bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis of the First Tellurium‐Derivatized Oligonucleotides for Structural and Functional Studies
Authors: Sheng Jia , Hassan Abdalla E. A. , Huang Zhen 
Published: August 2009

AbstractWe report here the first synthesis of Te‐nucleoside phosphoramidites and Te‐modified oligonucleotides. We protected the 2′‐tellurium functionality by alkylation and found that the Te functionality is compatible with solid‐phase synthesis and that the Te oligonucleotides are stable during deprotection and purification. In addition, the redox properties of the Te functionalities have been explored. We found that the telluride and telluoxide DNAs are interchangeable by redox reactions. At elevated temperature, the Te‐DNA can also be site‐specifically fragmented oxidatively or reductively when 2′‐TePh functionality is present, whereas elimination of the nucleobase is observed in the presence of 2′‐TeMe. Moreover, the stability of the DNA duplexes derivatized with the Te functionalities has been investigated. Our Te derivatization of nucleic acids provides a novel approach for investigating DNA damage as well as for structure and function studies of nucleic acids and their protein complexes.
Factors Affecting DNA–DNA Interstrand Cross‐Links in the Antiparallel 3′–3′ Sense: A Comparison with the 5′–5′ Directional Isomer
Authors: Ruhayel Rasha A. , Moniodis Joseph J. , Yang Xiaohong , Kasparkova Jana , Brabec Viktor , Berners‐Price Susan J. , Farrell Nicholas P. 
Published: August 2009

AbstractReported herein is a study of the unusual 3′–3′ 1,4‐GG interstrand cross‐link (IXL) formation in duplex DNA by a series of polynuclear platinum anticancer complexes. To examine the effect of possible preassociation through charge and hydrogen‐bonding effects the closely related compounds [{trans‐PtCl(NH3)2}2(μ‐trans‐Pt(NH3)2{NH2(CH2)6NH2}2)]4+ (BBR3464, 1), [{trans‐PtCl(NH3)2}2(μ‐NH2(CH2)6NH2)]2+ (BBR3005, 2), [{trans‐PtCl(NH3)2}2(μ‐H2N(CH2)3NH2(CH2)4)]3+ (BBR3571, 3) and [{trans‐PtCl(NH3)2}2{μ‐H2N(CH2)3‐N(COCF3)(CH2)4}]2+ (BBR3571‐COCF3, 4) were studied. Two different molecular biology approaches were used to investigate the effect of DNA template upon IXL formation in synthetic 20‐base‐pair duplexes. In the “hybridisation directed” method the monofunctionally adducted top strands were hybridised with their complementary 5′‐end labelled strands; after 24 h the efficiency of interstrand cross‐linking in the 5′–5′ direction was slightly higher than in the 3′–3′ direction. The second method involved “postsynthetic modification” of the intact duplex; significantly less cross‐linking was observed, but again a slight preference for the 5′–5′ duplex was present. 2D [1H, 15N] HSQC NMR spectroscopy studies of the reaction of [15N]‐1 with the sequence 5′‐d{TATACATGTATA}2 allowed direct comparison of the stepwise formation of the 3′–3′ IXL with the previously studied 5′–5′ IXL on the analogous sequence 5′‐d(ATATGTACATAT)2. Whereas the preassociation and aquation steps were similar, differences were evident at the monofunctional binding step. The reaction did not yield a single distinct 3′–3′ 1,4‐GG IXL, but numerous cross‐linked adducts formed. Similar results were found for the reaction with the dinuclear [15N]‐2. Molecular dynamics simulations for the 3′–3′ IXLs formed by both 1 and 2 showed a highly distorted structure with evident fraying of the end base pairs and considerable widening of the minor groove.
Why are pretreatment prostate‐specific antigen levels and biochemical recurrence poor predictors of prostate cancer survival?
Authors: Denham James W. , Steigler Allison , Wilcox Chantelle , Lamb David S. , Joseph David , Atkinson Chris , Tai Keen‐Hun , Spry Nigel A. , Gleeson Paul S. , D'Este Catherine 
Published: August 2009

