bluuebunny/crossref_metadata_2025_split huggingface dataset:
IDH1 mutations in grade II astrocytomas are associated with unfavorable progression‐free survival and prolonged postrecurrence survival
Authors: Thon Niklas , Eigenbrod Sabina , Kreth Simone , Lutz Juergen , Tonn Joerg‐Christian , Kretzschmar Hans , Peraud Aurelia , Kreth Friedrich‐Wilhelm 
Published: June 2011

AbstractBACKGROUND:The favorable prognostic impact of mutations in the IDH1 gene is well documented for malignant gliomas; its influence on World Health Organization (WHO) grade II astrocytomas, however, is still under debate.METHODS:A previously published database of 127 predominantly surgically treated patients harboring WHO grade II astrocytomas was revisited. Patients were screened for TP53 mutations (sequencing analysis), IDH1 mutations (pyrosequencing), and MGMT promoter methylation (methylation‐specific polymerase chain reaction and bisulfite sequencing). Endpoints were overall survival, progression‐free survival (PFS), time to malignant transformation, and postrecurrence survival. Radiotherapy was usually withheld until tumor progression/malignant transformation occurred.RESULTS:IDH1 mutations, TP53 mutations, and methylated MGMT promoters were seen in 78.1%, 51.2%, and 80.0% of the analyzed tumors, respectively. IDH1 mutations, which were significantly associated with TP53 mutations and/or MGMT promoter methylation (P < .001), resulted in shortened PFS (median, 47 vs 84 months; P = .004); postrecurrence survival, however, was significantly increased in those patients undergoing malignant transformation (median, 49 vs 13.5 months; P = .006). Overall survival was not affected by IDH1. A similar pattern of influence was seen for MGMT promoter methylation. Methylated tumors did significantly worse (better) in terms of PFS (postrecurrence survival); a low number of unmethylated tumors, however, limited the power of this analysis. Conversely, TP53 mutations were stringently associated with a worse prognosis throughout the course of the disease.CONCLUSIONS:IDH1 mutations are associated with a Janus headlike phenomenon; unfavorable prognostic influence on PFS turns into favorable impact on postrecurrence survival. A similar pattern of influence might exist for MGMT methylation. Cancer 2011;. © 2011 American Cancer Society.
Prophylactic recombinant erythropoietin therapy and thalidomide are predictors of venous thromboembolism in patients with multiple myeloma: limited effectiveness of thromboprophylaxis
Authors: Anaissie Elias J. , Coleman Elizabeth A. , Goodwin Julia A. , Kennedy Robert L. , Lockhart Kimberly D. , Stewart Carol B. , Coon Sharon K. , Bailey Clyde , Barlogie Bart 
Published: June 2011

AbstractBACKGROUND:Venous thromboembolism (VTE) is a significant but poorly understood complication in patients with newly diagnosed multiple myeloma (NDMM). As a result, most patients receive thromboprophylaxis with low molecular weight heparin (LMWH). The purpose of this retrospective study was to identify risk factors for VTE in NDMM and evaluate the effectiveness of LMWH.METHODS:A total of 604 patients with newly diagnosed myeloma completed 3 induction cycles with multiagent chemotherapy with up‐front randomization to thalidomide between 1998 and 2004. Prophylactic enoxaparin was given to thalidomide recipients beginning in June 2001, and 122 subjects received prophylactic epoetin alfa (EPO) as part of an exercise trial. The primary study endpoint was grades 3‐4 VTE.RESULTS:A total of 72 patients (11.9%) developed VTE (mostly deep venous thrombosis), with a higher incidence among EPO recipients (P = .001), although only significant for upper extremity DVT (P = .0002). The EPO‐treated patients had higher hemoglobin (Hb) levels throughout the study (P < .0005), although no relationship between higher Hb levels and increasing incidence of VTE could be shown. A history of VTE was a strong predictor of VTE on univariate analysis (P < .000005). Enoxaparin did not reduce the rate of VTE (P = .158). Logistic regression analysis identified thalidomide therapy (P = .001; odds ratio [OR], 2.428; 95% confidence interval [CI], 1.418‐4.159) and prophylactic EPO (P = .002; OR, 2.488; 95% CI, 1.432‐4.324) as risk factors for VTE. Myeloma response and survival were not negatively affected by prophylactic EPO or VTE.CONCLUSIONS:Prophylactic EPO, thalidomide therapy, and VTE history, but not higher Hb levels, were found to increase the risk of VTE among NDMM patients receiving multiagent chemotherapy. This risk was not found to be reduced in this population by LMWH thromboprophylaxis. Cancer 2011;. © 2011 American Cancer Society.
Distinct clinical features and outcomes in never‐smokers with nonsmall cell lung cancer who harbor EGFR or KRAS mutations or ALK rearrangement
Authors: Kim Hye Ryun , Shim Hyo Sup , Chung Jin‐Haeng , Lee Young Joo , Hong Yun Kyoung , Rha Sun Young , Kim Se Hoon , Ha Sang‐Jun , Kim Se Kyu , Chung Kyung Young , Soo Ross , Kim Joo Hang , Cho Byoung Chul 
Published: June 2011

