bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optical properties of pure and TM-doped single-walled ZnO nanotubes (8,0) (TM = V and Co) by first principles calculations
Authors: Mendi R. Taghavi , Sarmazdeh M. Majidiyan , Boochani A. , Elahi S. M. , Naderi S. 
Published: January 2016

In this paper, some optical properties of pure and transition metal-doped (TM = Co and V) single-walled ZnO nanotubes (8,0) (SWZnONT(8,0)) such as, real and imaginary parts of the dielectric function, optical conductivity, refractive index and optical reflectivity, were investigated. The calculations have been performed within framework of the density functional theory (DFT) using the full potential linearized augmented plane wave (FP-LAPW) and the generalized gradient approximation (GGA). The results show that, optical properties of SWZnONT(8,0) are anisotropic, especially at low energies and this anisotropy at low energies increases with doping of V in SWZnONT(8,0) while the Co-doped SWZnONT(8,0) behaves like pure SWZnONT(8,0). Doping of ZnO nanotubes has a significant impact on the value of the dielectric constant, so that due to the presence of V atom, the dielectric constant is increased up to three times. Study of the imaginary part of the dielectric function and optical conductivity showed that the important energy range for absorption processes and optical transitions is low energy range to 15 eV. The optical transitions have been studied based on band structure and density of states. The results of the optical reflectivity showed that these nanotubes are transparent in a wide energy ranges which provide them for using in transparent coatings. In addition, due to the reported magnetic properties for V- and Co-doped ZnO nanotubes, these nanotubes are suitable for using in spintronics and magneto-optic devices.
Active waveguides by low-fluence carbon implantation in Nd3+-doped fluorophosphate glasses
Authors: Liu Chun-Xiao , Luo Zhe-Yuan , Li Yu-Wen , Chen Meng , Xu Jun , Fu Li-Li , Yu Ke-Han , Zheng Rui-Lin , Zhou Zhi-Guang , Li Wei-Nan , Guo Hai-Tao , Lin She-Bao , Wei Wei 
Published: January 2016

A planar waveguide in the Nd[Formula: see text]-doped fluorophosphate glass is fabricated by a 6.0 MeV C[Formula: see text] ion implantation at a low-fluence of [Formula: see text] ions/cm2. The fluence is close to that in semiconductor industry. The dark mode spectra are recorded by a model 2010 prism coupler. The energy losses during the implantation process and the refractive index profile of the waveguide are simulated by the SRIM 2010 code and the reflectivity calculation method (RCM), respectively. The near-field light intensity profile and the propagation loss of the waveguide are measured by an end-face coupling system. The two-dimensional (2D) modal profile of transverse electric (TE) mode for the fabricated waveguide is calculated by the finite difference beam propagation method (FD-BPM). The results of microluminescence and optical absorption reveal that the spectroscopic characteristics of the Nd[Formula: see text]-doped fluorophosphate glass are nearly unaffected by the carbon ion implantation process. This work suggests that the carbon-implanted Nd[Formula: see text]-doped fluorophosphate glass waveguide is a promising candidate for integrated active devices.
Semi-supervised learning using ensembles of multiple 1D-embedding-based label boosting
Authors: Wang Jianzhong 
Published: January 2016