AbstractBACKGROUND:The value of pretreatment (initial) prostate‐specific antigen (iPSA) and biochemical recurrence (BR) as prognostic factors for survival remains unclear. The authors sought to determine why using randomized trial data with 7‐year minimum follow‐up.METHODS:In the Trans‐Tasman Radiation Oncology Group 96.01 trial, 802 men with T2b, T2c, T3, or T4 N0 prostate cancer (PC) were randomized to radiotherapy alone or with 3 or 6 months neoadjuvant androgen deprivation between 1996 and 2000. Cox modeling was used to identify outcome predictors at follow‐up landmark points.RESULTS:Higher iPSA was found to be a potent predictor of BR–free survival (P< .01) but was not prognostic for prostate cancer–specific survival (PCSS) from randomization. Patients experiencing BR had unfavorable initial prognostic factors compared with patients who did not. After BR, these factors were not prognostic for PC death in models adjusted for time to BR (TTBR). In these models, TTBR predicted PCSS more satisfactorily than the occurrence of BR itself. Survival probability 5 years after BR exceeded 90% for men with TTBR ≥4 years; however, it dropped to 44% ± 6% for men with TTBR <1 year. After BR, rapid PSA doubling time (DT), low iPSA, and short TTBR were identified as the most important predictors of inferior PCSS.CONCLUSIONS:When BR occurs, prognostic factors for survival change. Low iPSA, short TTBR, and rapid PSA DT take over at this point, providing reasons why iPSA and occurrence of BR alone predict PCSS unsatisfactorily. Cancer 2009. © 2009 American Cancer Society.
A randomized trial of external beam radiotherapy versus cryoablation in patients with localized prostate cancer
Authors: Robinson John W. , Donnelly Bryan J. , Siever Jodi E. , Saliken John C. , Ernst Scott D. , Rewcastle John C. , Trpkov Kiril , Lau Harold , Scott Cheryl , Thomas Bejoy 
Published: August 2009

AbstractBACKGROUND:A recent randomized trial to compare external beam radiation therapy (EBRT) to cryoablation for localized disease showed cryoablation to be noninferior to external beam EBRT in disease progression and overall and disease‐specific survival. We report on the quality of life (QOL) outcomes for this trial.METHODS:From December 1997 through February 2003, 244 men with newly diagnosed localized prostate cancer were randomly assigned to cryoablation or EBRT (median dose 68 Gy). All patients received neoadjuvant antiandrogen therapy. Patients completed the EORTC QLQ C30 and the Prostate Cancer Index (PCI) before treatment and at 1.5, 3, 6, 12, 18, 24, and 36 months post‐treatment.RESULTS:Regardless of treatment arm, participants reported high levels of QOL with few exceptions. cryoablation was associated with more acute urinary dysfunction (mean PCI urinary function cryoablation = 69.4; mean EBRT = 90.7; P < .001), which resolved over time. No late arising QOL issues were observed. Both EBRT and cryoablation participants reported decreases in sexual function at 3 months with the cryoablation patients reporting poorer functioning (mean cryoablation = 7.2: mean EBRT = 32.9; P < .001). Mean sexual function score was 15 points lower at 3 years for the cryoablation group and 13% more of the cryoablation men said that sexuality was a moderate or big problem.CONCLUSIONS:In this randomized trial, no long‐term QOL advantage for either treatment was apparent with the exception of poorer sexual function reported by those treated with cryoablation. Men who wish to increase their odds of retaining sexual function might be counseled to choose EBRT over cryoablation. Cancer 2009. © 2009 American Cancer Society.
Time to disease recurrence in basal‐type breast cancers
Authors: Dent Rebecca , Hanna Wedad M. , Trudeau Maureen , Rawlinson Ellen , Sun Ping , Narod Steven A. 
Published: August 2009

AbstractBACKGROUND:Basal‐like breast cancers are a subgroup of breast cancers defined by the absence of staining for estrogen‐receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER‐2/neu) and by positive staining for the cytokeratins (CKs) expressed in the myoepithelial cells of the ducts and lobules (CK5/CK6, CK14) and for epidermal growth factor receptor (EGFR). This class of tumors has an unusually aggressive course, and it is not clear whether conventional prognostic factors for breast cancers also predict outcome for patients who have the basal phenotype.METHODS:A panel of 962 breast cancers was stained for 5 markers (ER, PR, HER‐2/neu, CK5/CK6, and EGFR). The patients were followed for clinical outcomes for up to 15 years from diagnosis, and the rates of distant disease recurrence and death were compared by tumor size (≤2 cm or >2 cm) and by lymph node status within the subgroups of women with basal and nonbasal cancers.RESULTS:Of the 962 women with breast cancer, 116 cancers were basal (12%), 845 were nonbasal (88%), and 1 could not be classified as either basal or nonbasal and was excluded. In total, 426 tumors measured ≤2 cm (45%), and 530 tumors measured >2 cm (55%). Among women with nonbasal cancers, large tumor size was an adverse prognostic factor. Among women with basal cancers, a transient adverse effect of size on disease recurrence was observed; however, after 10 years, mortality rates were equal for women with small tumors and women with large tumors.CONCLUSIONS:Among women with basal breast cancers, the long‐term prognosis was similar for women with large tumors and women with small tumors. However, women with large basal tumors appeared to develop recurrent disease sooner. Cancer 2009. © 2009 American Cancer Society.
Bayesian statistics in oncology
Authors: Adamina Michel , Tomlinson George , Guller Ulrich 
Published: August 2009

