bluuebunny/crossref_metadata_2025_split huggingface dataset:
A combined molecular‐pathologic score improves risk stratification of thyroid papillary microcarcinoma
Authors: Niemeier Leo A. , Kuffner Akatsu Haruko , Song Chi , Carty Sally E. , Hodak Steven P. , Yip Linwah , Ferris Robert L. , Tseng George C. , Seethala Raja R. , LeBeau Shane O. , Stang Michael T. , Coyne Christopher , Johnson Jonas T. , Stewart Andrew F. , Nikiforov Yuri E. 
Published: September 2011

AbstractBACKGROUND:Thyroid papillary microcarcinoma (TPMC) is an incidentally discovered papillary carcinoma that measures ≤1.0 cm in size. Most TPMCs are indolent, whereas some behave aggressively. The objective of the study was to evaluate whether the combination of v‐raf murine sarcoma viral oncogene homolog B1 (BRAF) mutation and specific histopathologic features allows risk stratification of TPMC.METHODS:A group aggressive TPMCs was selected based on the presence of lymph node metastasis or tumor recurrence. Another group of nonaggressive tumors included TPMCs matched with the first group for age, sex, and tumor size, but with no extrathyroid spread. A molecular analysis was performed, and histologic slides were scored for multiple histopathologic criteria. A separate validation cohort of 40 TPMCs was evaluated.RESULTS:BRAF mutations were detected in 77% of aggressive TPMCs and in 32% of nonaggressive tumors (P = .001). Several histopathologic features differed significantly between the groups. By using multivariate regression analysis, a molecular‐pathologic (MP) score was developed that included BRAF status and 3 histopathologic features: superficial tumor location, intraglandular tumor spread/multifocality, and tumor fibrosis. By adding the histologic criteria to BRAF status, sensitivity was increased from 77% to 96%, and specificity was increased from 68% to 80%. In the independent validation cohort, the MP score stratified tumors into low‐risk, moderate‐risk, and high‐risk groups with the probability of lymph node metastases or tumor recurrence in 0%, 20%, and 60% of patients, respectively.CONCLUSIONS:BRAF status together with several histopathologic features allowed clinical risk stratification of TPMCs. The combined MP risk stratification model was a better predictor of extrathyroid tumor spread than either mutation or histopathologic findings alone. Cancer 2012;. © 2011 American Cancer Society.
Predictive factors for BRCA1/BRCA2 mutations in women with ductal carcinoma in situ
Authors: Bayraktar Soley , Elsayegh Nisreen , Gutierrez Barrera Angelica M. , Lin Heather , Kuerer Henry , Tasbas Tunc , Muse Kimberly I. , Ready Kaylene , Litton Jennifer , Meric‐Bernstam Funda , Hortobagyi Gabriel N. , Albarracin Constance T. , Arun Banu 
Published: September 2011

AbstractBACKGROUND:It is unclear whether women with ductal carcinoma in situ (DCIS), like their counterparts with invasive breast cancer, warrant genetic risk assessment and testing on the basis of high‐risk variables. The authors of this report identified predictive factors for mutations in the breast cancer‐susceptibility genes BRCA1 and BRCA2 in women who were diagnosed with DCIS.METHODS:One hundred eighteen women with DCIS who were referred for genetic counseling and underwent genetic testing for BRCA1/BRCA2 mutations between 2003 and 2010 were included in the study. Logistic regression models were fit to determine the associations between potential predictive factors and BRCA status.RESULTS:Of 118 high‐risk women with DCIS, 27% (n = 32) tested positive for BRCA1/BRCA2 mutations. Of those, 10% (n = 12) and 17% (n = 20) had BRCA1 and BRCA2 mutations, respectively. Age, race, and tumor characteristics did not differ between BRCA noncarriers and carriers. In a multivariate logistic model, ≥2 relatives with ovarian cancer (OC) (odds ratio [OR], 8.81; 95% confidence interval [CI], 1.38‐56.29; P = .034), and a score ≥10% according to the BRCAPRO mathematical model for calculating the probability that a particular family member carries a germline BRCA mutation (OR, 6.37; 95% CI, 2.23‐18.22; P = .0005) remained as independent significant predictors for a BRCA mutation. Fifty‐seven percent of mutation carriers but only 25% of noncarriers underwent prophylactic mastectomy(P = .0037). This difference remained significant for patients aged ≤40 years (P = .025).CONCLUSIONS:Women who had DCIS and a family history of OC or who had BRCAPRO scores ≥10% had a high rate of BRCA positivity regardless of age at diagnosis. These findings suggest that high‐risk patients with DCIS are appropriate candidates for genetic testing for BRCA mutations in the presence of predictive factors even if they do not have invasive breast cancer. Cancer 2011;. © 2011 American Cancer Society.
Changes in PSA kinetics predict metastasis‐free survival in men with PSA‐recurrent prostate cancer treated with nonhormonal agents
Authors: Antonarakis Emmanuel S. , Zahurak Marianna L. , Lin Jianqing , Keizman Daniel , Carducci Michael A. , Eisenberger Mario A. 
Published: September 2011

