bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the gantry sag on linear accelerators and introducing an MLC‐based compensation strategy
Authors: Du Weiliang , Gao Song , Wang Xiaochun , Kudchadker Rajat J. 
Published: March 2012

Purpose:Gantry sag is one of the well‐known sources of mechanical imperfections that compromise the spatial accuracy of radiation dose delivery. The objectives of this study were to quantify the gantry sag on multiple linear accelerators (linacs), to investigate a multileaf collimator (MLC)‐based strategy to compensate for gantry sag, and to verify the gantry sag and its compensation with film measurements.Methods:The authors used the Winston–Lutz method to measure gantry sag on three Varian linacs. A ball bearing phantom was imaged with megavolt radiation fields at 10° gantry angle intervals. The images recorded with an electronic portal imaging device were analyzed to derive the radiation isocenter and the gantry sag, that is, the superior–inferior wobble of the radiation field center, as a function of the gantry angle. The authors then attempted to compensate for the gantry sag by applying a gantry angle‐specific correction to the MLC leaf positions. The gantry sag and its compensation were independently verified using film measurements.Results:Gantry sag was reproducible over a six‐month measurement period. The maximum gantry sag was found to vary from 0.7 to 1.0 mm, depending on the linac and the collimator angle. The radiation field center moved inferiorly (i.e., away from the gantry) when the gantry was rotated from 0° to 180°. After the MLC leaf position compensation was applied at 90° collimator angle, the maximum gantry sag was reduced to <0.2 mm. The film measurements at gantry angles of 0° and 180° verified the inferior shift of the radiation fields and the effectiveness of MLC compensation.Conclusions:The results indicate that gantry sag on a linac can be quantitatively measured using a simple phantom and an electronic portal imaging device. Reduction of gantry sag is feasible by applying a gantry angle‐specific correction to MLC leaf positions at 90° collimator angle.
A filtered backprojection MAP algorithm with nonuniform sampling and noise modeling
Authors: Zeng Gengsheng L. 
Published: March 2012

Purpose:The goal of this paper is to extend our recently developed FBP (filtered backprojection) algorithm, which has the same characteristics of an iterative Landweber algorithm, to an FBP algorithm with the same characteristics of an iterative MAP (maximuma posteriori) algorithm. The newly developed FBP algorithm also works when the angular sampling interval is not uniform. The projection noise variance can be modeled using a view‐based weighting scheme.Methods:The new objective function contains projection noise model dependent weighting factors and image dependent prior (i.e., a Bayesian term). The noise weighting is view‐by‐view based. For the first time, the FBP algorithm is able to model the projection noise. Based on the formulation of the iterative Landweber MAP algorithm, a frequency‐domain window function is derived for each iteration of the Landweber MAP algorithm. As a result, the ramp filter and the windowing function are both modified by the Bayesian component. This new FBP algorithm can be applied to a projection data set that is not uniformly sampled.Results:Computer simulations show that the new FBP‐MAP algorithm with window function indexk and the iterative Landweber MAP algorithm with iteration number k give similar reconstructions in terms of resolution and noise texture. An example of transmission x‐ray CT shows that the noise modeling method is able to significantly reduce the streaking artifacts associated with low‐dose CT.Conclusions:View‐based noise weighting scheme can be introduced to the FBP algorithm as a weighting factor in the window function. The new FBP algorithm is able to provide similar results to the iterative MAP algorithm if the ramp filter is modified with a additive term. Nonuniform sampling and sensitivity can be accommodated by proper backprojection weighting.
Control of Entamoeba histolytica Adherence Involves Metallosurface Protease 1, an M8 Family Surface Metalloprotease with Homology to Leishmanolysin
Authors: Teixeira Jose E. , Sateriale Adam , Bessoff Kovi E. , Huston Christopher D. 
Published: March 2012