AbstractThe rise of evidence‐based medicine as well as important progress in statistical methods and computational power have led to a second birth of the >200‐year‐old Bayesian framework. The use of Bayesian techniques, in particular in the design and interpretation of clinical trials, offers several substantial advantages over the classical statistical approach. First, in contrast to classical statistics, Bayesian analysis allows a direct statement regarding the probability that a treatment was beneficial. Second, Bayesian statistics allow the researcher to incorporate any prior information in the analysis of the experimental results. Third, Bayesian methods can efficiently handle complex statistical models, which are suited for advanced clinical trial designs. Finally, Bayesian statistics encourage a thorough consideration and presentation of the assumptions underlying an analysis, which enables the reader to fully appraise the authors' conclusions. Both Bayesian and classical statistics have their respective strengths and limitations and should be viewed as being complementary to each other; we do not attempt to make a head‐to‐head comparison, as this is beyond the scope of the present review. Rather, the objective of the present article is to provide a nonmathematical, reader‐friendly overview of the current practice of Bayesian statistics coupled with numerous intuitive examples from the field of oncology. It is hoped that this educational review will be a useful resource to the oncologist and result in a better understanding of the scope, strengths, and limitations of the Bayesian approach. Cancer 2009. © 2009 American Cancer Society.
Lymph node density is a significant predictor of outcome in patients with oral cancer
Authors: Gil Ziv , Carlson Diane L. , Boyle Jay O. , Kraus Dennis H. , Shah Jatin P. , Shaha Ashok R. , Singh Bhuvanesh , Wong Richard J. , Patel Snehal G. 
Published: August 2009

AbstractBACKGROUND:The impact of lymph node metastases on prognosis in patients with oral cavity squamous cell carcinoma (OSCC) has been well recognized. However, accurate stratification of risk for recurrence among patients with lymph node metastases is difficult based on the existing staging systems. In the current study, the utility of lymph node density (LND) was evaluated as an alternative method for predicting survival.METHODS:Three hundred eighty‐six patients who underwent neck dissection were included. The median follow‐up was 67 months. Five‐year overall survival (OS), disease‐specific survival (DSS), and locoregional failure (LRF) rates were calculated using the Kaplan‐Meier method. LND (number of positive lymph nodes/total number of excised lymph nodes) and tumor‐node‐metastasis (TNM) staging variables were subjected to multivariate analysis.RESULTS:Using the median (LND = 0.06) as the cutoff point, LND was found to be significantly associated with outcome. For patients with LND ≤0.06, the OS was 58 percent versus 28 percent for patients with LND >0.06 (P < .001). Similarly, the DSS for patients with LND ≤0.06 was 65 percent and was 34 percent for those with LND >0.06 (P < .001). On univariate analysis, pathologic T and N classification, extracapsular spread, and LND were found to be significant predictors of outcome (P < .001). However, on multivariate analysis, LND remained the only independent predictor of OS (P = .02; hazards ratio, 2.0), DSS (P = .02; hazards ratio, 2.3), and LRF (P = .005; hazards ratio, 4.1). LND was also found to be the only significant predictor of outcome in patients receiving adjuvant radiotherapy (P < .05). Within individual subgroups of pN1 or pN2 patients, LND reliably stratified patients according to their risk of failure (P < .05).CONCLUSIONS:After surgery for OSCC, pathologic evaluation of the neck using LND was found to reliably stratify the risk of disease recurrence and survival. Cancer 2009. © 2009 American Cancer Society.
Task distribution models in grids: towards a profile‐based approach
Authors: Mury Antonio R. , Schulze Bruno , Gomes Antônio T. A. 
Published: August 2009

