMicrobial fuel cells (MFCs) and other bioelectrochemical systems are new technologies that require expertise in a variety of technical areas, ranging from electrochemistry to biological wastewater treatment. There are certain data and critical information that should be included in every MFC study, such as specific surface area of the electrodes, solution conductivity, and power densities normalized to electrode surface area and volumes. Electrochemical techniques such as linear sweep voltammetry can be used to understand the performance of the MFC, but extremely slow scans are required for these biological systems compared to more traditional fuel cells. In this Minireview, the critical information needed for MFC studies is provided with examples of how results can be better conveyed through a full description of materials, the use of proper controls, and inclusion of a more complete electrochemical analysis.
Case studies on ESA‐doping as revealed by the Biological Passport
Authors: Zorzoli Mario , Rossi Francesca 
Published: April 2012

Blood doping, through the increase of red cells, induces changes of hematological parameters. The aim of the Biological Passport is first to analyse individual longitudinal profiles in order to identify, through variations of the specific parameters, doping manipulations. Additionally, on the basis of abnormal values or profiles, athletes can be targeted for traditional anti‐doping tests in order to detect forbidden substances or methods.We report the experience of the International Cycling Union in applying the Biological Passport to target athletes for the presence of erythropoiesis stimulating agents. All positive results which have been reported between 2008 and 2010 concerning athletes enrolled in the Biological Passport program are presented. Four cases are discussed more in details. To conclude, we propose possible ways of using the Biological Passport in order to better understand athletes' doping modalities, so that testing programs efficiency can be improved. Copyright © 2012 John Wiley & Sons, Ltd.
Understanding degradation of phenolic compounds during olive oil processing by inhibitor addition
Authors: Migliorini Marzia , Cecchi Lorenzo , Cherubini Chiara , Trapani Serena , Cini Enrico , Zanoni Bruno 
Published: April 2012

AbstractThe aim of this work was to study, under different conditions, degradation of secoiridoids during extraction of extra virgin olive oil by following the effect of ascorbic and citric acid addition. Their effect was evaluated on oil obtained from both damaged olives and undamaged fresh olives. Addition of enzyme inhibitors to damaged olives during olive milling allowed us to obtain oil with a higher phenolic compound content. Conversely, addition of the same inhibitors to undamaged fresh olives, during oil milling, resulted in no significant improvement in the phenolic compound content of oil. A high presence of PPO was thus indirectly confirmed, as damaged olives were only found to be sensitive to action of inhibitors. Ascorbic acid was found to be more effective than citric acid in preserving phenolic compounds of oil. Trials on undamaged fresh olives confirmed occurrence of hydrolytic transformation phenomena for secoiridoids during extra virgin olive oil production process. In particular, the quantitatively most representative component for Frantoio cultivar was found to be 3,4‐DHPEA‐EDA. This compound may be considered a direct marker for the degree of transformation of secoiridoids during production process.Practical applications: The processing of undamaged olives resulted in the extraction of extra virgin olive oil with a higher phenol content. It could be indirectly inferred that a reduced activity of PPO caused a low secoiridoid degradation both before and after malaxation. Lightly scratched, overripe olives could be used in those markets where the addition of oxidation‐inhibiting substances is allowed. Using inhibitors can be suggested for olive washing step.
Plasma fibronectin deficiency impedes atherosclerosis progression and fibrous cap formation
Authors: Rohwedder Ina , Montanez Eloi , Beckmann Karsten , Bengtsson Eva , Dunér Pontus , Nilsson Jan , Soehnlein Oliver , Fässler Reinhard 
Published: April 2012

AbstractAtherosclerotic lesions are asymmetric focal thickenings of the intima of arteries that consist of lipids, various cell types and extracellular matrix (ECM). These lesions lead to vascular occlusion representing the most common cause of death in the Western world. The main cause of vascular occlusion is rupture of atheromatous lesions followed by thrombus formation. Fibronectin (FN) is one of the earliest ECM proteins deposited at atherosclerosis‐prone sites and was suggested to promote atherosclerotic lesion formation. Here, we report that atherosclerosis‐prone apolipoprotein E‐null mice lacking hepatocyte‐derived plasma FN (pFN) fed with a pro‐atherogenic diet display dramatically reduced FN depositions at atherosclerosis‐prone areas, which results in significantly smaller and fewer atherosclerotic plaques. However, the atherosclerotic lesions from pFN‐deficient mice lacked vascular smooth muscle cells and failed to develop a fibrous cap. Thus, our results demonstrate that while FN worsens the course of atherosclerosis by increasing the atherogenic plaque area, it promotes the formation of the protective fibrous cap, which in humans prevents plaques rupture and vascular occlusion.See accompanying article http://dx.doi.org/10.1002/emmm.201200238
Cross‐sectional profiles of sand ripples, megaripples, and dunes: a method for discriminating between formational mechanisms
Authors: Zimbelman James R. , Williams Steven H. , Johnston Andrew K. 
Published: April 2012