The paper continues the development of the multiple 1D-embedding-based (or, 1D multi-embedding) methods for semi-supervised learning, which is preliminarily introduced by the author in [J. Wang, Semi-supervised learning using multiple one-dimensional embedding based adaptive interpolation, Int. J. Wavelets, Multiresolut. Inform Process. 14(2) (2016) 11 pp.]. This paper puts the development in a more general framework and creates a new method, which employs the ensemble technique to integrate multiple 1D embedding-based regularization and label boosting for semi-supervised learning (SSL). It combines parallel ensemble and serial ensemble. In each stage of parallel ensemble, the dataset is first smoothly mapped onto multiple 1D sequences. On each 1D embedded data, a classical regularization method is applied to construct a weak classifier. All of these weak classifiers are then integrated to an ensemble of 1D labeler (E1DL), which together with a nearest neighbor cluster (NNC) algorithm extracts a newborn labeled subset from the unlabeled set. The subset is believed to be correctly labeled with a high confidence, so that it joins with the original labeled set for the next learning stage. Repeating this process, we gradually obtain a boosted labeled set and the process will not stopped until the updated labeled set reaches a certain size. Finally, we use E1DL to build the target classifier, which labels all points of the dataset. In this paper, we also set the universal parameters for all experiments to make the algorithm as a parameter-free one. The validity of our method in the classification of the handwritten digits is confirmed by several experiments. Comparing to several other popular SSL methods, our results are very promising.
An Endothelial Gene Signature Score Predicts Poor Outcome in Patients with Endocrine-Treated, Low Genomic Grade Breast Tumors
Authors: Tobin Nicholas P. , Wennmalm Kristian , Lindström Linda S. , Foukakis Theodoros , He Liqun , Genové Guillem , Östman Arne , Landberg Göran , Betsholtz Christer , Bergh Jonas 
Published: January 2016

Abstract
Purpose: The ability of vascular genes to provide treatment predictive information in breast cancer patients remains unclear. As such, we assessed the expression of genes representative of normal endothelial microvasculature (MV) in relation to treatment-specific patient subgroups.
Experimental Design: We used expression data from 993 breast tumors to assess 57 MV genes (summarized to yield an MV score) as well as the genomic grade index (GGI) and PAM50 signatures. MV score was compared with CD31 staining by correlation and gene ontology (GO) analysis, along with clinicopathologic characteristics and PAM50 subtypes. Uni-, multivariate, and/or t-test analyses were performed in all and treatment-specific subgroups, along with a clinical trial cohort of patients with metastatic breast cancer, seven of whom received antiangiogenic therapy.
Results: MV score did not correlate with microvessel density (correlation = 0.096), but displayed enrichment for angiogenic GO terms, and was lower in Luminal B tumors. In endocrine-treated patients, a high MV score was associated with decreased risk of metastasis [HR 0.58; 95% confidence interval (CI), 0.38–0.89], even after adjusting for histologic grade, but not GGI or PAM50. Subgroup analysis showed the prognostic strength of the MV score resided in low genomic grade tumors and MV score was significantly increased in metastatic breast tumors after treatment with sunitinib + docetaxel (P = 0.031).
Conclusions: MV score identifies two groups of better and worse survival in low-risk endocrine-treated breast cancer patients. We also show normalization of tumor vasculature on a transcriptional level in response to an angiogenic inhibitor in human breast cancer samples. Clin Cancer Res; 22(10); 2417–26. ©2016 AACR.
Not all NOTCH Is Created Equal: The Oncogenic Role of NOTCH2 in Bladder Cancer and Its Implications for Targeted Therapy
Authors: Hayashi Tetsutaro , Gust Kilian M. , Wyatt Alexander W. , Goriki Akihiro , Jäger Wolfgang , Awrey Shannon , Li Na , Oo Htoo Zarni , Altamirano-Dimas Manuel , Buttyan Ralph , Fazli Ladan , Matsubara Akio , Black Peter C. 
Published: January 2016