AbstractIn this paper we present an approach to task management—encompassing scheduling and fault recovery—in grid environments. The presented approach builds on user and resource profiles, which are continuously refined so as to allow estimates on the completion time of user tasks in specific grid resources. As shown in our simulation results, our approach reduces the average completion time of tasks by balancing the processing load on the grid resources, while allowing the detection of faults during task execution, and the reservation of grid resources in advance. Copyright © 2009 John Wiley & Sons, Ltd.
Direct Volumetric Measurement of Gas Oversolubility in Nanoliquids: Beyond Henry’s Law
Authors: Pera‐Titus Marc , El‐Chahal Rayan , Rakotovao Volainiana , Daniel Cécile , Miachon Sylvain , Dalmon Jean‐Alain 
Published: August 2009

AbstractThe properties of condensed matter are strongly affected by confinement and size effects at the nanoscale. Herein, we measured by microvolumetry the increased solubility of H2 in a series of solvents (CHCl3, CCl4, n‐hexane, ethanol, and water) when confined in the cavities of mesoporous solids (γ‐alumina, silica, and MCM‐41). Gas/liquid solubilities are enhanced by up to 15 times over the corresponding bulk values for nanoliquid sizes smaller than 15 nm as long as gas/liquid interfaces are mesoconfined in a porous network. Although Henry’s law constant apparently no longer applies under these confinement, the concentration of dissolved H2 still increases linearly with increasing pressure in the range 1–5 bar. We discuss the role and main implications of surface excess concentrations at mesoconfined gas/liquid interfaces in enhancing gas solubility.
Cytologic diagnosis of vulvar Paget's disease by means of brushing smear: Report of a case
Authors: Funamoto Yasunobu , Haba Reiji , Kobayashi Tadao K. , Kushida Yosio , Kouno Kouji , Matsunaga Toru , Shiota Atuko , Hata Toshiyuki 
Published: August 2009

AbstractPaget's disease of the vulva is a rare entity; since it may show the same clinical symptoms as benign chronic vulvitis, it may result in a delayed diagnosis. A 63‐year‐old woman was found to have an eczematoid pink to red lesion located in the vulva. Scraping cytology of the vulva showed isolated malignant cells of Paget type. The patient underwent wide local excision of the vulvar tumor and histopathological examination of resected specimens revealed that Paget cells were distributed singly or tended to form small nests in the epidermis. We consider vigorous brushing cytology to be a useful initial study for cancer screening of patients for any suspicious vulvar lesions. Diagn. Cytopathol. 2010. © 2009 Wiley‐Liss, Inc.
Acoustic techniques for studying soil‐surface seals and crusts
Authors: Leary Del , DiCarlo David A. , Hickey Craig J. 
Published: August 2009

AbstractThe impact of raindrops on a soil surface during a rainstorm may cause soil‐surface sealing and upon drying, soil crusting. Soil‐surface sealing is a result of the clogging of interaggregate pores by smaller suspended particles in the water and by structural deformation of the soil fabric, which reduces the infiltration capacity of soils. Soil‐surface crusting refers to the increase in soil strength or mechanical stiffness associated with near surface compaction, densification, or cementation. The formation of soil‐surface seals and crusts may have a profound influence on the erodability of soils, with the consensus being that the reduced hydraulic conductivity due to sealing is a highly significant contributing factor. In this article we discuss two acoustic techniques, one with sensitivity to changes in hydraulic properties (sealing) and the other to changes in mechanical stiffness (crusting). These non‐contact techniques excite the soil using a suspended loudspeaker to impinge acoustic energy from the air (sound) onto the sample. The response of the soil is quantified using a microphone to measure the total pressure above the soil surface and a laser Doppler vibrometer (LDV) to measure the surface solid particle velocity. Changes in soil‐surface hydraulic conductivity are examined by observing the relative change in total pressure at the soil surface. Soil‐surface stiffening is quantified by the ratio of LDV response to the measured total pressure and is referred to as the acoustic‐to‐seismic admittance. Measurements were made on two different soils having different erodability characteristics and subjected to a simulated rainstorm. A fiberglass mesh screen was used to reduce the kinetic energy from the raindrops on one half of the sample. The half of the rained‐on samples for both soils showed a lower acoustic‐to‐seismic admittance than the samples that were only wetted indicating that the raindrop impact produces a stiffer soil surface. The rained‐on side of both soils also has larger acoustic pressures than the wetted side indicating that the impact of raindrops also increases the flow resistivity (decreased hydraulic conductivity) of the surface. Copyright © 2009 John Wiley & Sons, Ltd.
Investigation of the near subsurface using acoustic to seismic coupling
Authors: Howard Wheeler , Hickey Craig J. 
Published: August 2009