ABSTRACTInvasive amebiasis due toEntamoeba histolyticainfection is an important cause of morbidity in developing countries. TheE. histolyticagenome contains two homologues to the metalloprotease leishmanolysin gene,Entamoeba histolytica MSP-1(EhMSP-1) andEhMSP-2, while the commensal amebaEntamoeba disparhas lostEhMSP-1. In this study, we sought to characterizeE. histolyticametallosurface protease 1 (EhMSP-1). Using immunoprecipitation and a model substrate, we found that EhMSP-1 was a functional metalloprotease. Confocal microscopy and flow cytometry revealed that EhMSP-1 localized to the cell surface and revealed the existence of distinct, nonclonal trophozoite populations with high and low EhMSP-1 surface abundance that became synchronized following serum starvation. Phenotypic assays were performed after silencingEhMSP-1. Adherence of EhMSP-1-deficient trophozoites to tissue culture cell monolayers was more than five times greater than that of control amebas, but surface staining of several antigens, including the galactose adherence lectin, was unchanged.EhMSP-1silencing similarly increased adherence to both viable and apoptotic Jurkat lymphocytes. Tissue culture cell monolayer destruction was reduced byEhMSP-1silencing, although it was blocked almost completely by inhibiting cysteine proteases. Consistent with a primary defect in regulation of amebic adherence,EhMSP-1silencing also resulted in reduced mobility on tissue culture cell monolayers and in increased phagocytosis. In conclusion, EhMSP-1 was shown to be a surface metalloprotease involved in regulation of amebic adherence, with additional effects on cell motility, cell monolayer destruction, and phagocytosis.
Complete Genome Sequence of Lactococcus lactis IO-1, a Lactic Acid Bacterium That Utilizes Xylose and Produces High Levels of
l
-Lactic Acid
Authors: Kato Hiroaki , Shiwa Yuh , Oshima Kenshiro , Machii Miki , Araya-Kojima Tomoko , Zendo Takeshi , Shimizu-Kadota Mariko , Hattori Masahira , Sonomoto Kenji , Yoshikawa Hirofumi 
Published: March 2012

ABSTRACT

We report the complete genome sequence of
Lactococcus lactis
IO-1 (= JCM7638). It is a nondairy lactic acid bacterium, produces nisin Z, ferments xylose, and produces predominantly
l
-lactic acid at high xylose concentrations. From ortholog analysis with other five
L. lactis
strains, IO-1 was identified as
L. lactis
subsp.
lactis
.
Genome Sequence of Paenibacillus sp. Strain Aloe-11, an Endophytic Bacterium with Broad Antimicrobial Activity and Intestinal Colonization Ability
Authors: Li Neng-Zhang , Xia Tian , Xu Ya-Li , Qiu Rong-Rong , Xiang Heng , He Dan , Peng Yuan-Yi 
Published: March 2012

ABSTRACT

Paenibacillus
sp. strain Aloe-11, a Gram-positive, spore-forming, facultatively anaerobic bacterium isolated from the root of
Aloe chinensis
in the southwest region of China, has excellent antibiotic activity and intestine colonization ability. Here, we present the 5.8-Mb draft genome sequence of
Paenibacillus
sp. strain Aloe-11.
Genome Sequence of Extracellular-Protease-Producing Alishewanella jeotgali Isolated from Traditional Korean Fermented Seafood
Authors: Jung Jaejoon , Chun Jongsik , Park Woojun 
Published: March 2012

ABSTRACT

Alishewanella jeotgali
MS1
T
(= KCTC 22429
T
= JCM 15561
T
) was isolated from a traditional Korean fermented seafood, gajami sikhae (jeotgal), and has been reported as a novel species.
A. jeotgali
was proven to have extracellular proteolytic activity, which may play an important role in the fermentation environment of food containing fish flesh. Here, we present the genome sequence of
Alishewanella jeotgali
MS1
T
as the first sequenced strain in the genus
Alishewanella
and its taxonomic relatives.
Real-Time Monitoring of Rare Circulating Hepatocellular Carcinoma Cells in an Orthotopic Model byIn VivoFlow Cytometry Assesses Resection on Metastasis
Authors: Fan Zhi-Chao , Yan Jun , Liu Guang-Da , Tan Xiao-Ying , Weng Xiao-Fu , Wu Wei-Zhong , Zhou Jian , Wei Xun-Bin 
Published: March 2012

AbstractThe fate of circulating tumor cells (CTC) is an important determinant of metastasis and recurrence, which leads to most deaths in hepatocellular carcinoma (HCC). Therefore, quantification of CTCs proves to be an emerging tool for diagnosing, stratifying, and monitoring patients with metastatic diseases. In vivo flow cytometry has the capability to monitor the dynamics of fluorescently labeled CTCs continuously and noninvasively. Here, we combine in vivo flow cytometry technique and a GFP-transfected HCC orthotopic metastatic tumor model to monitor CTC dynamics. Our in vivo flow cytometry has approximately 1.8-fold higher sensitivity than whole blood analysis by conventional flow cytometry. We found a significant difference in CTC dynamics between orthotopic and subcutaneous tumor models. We also investigated whether liver resection promotes or restricts hematogenous metastasis in advanced HCC. Our results show that the number of CTCs and early metastases decreases significantly after the resection. The resection prominently restricts hematogenous metastasis and distant metastases. CTC dynamics is correlated with tumor growth in our orthotopic tumor model. The number and size of distant metastases correspond to CTC dynamics. The novel in vivo flow cytometry technique combined with orthotopic tumor models might provide insights to tumor hematogenous metastasis and guidance to cancer therapy. Cancer Res; 72(10); 2683–91. ©2012 AACR.
Survival of 1,181 Patients in a Phase I Clinic: The MD Anderson Clinical Center for Targeted Therapy Experience
Authors: Wheler Jennifer , Tsimberidou Apostolia M. , Hong David , Naing Aung , Falchook Gerald , Piha-Paul Sarina , Fu Siqing , Moulder Stacy , Stephen Bettzy , Wen Sijin , Kurzrock Razelle 
Published: March 2012