Abstract
Purpose: Recent molecular analyses of bladder cancer open the door to significant advances in targeted therapies. NOTCH has been identified as a tumor suppressor in bladder cancer, but prior reports have focused on NOTCH1. Here we hypothesized that NOTCH2 is an oncogene suitable for therapeutic targeting in bladder cancer.
Experimental design: We studied genomic aberrations of NOTCH, compared survival and tumor progression according to NOTCH2 expression levels, and studied NOTCH2 function in vitro and vivo.
Results: We report a high rate of NOTCH2 copy number gain in bladder cancer. High NOTCH2 expression was identified especially in the basal subtype and in mesenchymal tumors. NOTCH2 activation correlated with adverse disease parameters and worse prognosis by immunohistochemistry. Forced overexpression of the intracellular domain of NOTCH2 (N2ICD) induced cell growth and invasion by cell-cycle progression, maintenance of stemness and epithelial-to-mesenchymal transition (EMT). These effects were abrogated by silencing of CSL, indicating that the effects were mediated through the canonical NOTCH signaling pathway. In an orthotopic xenograft model, forced overexpression of N2ICD increased growth, invasion, and metastasis. To explore the potential for therapeutic targeting of NOTCH2, we first silenced the receptor with shRNA and subsequently treated with a specific inhibitory antibody. Both interventions decreased cell growth, invasion, and metastasis in vitro and in the orthotopic xenograft model.
Conclusions: We have demonstrated that NOTCH2 acts as an oncogene that promotes bladder cancer growth and metastasis through EMT, cell-cycle progression, and maintenance of stemness. Inhibition of NOTCH2 is a rational novel treatment strategy for invasive bladder cancer. Clin Cancer Res; 22(12); 2981–92. ©2016 AACR.
Choline Kinase Alpha (CHKα) as a Therapeutic Target in Pancreatic Ductal Adenocarcinoma: Expression, Predictive Value, and Sensitivity to Inhibitors
Authors: Mazarico José M. , Sánchez-Arévalo Lobo Victor J. , Favicchio Rosy , Greenhalf William , Costello Eithne , Carrillo-de Santa Pau Enrique , Marqués Miriam , Lacal Juan C. , Aboagye Eric , Real Francisco X. 
Published: January 2016

Abstract
Choline kinase α (CHKα) plays a crucial role in the regulation of membrane phospholipid synthesis and has oncogenic properties in vitro. We have analyzed the expression of CHKα in cell lines derived from pancreatic ductal adenocarcinoma (PDAC) and have found increased CHKα expression, associated with differentiation. CHKα protein expression was directly correlated with sensitivity to MN58b, a CHKα inhibitor that reduced cell growth through the induction of apoptosis. Accordingly, CHKα knockdown led to reduced drug sensitivity. In addition, we found that gemcitabine-resistant PDAC cells displayed enhanced sensitivity to CHKα inhibition and, in vitro, MN58b had additive or synergistic effects with gemcitabine, 5-fluorouracil, and oxaliplatin, three active drugs in the treatment of PDAC. Using tissue microarrays, CHKα was found to be overexpressed in 90% of pancreatic tumors. While cytoplasmic CHKα did not relate to survival, nuclear CHKα distribution was observed in 43% of samples and was associated with longer survival, especially among patients with well/moderately differentiated tumors. To identify the mechanisms involved in resistance to CHKα inhibitors, we cultured IMIM-PC-2 cells with increasingly higher concentrations of MN58b and isolated a subline with a 30-fold higher IC50. RNA-Seq analysis identified upregulation of ABCB1 and ABCB4 multidrug resistance transporters, and functional studies confirmed that their upregulation is the main mechanism involved in resistance. Overall, our findings support the notion that CHKα inhibition merits further attention as a therapeutic option in patients with PDAC and that expression levels may predict response. Mol Cancer Ther; 15(2); 323–33. ©2016 AACR.
Congenital Heart Defects and Indices of Fetal Cerebral Growth in a Nationwide Cohort of 924 422 Liveborn Infants
Authors: Matthiesen Niels B. , Henriksen Tine B. , Gaynor J. William , Agergaard Peter , Bach Cathrine C. , Hjortdal Vibeke E. , Østergaard John R. 
Published: January 2016

Background—
Neurodevelopmental disorders are the most common and distressful comorbidities associated with congenital heart defects (CHD). Head circumference at birth (HC), a proxy for prenatal cerebral growth, is an established risk factor for neurodevelopmental disorders.

Methods and Results—

In a nationwide cohort, we included all 924 422 liveborn Danish singletons, 1997 to 2011. CHD was present in 5519. The association between CHD and growth indices was analyzed by multivariable linear regression, adjusted for potential confounders. We report mean differences in gestational age–specific
z
scores in comparison with the general population. CHD was associated with lower HC
z
scores, –0.10 (95% confidence interval [CI], –0.13 to –0.08). Several CHD subtypes were associated with smaller HC, eg, hypoplastic left heart syndrome, –0.39 (95% CI, –0.58 to –0.21); common arterial trunk, –0.41 (95% CI, –0.74 to –0.09); and major ventricular septal defects, –0.25 (95% CI, –0.35 to –0.15). Other single-ventricle defects, transposition of the great arteries, tetralogy of Fallot, and anomalous pulmonary venous return, were also associated with smaller HC. Transposition of the great arteries was associated with smaller HC relative to birth weight, –0.26 (95% CI, –0.39 to –0.13). Major ventricular septal defects were associated with larger HC relative to birth weight. The results were consistent under various conditions, eg, when siblings of infants with CHD (n=5311) or infants with other major malformations (n=24 974) were used as the reference.