AbstractAgricultural, hydrological and civil engineering applications have realized a need for information of the near subsurface over large areas. In order to obtain this spatially distributed data over such scales, the measurement technique must be highly mobile with a short acquisition time. Therefore, some type of remote sensing or geophysical technique must be utilized. Geophysical measurements are sensitive to the distribution of physical properties, such as the electrical conductivity, dielectric constant, mass density, mechanical properties, etc., of the ground. In most instances, the geophysical properties must be reconciled with physical properties used by the soil scientist. This paper presents a preliminary investigation of the use of acoustic to seismic (A/S) coupling measurements for measuring the depth to the top of the fragipan horizon. Fragipans influence the hydrology and ecohydrology of the soil on a field scale. A suite of traditional geophysical measurements was taken to characterize the soils at two sites with different depths to the fragipan horizon. Data at these two field sites indicate that this A/S technique is sensitive to the spatial variability of the depth to the fragipan horizon. At present, inversion of the A/S data for the fragipan depth requires use of data from a separate geophysical measurement or soil cores to provide a field calibration. Copyright © 2009 John Wiley & Sons, Ltd.
Inter‐ and intraspecific variation of stemflow production from Fagus grandifolia Ehrh. (American beech) and Liriodendron tulipifera L. (yellow poplar) in relation to bark microrelief in the eastern United States
Authors: Van Stan J. Toland , Levia Delphis F. 
Published: August 2009

AbstractStemflow is a spatially concentrated hydrologic input at the tree base. Prior work has documented the differential effects of stemflow from a wide range of plant species on ecohydrological processes, such as the alteration of soil pH and spatial patterning of understory vegetation. No known work has coupled stemflow yield with high resolution measurements of bark microrelief that definitively ascribe differential stemflow yield to bark microrelief. As such, our research objectives were to: (1) correlate inter‐ and intraspecific variation in stemflow yield to a quantitative bark microrelief scale and (2) compare and contrast stemflow for two co‐occurring deciduous species—Fagus grandifolia Ehrh. (American beech) and Liriodendron tulipifera L. (yellow poplar). Using a newly developed instrument to measure bark microrelief, namely the LaserBark™ automated tree measurement system, in combination with an 11‐month stemflow database for a broadleaved deciduous forest in eastern North America, it was found that bark microrelief values significantly differed between the two species [P = 0·000, F (1,19) = 49·32]. Funneling ratios [P = 0·000, H (1, 990) = 339·20] and stemflow generation [P = 0·000, H (1, 990) = 146·75] also significantly differed between the two species. Our results indicate that bark microrelief exerts a considerable effect on stemflow yield from F. grandifolia and L. tulipifera, possibly affecting water and solute flux to the forest floor. Copyright © 2009 John Wiley & Sons, Ltd.
Reduction of cyclic speed change using a bandpass filter for compressor PMSM sine‐wave position sensorless drives
Authors: Fukumoto Tetsuya , Hamane Hiroto , Hayashi Yoichi 
Published: August 2009

AbstractPosition sensorless vector control has been applied to compressor drive systems using an IPMSM to realize higher efficiency. In this paper, reduction control of cyclic speed change is proposed in order to achieve improved performance, including low vibration and low acoustic noise. Designing a speed estimator by using an adaptive observer with a wide frequency band, the fundamental frequency component of the cyclic speed change is calculated by a bandpass filter. The proposed compensation method recognizing the fundamental component can reduce the cyclic speed change to an acceptable level. The principle of the compensation method is presented along with experimental results. © 2009 Wiley Periodicals, Inc. Electr Eng Jpn, 169(4): 75–84, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/eej.20765
FDTD simulation of nonlinear ultrasonic pulse propagation in ESWL using equations including Lagrangian
Authors: Fukuhara Keisuke , Morita Nagayoshi 
Published: August 2009

AbstractA new FDTD algorithm is proposed for analyzing ultrasonic pulse propagation in the human body, a problem connected with ESWL (extracorporeal shock wave lithotripsy). In this method, we do not use plane wave approximation but directly employ the original equations, taking into account the Lagrangian to derive new FDTD algorithms. This method is applied to an experimental setup and its numerical model that resembles an actual treatment situation in order to compare the sound pressure distributions obtained numerically with those obtained experimentally. The present method is shown to give clearly better results than the earlier method, from the point of view of the numerical reappearance of a strongly nonlinear waveform. © 2009 Wiley Periodicals, Inc. Electr Eng Jpn, 169(4): 29–36, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/eej.20819