AbstractBACKGROUND:Several phase II trials in men with noncastrate PSA‐recurrent prostate cancer have assessed the impact of novel nonhormonal agents on PSA kinetics. However, it is unknown whether changes in PSA kinetics influence metastasis‐free survival (MFS).METHODS:We performed a retrospective post hoc analysis of 146 men treated in 4 phase II trials examining the investigational agents marimastat (a matrix metalloproteinase inhibitor; n = 39), imatinib (a tyrosine kinase inhibitor; n = 25), ATN‐224 (a copper/zinc‐superoxide dismutase inhibitor; n = 22), and lenalidomide (an antiangiogenic/immunomodulatory drug; n = 60). We investigated factors influencing MFS, including within‐subject changes in PSA kinetics (PSA slope, doubling time, and velocity) before and after treatment initiation.RESULTS:After a median follow‐up of 16.8 months, 70 patients (47.9%) developed metastases. In multivariable Cox regression models, factors that were independently predictive of MFS after adjusting for age and other clinical prognostic variables were baseline PSA doubling time (PSADT) (P = .05), baseline PSA slope (P = .01), on‐study change in PSADT (P = .02), and on‐study change in PSA slope (P = .03). In a landmark Kaplan‐Meier analysis, median MFS was 63.5 months (95% confidence interval [CI], 34.6‐not reached) and 28.9 months (95% CI, 13.5‐68.0) for men with or without any decrease in PSA slope by 6 months after treatment, respectively.CONCLUSIONS:This hypothesis‐generating analysis suggests that within‐subject changes in PSADT and PSA slope after initiation of experimental therapy may correlate with MFS in men with biochemically recurrent prostate cancer. If validated in prospective trials, changes in PSA kinetics may represent a reasonable intermediate end point for screening new agents in these patients. Cancer 2011;. © 2011 American Cancer Society.
CAPER‐α alternative splicing regulates the expression of vascular endothelial growth factor165 in Ewing sarcoma cells
Authors: Huang Gangxiong , Zhou Zhichao , Wang Hua , Kleinerman Eugenie S. 
Published: September 2011

AbstractBACKGROUND:TC‐71 Ewing sarcoma cells overexpress vascular endothelial growth factor (VEGF) with a shift from the 189 to the 165 isoform.METHODS:The effect of CAPER‐α on the expression of the VEGF isoforms, tumor growth, and vessel density was analyzed after transfection of TC‐71 cells with CAPER‐α cDNA or siRNA.RESULTS:CAPER‐α correlated inversely with the VEGF165/VEGF189 mRNA ratio. Up‐regulation of CAPER‐α resulted in decreased tumor growth, tumor vessel density, and chemotactic activity of the cell's supernatant. CAPER‐α expression was regulated by EWS/FLI‐1 through a protein‐protein interaction.CONCLUSIONS:Increased VEGF165 expression is secondary to the down‐regulation of CAPER‐α by EWS/FLI‐1. CAPER‐α mediates alternative splicing and controls the shift from VEGF189 to VEGF165. Cancer 2012;. © 2011 American Cancer Society.
Design of optimally smoothing multistage schemes for the euler equations
Authors: van Leer Bram , Lee Wen‐Tzong , Roe Philip L. , Powell Kenneth G. , Tai Chang‐Hsien 
Published: September 2011

AbstractA recently derived local preconditioning of the Euler equations is shown to be useful in developing multistage schemes suited for multigrid use. The effect of the preconditioning matrix on the spatial Euler operator is to equalize the characteristic speeds. When applied to the discretized Euler equations, the preconditioning has the effect of strongly clustering the operator's eigenvalues in the complex plane. This makes possible the development of explicit marching schemes that effectively damp most high‐frequency Fourier modes, as desired in multigrid applications. The technique is the same as developed earlier for scalar convection schemes: placement of the zeros of the amplification factor of the multistage scheme in locations where eigenvalues corresponding to high‐frequency modes abound.
Ab Initio Multireference Investigation of Disjoint Diradicals: Singlet versus Triplet Ground States
Authors: Chattopadhyay Sudip , Chaudhuri Rajat K. , Sinha Mahapatra Uttam 
Published: September 2011