Abstract
Purpose: To determine whether the Royal Marsden Hospital (RMH; London, UK) prognostic score for phase I patients can be validated in a large group of individuals seen in a different center and whether other prognostic variables are also relevant, we present an analysis of 1,181 patients treated in the MD Anderson Cancer Center (MDACC; Houston, TX) phase I clinic.
Experimental Design: Medical records of 1,181 consecutive patients who were treated on at least one trial in the phase I clinic were reviewed.
Results: The median age was 58 years and 50% were women. The median number of prior therapies was four and median survival 10 months [95% confidence interval (CI), 9.1–10.9 months]. Independent factors that predicted shorter survival in a multivariate Cox model and could be internally validated included RMH score of &gt;1 (P &lt; 0.0001; albumin &lt;3.5 g/dL; lactate dehydrogenase &gt;upper limit of normal, and &gt;two sites of metastases), gastrointestinal tumor type (P &lt; 0.0001), and Eastern Cooperative Oncology Group performance status ≥1 (P = 0.0004). The median survival was 24.0, 15.2, 8.4, 6.2, and 4.1 months for patients with 0, 1, 2, 3, and 4 or 5 of the above risk factors, respectively.
Conclusion: The RMH score was validated in a large group of patients at MDACC. Internal validation of the independent prognostic factors for survival led to the development of the MDACC prognostic score, a modification of the RMH score that strengthens it. Clin Cancer Res; 18(10); 2922–9. ©2012 AACR.
Prognostic and Predictive Role of JWA and XRCC1 Expressions in Gastric Cancer
Authors: Wang Shouyu , Wu Xuming , Chen Yansu , Zhang Jianbing , Ding Jingjing , Zhou Yan , He Song , Tan Yongfei , Qiang Fulin , Bai Jin , Zeng Jinyan , Gong Zhenghua , Li Aiping , Li Gang , Røe Oluf Dimitri , Zhou Jianwei 
Published: March 2012

Abstract
Purpose: To investigate the expression pattern and significance of DNA repair genes JWA and X-ray repair cross complement group 1 (XRCC1) in gastric cancer.
Experimental Design: Expressions of JWA and XRCC1 were assessed by immunohistochemistry in a training cohort and they went into a second testing cohort and finally to a validating cohort. Prognostic and predictive role of JWA and XRCC1 expression status in cases treated with surgery alone or combined with adjuvant chemotherapy was evaluated, respectively.
Results: JWA and XRCC1 protein levels were significantly downregulated in gastric cancer lesions compared with adjacent noncancerous tissues. Low tumoral JWA or XRCC1 expression significantly correlated with shorter overall survival (OS), as well as with clinicopathologic characteristics in patients without adjuvant treatment. Multivariate regression analysis showed that low JWA and XRCC1 expressions, separately and together, were independent negative markers of OS. Adjuvant fluorouracil-leucovorin-oxaliplatin (FLO) significantly improved OS compared with surgery alone (log-rank test, P = 0.01). However, this effect was evident only in the JWA or XRCC1 low expression group (HR = 0.44; 95% CI: 0.26–0.73; P = 0.002, and HR = 0.44, 95% CI: 0.26–0.75; P = 0.002, respectively); Adjuvant fluorouracil-leucovorin-platinol (FLP) did not improve OS, except in the patients with low JWA and XRCC1 expressions (P = 0.010 for JWA and 0.024 for XRCC1, respectively).
Conclusions: JWA and XRCC1 protein expressions in tumor are novel candidate prognostic markers and predictive factors for benefit from adjuvant platinum-based chemotherapy (FLO or FLP) in resectable human gastric carcinoma. Clin Cancer Res; 18(10); 2987–96. ©2012 AACR.
Correlation of ERG Expression and DNA Methylation Biomarkers with Adverse Clinicopathologic Features of Prostate Cancer
Authors: Kron Ken , Liu Liyang , Trudel Dominique , Pethe Vaijayanti , Trachtenberg John , Fleshner Neil , Bapat Bharati , van der Kwast Theodorus 
Published: March 2012