AbstractBACKGROUND:The objectives of this study were to determine the proportions of major oncogenic alterations and to examine survival in genotype‐specific subsets of never‐smokers with nonsmall cell lung cancer (NSCLC).METHODS:The authors concurrently analyzed mutations in the epidermal growth factor receptor (EGFR) and v‐Ki‐ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) genes and investigated anaplastic lymphoma kinase (ALK) gene rearrangements in samples from 229 never‐smokers with NSCLC. ALK rearrangements were identified by fluorescent in situ hybridization and were confirmed by immunohistochemistry. Mutations in EGFR (exons 18 to 21) and KRAS (codons 12 and 13) were determined by direct sequencing.RESULTS:Of 229 tumors, the frequency of EGFR mutations, ALK rearrangements, KRAS mutations, and no mutations (wild type [WT]) in any of the 3 genes (WT/WT/WT) was 48%, 8.3%, 3.5%, and 40.2%, respectively. All genetic alterations were mutually exclusive. The median progression‐free survival after treatment with EGFR tyrosine kinase inhibitors (TKIs) was 12.8 months, 6.3 months, 2.1 months, and 1.6 months in patients with EGFR mutations, the WT/WT/WT genotype, KRAS mutations, and ALK rearrangements, respectively. In a Cox regression model, the adjusted hazard ratio for the risk of disease progression after treatment with EGFR TKIs was 0.59 (95% confidence interval [CI], 0.40‐0.87; P = .008) for patients with EGFR mutations, 4.58 (95% CI, 2.07‐10.15; P < .001) for patients with ALK rearrangements, and 4.23 (95% CI, 1.65‐10.8; P = .003) for patients with KRAS mutations. Overall survival also differed significantly among genotypes.CONCLUSIONS:To the authors' knowledge, this was the largest comprehensive and concurrent analysis to date of 3 major oncogenic alterations in a cohort of East Asian never‐smokers with NSCLC. Because survival outcomes differed among genotypes, and drugs that target specific alterations currently are available, genetic profiling to identify genotype‐specific subsets can lead to successful treatment with appropriate kinase inhibitors. Cancer 2012;. © 2011 American Cancer Society.
Can radicality of surgery be safely modulated on the basis of MRI and PET/CT imaging in locally advanced cervical cancer patients administered preoperative treatment?
Authors: Ferrandina Gabriella , Petrillo Marco , Restaino Gennaro , Rufini Vittoria , Macchia Gabriella , Carbone Arnaldo , Zannoni Gian Franco , Lucidi Alessandro , D'Angelo Giorgia , Scambia Giovanni 
Published: June 2011

AbstractBACKGROUND:The goal of this study was to prospectively analyze the diagnostic performances of magnetic resonance imaging (MRI) and positron emission tomography (PET)/computed tomography (CT) in predicting pathologically assessed residual disease in a large, single‐institution series of locally advanced cervical cancer (LACC) patients triaged to neoadjuvant treatments followed by radical surgery.METHODS:Between April 2007 and March 2010, 96 patients with histologically documented cervical cancer (any histology) and FIGO stage IB2‐IVA were enrolled. MRI and PET/CT were recommended to be performed within 4‐6 weeks from the end of treatment, and histology was the reference standard. Sensitivity, specificity, and accuracy were compared using the McNemar test.RESULTS:For residual disease in the cervix, sensitivity was higher for MRI than for PET/CT (86.1% vs 63.1%; P = .002), while specificity was significantly higher for PET/CT compared with MRI (P = .002). There was no difference in accuracy values between the 2 imaging modalities. For MRI analysis of lymph node groups, sensitivity, specificity, and accuracy were 35.7%, 95.9%, and 88.0%, respectively. Conversely, sensitivity, specificity, and accuracy for PET/CT were 28.6%, 97.8%, and 88.7%, respectively. Absence of follicular structures replaced by prevalent sclerosis and/or sinus histiocytosis was the most frequently documented morphological pattern in false‐positive cases.CONCLUSION:Neither MRI nor PET/CT accurately detected residual disease in LACC patients triaged to radical surgery after neoadjuvant treatment, disallowing the option of avoiding or modulating completion surgery. Cancer 2011;. © 2011 American Cancer Society.
Individualizing antimetabolic treatment strategies for head and neck squamous cell carcinoma based on TP53 mutational status
Authors: Sandulache Vlad C. , Skinner Heath D. , Ow Thomas J. , Zhang Aijun , Xia Xuefeng , Luchak James M. , Wong Lee‐Jun C. , Pickering Curtis R. , Zhou Ge , Myers Jeffrey N. 
Published: June 2011