AbstractWe present improved virtual orbital (IVO) complete active space (CAS) configuration interaction (IVO‐CASCI) and IVO‐CASCI‐based multireference Møller–Plesset perturbation theory (MRMPPT) calculations with an aim to elucidate the electronic structure of tetramethyleneethane (TME) in its lowest singlet and triplet state and to quantify their order and extent of splitting. The potential surfaces of singlet and triplet states for the twisting of TME are also studied. We found that the triplet state is higher in energy than the singlet one in the whole range of twisting angles with the energy gap minimum at a twisting angle of about 45°. Harmonic vibrational frequencies of TME have also been calculated for both the states. We also report the ground to first excited triplet state transition energies. Our results are analyzed with respect to the results available in the literature to illustrate the efficacy of our methods employed. We also demonstrate that the spin character of the ground state of disjoint, TME‐like diradicals can be manipulated by using appropriate selection of annulenic spacer to separate the allyl groups of TME.
Influence of Electron Doping on the Hydrogenation of Fullerene C60: A Theoretical Investigation
Authors: Dral Pavlo O. , Shubina Tatyana E. , Hirsch Andreas , Clark Timothy 
Published: September 2011

AbstractThe influence of electron attachment on the stability of the mono‐ and dihydrogenated buckminsterfullerene C60 was studied using density functional theory and semiempirical molecular orbital techniques. We have also assessed the reliability of computationally accessible methods that are important for investigating the reactivity of graphenic species and surfaces in general. The B3LYP and M06L functionals with the 6‐311+G(d,p) basis set and MNDO/c are found to be the best methods for describing the electron affinities of C60 and C60H2. It is shown that simple frontier molecular orbital analyses at both the AM1 and B3LYP/6‐31G(d) levels are useful for predicting the most favourable position of protonation of C60H−, that is, formation of the kinetically controlled product 1,9‐dihydro[60]fullerene, which is also the thermodynamically controlled product, in agreement with experimental and previous theoretical studies. We have shown that reduction of exo‐ and endo‐C60H makes them more stable in contrast to the reduction of the exo,exo‐1,9‐C60H2, reduced forms of which decompose more readily, in agreement with experimental electrochemical studies. However, most other dihydro[60]fullerenes are stabilized by reduction and the regioselectivity of addition is predicted to decrease as the less stable isomers are stabilized more by the addition of electrons than the two most stable ones (1,9 and 1,7).
A Comparison of Mood‐Dependent Memory in Bipolar Disorder and Normal Controls
Authors: Nutt Rachel M. , Lam Dominic 
Published: September 2011

Mood‐dependent memory was investigated in a sample of 28 individuals, with a diagnosis of bipolar disorder I but not during acute episodes, and 30 non‐clinical controls by using the word lists from Wechsler Memory Scale—Third Edition and abstract inkblot recognition. Positive or negative mood induction procedures were used prior to and after the stimuli were presented. After either the same or contrasting high or low mood inductions, participants attempted to recall the word list and performed an inkblot recognition task. Bipolar patients were significantly better at the inkblot recognition in the same mood state, showing mood‐dependent memory. No differences were found in the verbal recall task. This study paves the way for further investigation into memory differences of this sort in mood disorders. Copyright © 2011 John Wiley & Sons, Ltd.Key Practitioner MessageSince there is evidence that bipolar patients are better at visual mood‐dependent memory, clinicians should explore imagery more frequently in state‐dependent memory.
Hydrothermal synthesis of anatase flower‐like nanostructures for photocatalytic degradation of dye
Authors: Zhang Li , Ding Qianqian , Zhou Ying 
Published: September 2011

AbstractFlower‐like hierarchical nanostructures of titanium dioxide (TiO2) have been synthesized in large scale by a facile and controlled hydrothermal and after annealing process. The morphologies of flower‐like hierarchical nanostructures are formed by self‐organization of several tens of radially distributed thin flakes with a thickness of several nanometers holding a larger surface area. The materials are characterized by Scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X‐ray diffraction (XRD). The ultraviolet photocatalytic degradation of R6G dyes has been studied over this flower‐like hierarchical nanostructures and the activity is compared with that of commercial P25 TiO2 under same conditions. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Hydrothermal synthesis of MoO3 nanobelt‐graphene composites
Authors: Yang Xiaofei , Ding Heyi , Zhang Du , Yan Xuehua , Lu Chunyu , Qin Jieling , Zhang Rongxian , Tang Hua , Song Haojie 
Published: September 2011