Abstract
Purpose: Fusion of the TMPRSS2 gene with the ERG oncogene and aberrant DNA methylation patterns are commonly found in prostate cancer. The aim of this study was to analyze the relationship between ERG expression, DNA methylation of three biomarkers, and clinicopathologic features of prostate cancer.
Experimental Design: Immunohistochemistry for ERG protein was conducted as a surrogate for TMPRSS2-ERG fusions. We analyzed methylation of CYP26A1, TBX15, and HOXD3 in 219 prostatectomy specimens by the quantitative MethyLight assay. DNA methylation was compared between ERG-positive and -negative cases and correlations of ERG and DNA methylation with clinicopathologic features were analyzed using χ2, Spearman correlation, logistic regression, and Cox regression.
Results: ERG expression varied according to Gleason pattern (almost absent in pattern II, highest in pattern III, and lower in pattern IV/V) and showed a strong positive correlation with methylation levels of CYP26A1, TBX15, and HOXD3 (Spearman P &lt; 0.005). TBX15 and HOXD3 methylation were significantly associated with pathologic stage, Gleason score, and Gleason pattern (P ≤ 0.015). In multivariate regression analysis, PSA, TBX15 high methylation, and HOXD3 high methylation were significantly associated with stage (P &lt; 0.05), whereas ERG expression was negatively correlated with Gleason score (P = 0.003). In univariate time-to-recurrence analysis, a combination of HOXD3/TBX15 high methylation predicted recurrence in ERG-positive and -negative cases (P &lt; 0.05).
Conclusions: CYP26A1, TBX15, and HOXD3 are methylation markers of prostate cancer associated with ERG expression and clinicopathologic variables, suggesting that incorporation of these markers may be useful in a pre- and posttreatment clinical setting. Clin Cancer Res; 18(10); 2896–904. ©2012 AACR.
Antitumor Activity of Src Inhibitor Saracatinib (AZD-0530) in Preclinical Models of Biliary Tract Carcinomas
Authors: Cavalloni Giuliana , Peraldo-Neia Caterina , Sarotto Ivana , Gammaitoni Loretta , Migliardi Giorgia , Soster Marco , Marchiò Serena , Aglietta Massimo , Leone Francesco 
Published: March 2012

Abstract
Biliary tract carcinoma (BTC) has a poor prognosis due to limited treatment options. There is, therefore, an urgent need to identify new targets and to design innovative therapeutic approaches. Among potential candidate molecules, we evaluated the nonreceptor tyrosine kinase Src, observing promising antitumor effects of its small-molecule inhibitor saracatinib in BTC preclinical models. The presence of an active Src protein was investigated by immunohistochemistry in 19 surgical samples from patients with BTC. Upon saracatinib treatment, the phosphorylation of Src and of its downstream transducers was evaluated in the BTC cell lines TFK-1, EGI-1, HuH28, and TGBC1-TKB. The effect of saracatinib on proliferation and migration was analyzed in these same cell lines, and its antitumor activity was essayed in EGI-1 mouse xenografts. Saracatinib-modulated transcriptome was profiled in EGI-1 cells and in tumor samples of the xenograft model. Src was activated in about 80% of the human BTC samples. In cultured BTC cell lines, low-dose saracatinib counteracted the activation of Src and of its downstream effectors, increased the fraction of cells in G0–G1 phase, and inhibited cell migration. At high concentrations (median dose from 2.26–6.99 μmol/L), saracatinib was also capable of inhibiting BTC cell proliferation. In vivo, saracatinib treatment resulted in delayed tumor growth, associated with an impaired vascular network. Here, we provide a demonstration that the targeted inhibition of Src kinase by saracatinib is of therapeutic benefit in preclinical models of BTC. We propose our results as a basis for the design of saracatinib-based clinical applications. Mol Cancer Ther; 11(7); 1528–38. ©2012 AACR.
Paying Attention through Eye Movements: A Computational Investigation of the Premotor Theory of Spatial Attention
Authors: Casarotti Marco , Lisi Matteo , Umiltà Carlo , Zorzi Marco 
Published: March 2012