ABSTRACTCross‐sectional profiles of sand ripples, megaripples, and sand dunes provide a useful tool for discriminating between formation by ripple and dune processes. Feature width, defined as the basal break in slope along the profile to either side of the crest, represents a good standard for comparison of profile attributes across more than three orders of magnitude. Aspect ratio (height/width) as a function of log width separates measurements into clusters representing differing mechanisms of formation. Scaling both height and distance for individual profiles by feature width facilitates comparison of profile shapes across three orders of magnitude in width. The data presented here should prove useful for evaluating possible mechanisms of origin for aeolian features observed remotely, including on planetary bodies. Copyright © 2012 John Wiley & Sons, Ltd.
Comparison of methods for quantifying active layer dynamics and bedload discharge in armoured gravel‐bed rivers
Authors: Houbrechts Geoffrey , Van Campenhout Jean , Levecq Yannick , Hallot Eric , Peeters Alexandre , Petit Francois 
Published: April 2012

ABSTRACTSeveral methods were employed in the Ardennian rivers (Belgium) to determine the depth of the active layer mobilized during floods and to evaluate the bedload discharge associated with these events. The use of scour chains has shown that the depth of the active layer is systematically less than the b‐axis of the average particle size (D50) of the elements which compose the surface layer of the riffles. This indicates that only a partial transport exists during low magnitude floods. The bedload discharge has been evaluated by combining data obtained using the scour chains technique and the distance covered by tracers. Quantities of sediment transported during frequent floods are relatively low (0·02 t km–2) due to the armour layer which protects the subsurface material. These low values are also related to the fact that the distance calculated for mobilized bedload only applies to tracers fitted with PIT (passive integrated transponder)‐tags (diameter > 20 mm), whereas part of the bedload discharge is composed of sand and fine gravel transported over greater distances than the pebbles. The break‐up of the armour layer was observed only once, for a decennial discharge. During this event, the bedload discharge increased considerably (2 t km–2). The use of sediment traps, data from dredging and a Helley–Smith sampler confirm the low bedload transport in Ardennian rivers in comparison to the bedload transport in other geomorphological contexts. This difference is explained by the presence of an armoured layer but also by the imbricated structures of flat bed elements which increase the resistance to the flow. Finally, the use of the old iron industry wastes allowed to quantify the thickness of the bed reworked over the past centuries. In the Lembrée River, the river‐bed contains slag elements up to a depth of about 50 cm, indicating that exceptional floods may rework the bed to a considerable depth. Copyright © 2012 John Wiley & Sons, Ltd.
A Degradation Model for Solid Oxide Fuel Cell Anodes due to Impurities in Coal Syngas: Part I Theory and Validation
Authors: Cayan F. N. , Pakalapati S. R. , Celik I. , Xu C. , Zondlo J. 
Published: April 2012

AbstractA new phenomenological one‐dimensional model is formulated to simulate the typical degradation patterns observed in solid oxide fuel cell (SOFC) anodes due to coal syngas contaminants such as arsenic (As) and phosphorous (P). The model includes gas phase diffusion and surface diffusion within the anode and the adsorption reactions on the surface of the Ni‐YSZ‐based anode. Model parameters such as reaction rate constants for the adsorption reactions are obtained through indirect calibration to match the degradation rates reported in the literature for arsine (AsH3), phosphine (PH3), hydrogen sulfide (H2S), and hydrogen selenide (H2Se) under accelerated testing conditions. Results from the model demonstrate that the deposition of the impurity on the Ni catalyst starts near the fuel channel/anode interface and slowly moves toward the active anode/electrolyte interface as observed in the experiments. Parametric studies performed at different impurity concentrations and operating temperatures show that the coverage rate increases with increasing temperature and impurity concentration, as expected. The calibrated model was then used for prediction of the performance curves at different impurity concentrations and operating temperatures. Good agreement is obtained between the predicted results and the experimental data reported in the literature.