AbstractA composite of graphene sheets decorated with molybdenum trioxide (MoO3) nanobelts has been fabricated via a facile and efficient hydrothermal route in the presence of NaCl. The structure, morphology of these promising composites were investigated by means of field‐emission scanning electron microscopy (FE‐SEM), transmission electron microscopy (TEM), X‐ray diffraction (XRD), Raman spectroscopy and thermogravimetric (TG) analysis. FESEM and TEM studies suggest the presence of uniform crystalline MoO3 nanobelts and graphene sheets in as‐prepared hybrid materials. XRD and Raman results confirm the reduction of graphite oxide (GO) sheets to graphene sheets accompanying by the formation of MoO3 nanobelts. Moreover, thermal properties of GO and MoO3 nanobelt‐graphene composites reveal that thermal stability of the obtained MoO3 nanobelt‐graphene composites is obviously higher than that of GO due to the transformation of GO sheets to highly stable graphene sheets in the hybrids. This work could provide new insights into the fabrication of high quality MoO3‐graphene hybrid nanomaterials and facilitate their potential applications in different fields. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Magnetic properties and X‐ray photoelectron spectroscopy of nanocrystalline Ho3Al5O12
Authors: Petrov D. , Angelov B. , Lovchinov V. 
Published: September 2011

AbstractNanocrystalline holmium aluminium garnet (Ho3Al5O12) has been prepared for the first time by modified Pechini's reaction after sintering the precursor gel at 1223 K. The nanomaterial has been characterized by X‐ray diffraction (XRD), selected area electron diffraction (SAED) and high resolution transmission electron microscopy (HRTEM). The XRD pattern confirms the formation of single‐phase Ho3Al5O12; the average size of the nanoparticles has also been determined. X‐ray photoelectron spectroscopy (XPS) has been used to study the chemical composition and bonding in the as‐prepared samples. The binding energies of core‐level electrons in Ho, Al and O in the title material have been found slightly shifted compared to the values of the respective elements. DC magnetic susceptibility has been measured in the temperature range 2 – 260 K. Low effective magnetic moment of Ho3+, μeff = 1.35 µB and Weiss constant have been derived from the inverse magnetic susceptibility–temperature linear plot. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Hydrothermal synthesis and characterization of micro/nanostructured ZnSn(OH)6/ZnO composite architectures
Authors: Yu Xiujun , Lu Hongxia , Li Qi , Zhao Yunlong , Zhang Liwei , Fan Bingbing , Chen Deliang , Wang Hailong , Xu Hongliang , Zhang Rui 
Published: September 2011

AbstractMicro/nanostructured ZnSn(OH)6/ZnO composite architectures were synthesized through a simple one‐step hydrothermal method. Phase structure and morphology of the products were characterized by using X‐ray diffraction (XRD), scanning electron microscope (SEM) and transmission electron microscope (TEM). ZnSn(OH)6 microcubes and ZnO nanorods with uniform size were interconnected to form the micro/nanostructured architectures. ZnO nanorods preferentially grow at edges and corners of the microcubes. Morphology of the products was susceptible to concentration of the reactants. With increasing reactant concentration, the ZnO nanorods grown on the surfaces of ZnSn(OH)6 microcubes disappeared. Meanwhile, the smooth surfaces of the ZnSn(OH)6 microcubes become coarsened and were etched to spherical outlines. Growth mechanism of the micro/nanostructured ZnSn(OH)6/ZnO composite architectures was discussed and thermal decomposition properties of the micro/nanostructured ZnSn(OH)6/ZnO composite architectures at high temperature were examined. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Hyperspectral cytometry at the single‐cell level using a 32‐channel photodetector
Authors: Grégori Gérald , Patsekin Valery , Rajwa Bartek , Jones James , Ragheb Kathy , Holdman Cheryl , Robinson J. Paul 
Published: September 2011