AbstractBACKGROUND:Mutations in the tumor protein 53 (TP53) tumor suppressor gene are common in head and neck squamous cell carcinoma (HNSCC) and correlate with radioresistance. Currently, there are no clinically available therapeutic approaches targeting p53 in HNSCC. In this report, the authors propose a strategy that uses TP53 mutational status to individualize antimetabolic strategies for the potentiation of radiation toxicity in HNSCC cells.METHODS:Glycolytic flux and mitochondrial respiration were evaluated in wild‐type (wt) and mutant (mut) TP53 HNSCC cell lines. Sensitivity to external‐beam radiation (XRT) was measured using a clonogenic assay.RESULTS:HNSCC cells that expressed mutTP53 demonstrated radioresistance compared with HNSCC cells that expressed wtTP53. Glycolytic inhibition potentiated radiation toxicity in mutTP53‐expressing, but not wtTP53‐expressing, HNSCC cells. The relative sensitivity of mutTP53 HNSCC cells to glycolytic inhibition was caused by a glycolytic dependence associated with decreased mitochondrial complex II and IV activity. The wtTP53‐expressing cells maintained mitochondrial reserves and were relatively insensitive to glycolytic inhibition. Inhibition of respiration using metformin increased glycolytic dependence in wtTP53‐expressing cells and potentiated the effects of glycolyic inhibition on radiation toxicity.CONCLUSIONS:TP53 mutation in HNSCC cells was correlated with a metabolic shift away from mitochondrial respiration toward glycolysis, resulting in increased sensitivity to the potentiating effects of glycolytic inhibition on radiation toxicity. In contrast, wtTP53‐expressing cells required inhibition of both mitochondrial respiration and glycolysis to become sensitized to radiation. Therefore, the authors concluded that TP53 mutational status may be used as a marker of altered tumor cell metabolism to individualize HNSCC treatment selection of specific, targeted metabolic agents that can overcome cellular resistance to radiation therapy. Cancer 2012;. © 2011 American Cancer Society.
Molecular organization and timing of Wnt1 expression define cohorts of midbrain dopamine neuron progenitors in vivo
Authors: Brown Ashly , Machan Jason T. , Hayes Lindsay , Zervas Mark 
Published: June 2011

AbstractMidbrain dopamine (MbDA) neurons are functionally heterogeneous and modulate complex functions through precisely organized anatomical groups. MbDA neurons are generated from Wnt1‐expressing progenitors located in the ventral mesencephalon (vMes) during embryogenesis. However, it is unclear whether the progenitor pool is partitioned into distinct cohorts based on molecular identity and whether the timing of gene expression uniquely identifies subtypes of MbDA neurons. In this study we show that Wnt1‐expressing MbDA progenitors from embryonic day (E)8.5–12.5 have dynamic molecular identities that correlate with specific spatial locations in the vMes. We also tested the hypothesis that the timing of Wnt1 expression in progenitors is related to the distribution of anatomically distinct cohorts of adult MbDA neurons using genetic inducible fate mapping (GIFM). We demonstrate that the Wnt1 lineage contributes to specific cohorts of MbDA neurons during a 7‐day epoch and that the contribution to MbDA neurons predominates over other ventral Mb domains. In addition, we show that calbindin‐, GIRK2‐, and calretinin‐expressing MbDA neuron subtypes are derived from Wnt1‐expressing progenitors marked over a broad temporal window. Through GIFM and quantitative analysis we demonstrate that the Wnt1 lineage does not undergo progressive lineage restriction, which eliminates a restricted competence model of generating MbDA diversity. Interestingly, we uncover that two significant peaks of Wnt1 lineage contribution to MbDA neurons occur at E9.5 and E11.5. Collectively, our findings delineate the temporal window of MbDA neuron generation and show that lineage and timing predicts the terminal distribution pattern of MbDA neurons. J. Comp. Neurol. 519:2978–3000, 2011. © 2011 Wiley‐Liss, Inc.
Cloud computing paradigms for pleasingly parallel biomedical applications
Authors: Gunarathne Thilina , Wu Tak‐Lon , Choi Jong Youl , Bae Seung‐Hee , Qiu Judy 
Published: June 2011