Abstract
Growing evidence indicates that planning eye movements and orienting visuospatial attention share overlapping brain mechanisms. A tight link between endogenous attention and eye movements is maintained by the premotor theory, in contrast to other accounts that postulate the existence of specific attention mechanisms that modulate the activity of information processing systems. The strong assumption of equivalence between attention and eye movements, however, is challenged by demonstrations that human observers are able to keep attention on a specific location while moving the eyes elsewhere. Here we investigate whether a recurrent model of saccadic planning can account for attentional effects without requiring additional or specific mechanisms separate from the circuits that perform sensorimotor transformations for eye movements. The model builds on the basis function approach and includes a circuit that performs spatial remapping using an “internal forward model” of how visual inputs are modified as a result of saccadic movements. Simulations show that the latter circuit is crucial to account for dissociations between attention and eye movements that may be invoked to disprove the premotor theory. The model provides new insights into how spatial remapping may be implemented in parietal cortex and offers a computational framework for recent proposals that link visual stability with remapping of attention pointers.
Observed Structure of Convectively Coupled Waves as a Function of Equivalent Depth: Kelvin Waves and the Madden–Julian Oscillation
Authors: Roundy Paul E. 
Published: March 2012

Abstract
The view that convectively coupled Kelvin waves and the Madden–Julian oscillation (MJO) are distinct modes is tested by regressing data from the Climate Forecast System Reanalysis against satellite outgoing longwave radiation data filtered for particular zonal wavenumbers and frequencies by wavelet analysis. Results confirm that nearly dry Kelvin waves have horizontal structures consistent with their equatorial beta-plane shallow-water-theory counterparts, with westerly winds collocated with the lower-tropospheric ridge, while the MJO and signals along Kelvin wave dispersion curves at low shallow-water-model equivalent depths are characterized by geopotential troughs extending westward from the region of lower-tropospheric easterly wind anomalies through the region of lower-tropospheric westerly winds collocated with deep convection. Results show that as equivalent depth decreases from that of the dry waves (concomitant with intensification of the associated convection), the ridge in the westerlies and the trough in the easterlies shift westward. The analysis therefore demonstrates a continuous field of intermediate structures between the two extremes, suggesting that Kelvin waves and the MJO are not dynamically distinct modes. Instead, signals consistent with Kelvin waves become more consistent with the MJO as the associated convection intensifies. This result depends little on zonal scale. Further analysis also shows how activity in synoptic-scale Kelvin waves characterized by particular phase speeds evolves with the planetary-scale MJO.
A Novel Approach for the High-Resolution Interpolation of In Situ Sea Surface Salinity
Authors: Nardelli Bruno Buongiorno 
Published: March 2012

Abstract
A novel technique for the high-resolution interpolation of in situ sea surface salinity (SSS) observations is developed and tested. The method is based on an optimal interpolation (OI) algorithm that includes satellite sea surface temperature (SST) in the covariance estimation. The covariance function parameters (i.e., spatial, temporal, and thermal decorrelation scales) and the noise-to-signal ratio are determined empirically, by minimizing the root-mean-square error and mean error with respect to fully independent validation datasets. Both in situ observations and simulated data extracted from a numerical model output are used to run these tests. Different filters are applied to sea surface temperature data in order to remove the large-scale variability associated with air–sea interaction, because a high correlation between SST and SSS is expected only at small scales. In the tests performed on in situ observations, the lowest errors are obtained by selecting covariance decorrelation scales of 400 km, 6 days, and 2.75°C, respectively, a noise-to-signal ratio of 0.01 and filtering the scales longer than 1000 km in the SST time series. This results in a root-mean-square error of ~0.11 g kg−1 and a mean error of ~0.01 g kg−1, that is, reducing the errors by ~25% and ~60%, respectively, with respect to the first guess.
Removing the Laser-Chirp Influence from Coherent Doppler Lidar Datasets by Two-Dimensional Deconvolution
Authors: Bühl Johannes , Engelmann Ronny , Ansmann Albert 
Published: March 2012

Abstract
A chirped laser pulse can introduce artifacts into datasets of coherent Doppler wind lidars. At close vicinity of strong signal peaks undesired artificial velocities can be measured and continuous signals can be shifted by a constant factor. It is shown how to remove these artifacts and how to retrieve accurate velocity estimations from both clouds and the planetary boundary layer. Therefore, a two-dimensional deconvolution technique is applied to the wind lidar datasets in order to correct the chirp effect in the range and frequency space. The chirp correction for a 1-h measurement of vertical velocities in the atmosphere is presented. The method is applied to the averaged Doppler spectra. Therefore, no access to the raw heterodyne signal is necessary. The complexity of the data acquisition software and the amount of data to be stored is hereby significantly reduced. Simulations suggest that the remaining velocity error resulting from the laser pulse chirp is smaller than 0.02 m s−1 and chirp-induced artifacts are removed reliably. The method also increases the signal resolution in the range and frequency dimension and can be applied for this intent even if there is no chirp.