AbstractDespite recent progress in cell‐analysis technology, rapid classification of cells remains a very difficult task. Among the techniques available, flow cytometry (FCM) is considered especially powerful, because it is able to perform multiparametric analyses of single biological particles at a high flow rate–up to several thousand particles per second. Moreover, FCM is nondestructive, and flow cytometric analysis can be performed on live cells. The current limit for simultaneously detectable fluorescence signals in FCM is around 8–15 depending upon the instrument. Obtaining multiparametric measurements is a very complex task, and the necessity for fluorescence spectral overlap compensation creates a number of additional difficulties to solve. Further, to obtain well‐separated single spectral bands a very complex set of optical filters is required. This study describes the key components and principles involved in building a next‐generation flow cytometer based on a 32‐channel PMT array detector, a phase‐volume holographic grating, and a fast electronic board. The system is capable of full‐spectral data collection and spectral analysis at the single‐cell level. As demonstrated using fluorescent microspheres and lymphocytes labeled with a cocktail of antibodies (CD45/FITC, CD4/PE, CD8/ECD, and CD3/Cy5), the presented technology is able to simultaneously collect 32 narrow bands of fluorescence from single particles flowing across the laser beam in <5 μs. These 32 discrete values provide a proxy of the full fluorescence emission spectrum for each single particle (cell). Advanced statistical analysis has then been performed to separate the various clusters of lymphocytes. The average spectrum computed for each cluster has been used to characterize the corresponding combination of antibodies, and thus identify the various lymphocytes subsets. The powerful data‐collection capabilities of this flow cytometer open up significant opportunities for advanced analytical approaches, including spectral unmixing and unsupervised or supervised classification. © 2011 International Society for Advancement of Cytometry
Combined normal donor and CLL: Single tube ZAP‐70 analysis
Authors: Degheidy Heba A. , Venzon David J. , Farooqui Mohammed Z. H. , Abbasi Fatima , Arthur Diane C. , Wilson Wyndham H. , Wiestner Adrian , Stetler‐Stevenson M. A. , Marti Gerald E. 
Published: September 2011

AbstractIntroduction:Zeta‐chain‐associated protein kinase 70 (ZAP‐70) has been identified as an independent prognostic marker in chronic lymphocytic leukemia (CLL). Based on our previous studies, we have developed a combined one‐tube technology with multiple internal controls to optimize ZAP‐70 assessment.Methods:Forty‐eight untreated CLL cases were examined for ZAP‐70 expression using a modified 7‐color one‐tube assay. Normal donor (ND) whole blood is stained with CD3 APC‐Cy7 and CD19 APC. In a second tube, patient whole blood is stained with CD5 PE‐Cy7, CD19 PerCP‐Cy5.5, and CD20 eFluor450. After surface staining and fixation, these two tubes are combined. After saponin permeabilization, the cells were stained with two anti‐ZAP‐70 clones (1E7.2/AF488 and SBZAP/PE). The results obtained from this modified tube were compared with those obtained concurrently using the non‐mixed single sample tubes. Five different methods of ZAP‐70 expression analysis were evaluated: percentage positive cells using ND T‐cells as a reference; the internal patient T‐cell/clone ratio; ND T‐cell/clone ratio; clone/ND B‐cell ratio; and modified Z‐index.Result:Overall, the combined patient and ND mix tube performed better than the non‐mixed single sample tube. The strongest correlations between ZAP‐70 expression and immunoglobulin heavy chain variable (IGHV) mutational status were seen with percentage positive ND T‐cell, ND T‐cell/clone ratio, and clone/ND B‐cell ratio for both 1E7.2 and SBZAP clone (P < 0.0001).Conclusion:The modified one tube method combining the ND and patient sample provides highly reliable results that correlate with the IGHV mutational status. This method should be considered as part of the next step in standardization of the ZAP‐70 assay in CLL. Published 2011 Wiley Periodicals, Inc.
Efficient probe selection for fault localization using the property of submodularity
Authors: Qiao Yan , Qiu Xuesong , Meng Luoming 
Published: September 2011

SUMMARYAs the computer network increasingly grows larger and more complex, fault diagnosis has become a challenging task. Active probing is an efficient tool for fault localization. By implementing some test programs and analyzing the results, active‐probing‐based techniques can perform diagnosis efficiently and adaptively. Because probes may generate additional traffic overhead, it is important to appropriately select small number of probes to reach the desired diagnostic capability. However, the computation of probe selection problem in such environment is extremely expensive. Most of the past works purchase the speed at the cost of diagnostic accuracy. In this paper, we first verify that probe selection problem satisfies the property of submodularity. Then we take the use of the property and develop a submodularity‐based selection algorithm with following novel features: (i) it is cost effective, failure resistant and more accurate; (ii) it could deal with the uncertainties about the network structures and the observations; and (iii) it can select the required probes in near‐linear time. Finally, we implement submodularity‐based selection algorithm and other two representative probe selection algorithms (bounded path enumeration approximation algorithm and greedy search algorithm) on different settings of networks. The results have shown how the new algorithm outperforms the former two algorithms. Copyright © 2011 John Wiley & Sons, Ltd.