SUMMARYCloud computing offers exciting new approaches for scientific computing that leverage major commercial players’ hardware and software investments in large‐scale data centers. Loosely coupled problems are very important in many scientific fields, and with the ongoing move towards data‐intensive computing, they are on the rise. There exist several different approaches to leveraging clouds and cloud‐oriented data processing frameworks to perform pleasingly parallel (also called embarrassingly parallel) computations. In this paper, we present three pleasingly parallel biomedical applications: (i) assembly of genome fragments; (ii) sequence alignment and similarity search; and (iii) dimension reduction in the analysis of chemical structures, which are implemented utilizing a cloud infrastructure service‐based utility computing models of Amazon Web Services (http://Amazon.com Inc., Seattle, WA, USA) and Microsoft Windows Azure (Microsoft Corp., Redmond, WA, USA) as well as utilizing MapReduce‐based data processing frameworks Apache Hadoop (Apache Software Foundation, Los Angeles, CA, USA) and Microsoft DryadLINQ. We review and compare each of these frameworks, performing a comparative study among them based on performance, cost, and usability. High latency, eventually consistent cloud infrastructure service‐based frameworks that rely on off‐the‐node cloud storage were able to exhibit performance efficiencies and scalability comparable to the MapReduce‐based frameworks with local disk‐based storage for the applications considered. In this paper, we also analyze variations in cost among the different platform choices (e.g., Elastic Compute Cloud instance types), highlighting the importance of selecting an appropriate platform based on the nature of the computation. Copyright © 2011 John Wiley & Sons, Ltd.
Hydrogen Electrocatalysis on Single Crystals and on Nanostructured Electrodes
Authors: Santos Elizabeth , Hindelang Peter , Quaino Paola , Schulz Eduardo N. , Soldano Germán , Schmickler Wolfgang 
Published: June 2011

AbstractWe investigate hydrogen evolution on plain and nanostructured electrodes with a theory developed by us. On electrodes involving transition metals the most strongly adsorbed hydrogen is often only a spectator, while the reaction proceeds via a weakly adsorbed species. For Pt(111) the isotherms for both species are calculated. We explain why a nanostructure consisting of a monolayer of Pd on Au(111) is a good catalysts, and predict that Rh/Au(111) should be even better. Our calculations for a fair number of metals are in good agreement with experiment.
Generalized graph entropies
Authors: Dehmer Matthias , Mowshowitz Abbe 
Published: June 2011

AbstractThis article deals with generalized entropies for graphs. These entropies result from applying information measures to a graph using various schemes for defining probability distributions over the elements (e.g., vertices) of the graph. We introduce a new class of generalized measures, develop their properties, compute the measures for selected graphs, and briefly discuss potential applications to classification and clustering problems. © 2011 Wiley Periodicals, Inc. Complexity, 17,45–50, 2011
Formation of oxygen deficient BaPbO3‐x by oxalate decomposition
Authors: Franz A. , Klimm D. , Schmitz W. , Haferkorn I. , Bente K. 
Published: June 2011

AbstractBaPbO3 is assumed to be oxygen deficient but the exact determination has never been reported. The aim of this study is to investigate the correlation between synthetic conditions and the resulting oxygen deficiency of BaPbO3‐x. The formation of BaPbO3‐x by decomposition of barium‐ and lead oxalate up to 850 °C is significantly faster compared to conventional high temperature solid state reactions of oxide compounds. The discrete reaction steps were studied by simultaneous thermal analysis and X‐ray powder diffraction. The oxygen content was determined by temperature‐programmed reduction analysis. It is shown that the formation process is very sensitive to the chosen starting materials leading to different oxygen deficits caused by partial oxidation from Pb2+ to Pb4+. The resulting perovskites show chemical compositions of BaPbO2.74 and BaPbO2.82. The varying oxygen deficits should have an effect on structural properties. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Morphology control of CuO micro‐particles using Zn2+ ion and ultrasonic treatment
Authors: Si Limin , Yue Linhai , Jin Dalai 
Published: June 2011

AbstractNovel tomato‐shaped copper oxide crystals has been prepared by a simple hydrothermal method with the presence of Zn2+ ion. The ultrasonic pretreatment has proved to be the key factor during the synthesis process. Scanning electron microscope, energy dispersive X‐ray spectrometry and powder X‐ray diffraction were used to characterize the microstructure and morphology of the as‐prepared products. The obtained tomato‐shaped CuO particles were constructed by nanorods with the diameter of about 20 nm. The possible growth mechanism was proposed based on the experimental results. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Modeling of flame assisted chemical vapor deposition of silicon films
Authors: Masi M. , Cavallotti C. , Raffa E. 
Published: June 2011

AbstractThe simulation of a flame assisted chemical vapor deposition (FACVD) process is here proposed with reference to the growth of silicon thin films through the silane/chlorosilanes/hydrogen/chlorine route. The goal is to design a reactor able to deposit micromorphous or multicrystalline films at the high growth rates necessary for photovoltaic applications. In fact, since FACVD processes can operate in atmospheric conditions and in auto‐thermal mode, they present significant energetic advantages with respect to the plasma assisted technology used today. This work is in particular devoted to illustrate the multi‐hierarchical modeling procedure adopted to determine the process optimal operating conditions and to design the deposition chamber. Different burner geometries (single, porous or multiple nozzles burner) were investigated in order to exploit the advantages of the two classical stagnation flow and Bunsen stretched flames. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Photoluminescence from screen printed ZnO based nanocrystalline films
Authors: Srivastava A. , Shukla R. K. , Misra K. P. 
Published: June 2011

AbstractPhotoluminescence from ZnO based films deposited by screen printing is studied. PL spectra of undoped films show strong broad green emission around 500 nm and a weak (nearly one fourth of visible) UV emission around 398 nm. Further enhancement of 30% in the green emission is observed as 5 at.% Ca is doped in ZnO which for higher dopant concentration falls monotonously. The films are polycrystalline and the particle size lies between 33 to 47 nm as determined by Debye‐Scherrer method. Film with 5 at.% doping is under tensile strain and the others are under compressive strain. SEM shows microclusters, consisting of nanoparticles, scattered throughout the substrate which club together with increase in dopant amount. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The effect of diluting crystallization droplets on protein crystallization in vapor diffusion method
Authors: Lu Qin‐Qin , Yin Da‐Chuan , Xie Si‐Xiao , Liu Yong‐Ming , Chen Rui‐Qing 
Published: June 2011

AbstractIn this study, effects of diluting either protein or crystallization agents in the droplets on the success rate of protein crystallization was investigated. Diluting the crystallization agent was found to increase the success rate of protein crystallization. Theoretical analysis showed that, concentration ranges of both protein and crystallization agent that can be scanned during the vapor diffusion process are wider with diluting the crystallization agent than that without dilution, resulting in more opportunities for the crystallization solution to be in the nucleation zone. On the other hand, diluting protein could lead to controversial results depending on the location of the initial concentration relative to that of the nucleation zone in the phase diagram. The method of diluting the crystallization agent is therefore proposed as an alternative modification to the conventional vapor diffusion method for obtaining more crystallization conditions in protein crystallization screening. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Channel capacity per user in a power and rate adaptive hybrid DS/FFH‐CDMA cellular system over Rayleigh fading channels
Authors: Varzakas P. 
Published: June 2011

SUMMARYThe theoretically achievable average channel capacity (in the Shannon sense) per user of a hybrid cellular direct sequence/fast frequency hopping code‐division multiple‐access (DS/FFH‐CDMA) system, operating in a Rayleigh fading environment, was examined. The analysis covers the downlink transmission and leads to the derivation of a novel expression between the average channel capacity available to each system's user under simultaneous optimal power and rate adaptation and the system's parameters, providing an optimistic upper bound, useful for practical modulation and coding schemes. The final derived closed‐form expression can be useful for the design of the DS/FFH‐CDMA system because it provides a theoretical tool for the initial quantitative analysis. Finally, avoiding the application of complex theoretical algorithm or lengthy simulation, we theoretically derived numerical results to illustrate the presented analysis. Copyright © 2011 John Wiley & Sons, Ltd.
Urine cytopathology: Challenges, pitfalls, and mimics
Authors: Thiryayi, S. A. , Rana D. N. 
Published: June 2011

AbstractUrine cytopathology is a useful and noninvasive tool in the diagnosis and follow‐up of urothelial neoplasia, which remains complementary to emerging molecular tests. These specimens may be challenging and there are numerous mimics and diagnostic pitfalls with which to contend. This review discusses these various entities and includes consideration of ancillary tests that may be useful in the diagnostic procedure. Diagn. Cytopathol. 2012. © 2011 Wiley Periodicals, Inc.