Conclusions—
Several subtypes of CHD were associated with smaller HC. The associations with major ventricular septal defects, common arterial trunk, and anomalous pulmonary venous return have not previously been described. Only infants with transposition of the great arteries had smaller HC relative to birth weight.
Thrombus Length Estimation on Delayed Gadolinium–Enhanced T1
Authors: Yan Shenqiang , Chen Qingmeng , Xu Mengjun , Sun Jianzhong , Liebeskind David S. , Lou Min 
Published: January 2016

Background and Purpose—
Previous studies revealed a close relationship between thrombus length and recanalization rate after intravenous thrombolysis (IVT). As a novel approach, we prospectively adjusted the order of sequence acquisition to obtain delayed gadolinium–enhanced T1 (dGE-T1) and thereby assess thrombus length on dGE-T1 to evaluate its predictive value for recanalization after IVT.

Methods—
We reviewed prospectively collected clinical and imaging data from acute ischemic stroke patients with middle cerebral artery occlusion who underwent multimodal magnetic resonance imaging before and 24 hours after IVT. Perfusion-weighted imaging was performed followed by conventional T1. We measured thrombus length on dGE-T1 and examined its association with middle cerebral artery recanalization.

Results—

Of the included 74 patients, the median age was 66 years and 28 (37.8%) were women. Thrombus length was 8.18±4.56 mm on dGE-T1, which was an acceptable predictor for no recanalization (odds ratio, 1.196; 95% confidence interval, 1.015–1.409;
P
=0.033), with a receiver–operator characteristic of 0.732 (95% confidence interval, 0.619–0.845;
P
=0.001). The optimal cut-off point was identified at 6.77 mm, which yielded a sensitivity of 77.8%, a specificity of 57.9%, and an odds ratio of 4.81 (95% confidence interval, 1.742–13.292;
P
=0.002). Moreover, no one achieved recanalization after IVT when length of thrombus exceeded 14 mm on dGE-T1.

Conclusions—
The dGE-T1, obtained by simply adjusting scanning order in multimodal magnetic resonance imaging protocol, is a useful tool for thrombus length estimation and middle cerebral artery recanalization prediction after IVT.
Perspectives on Moist Baroclinic Instability: Implications for the Growth of Monsoon Depressions
Authors: Cohen Naftali Y. , Boos William R. 
Published: January 2016

AbstractLittle is known about the genesis and growth mechanisms of monsoon depressions, despite the great importance of these storms for the hydrological cycle of the Asian–Australian monsoon region. Of the few theoretical studies that have examined this issue, most have attributed the amplification of monsoon depressions to some form of baroclinic instability or stable baroclinic growth, highly modified by the diabatic effects of moist convection. Here, a simple criterion—namely, the upshear tilt of potential vorticity anomalies—is argued be necessary for dry or moist baroclinic growth. Reanalysis data are then used to assess whether a large ensemble of South Asian monsoon depressions has vertical structures consistent with this criterion. The evolution of these monsoon depressions is compared with that of ensembles of hurricanes and diabatic Rossby waves, the latter being prototypical examples of moist baroclinic instability. During their amplification phase, monsoon depressions do not exhibit an upshear tilt of potential vorticity anomalies. Many similarities are found between developing monsoon depressions and hurricanes but few with diabatic Rossby waves. Thus, the mechanism responsible for the intensification of monsoon depressions remains unknown, but these results indicate greater similarity with the general process of tropical depression spinup than with moist convectively coupled baroclinic instability.
Response of Tropical Cyclone Tracks to Sea Surface Temperature in the Western North Pacific
Authors: Katsube Kotaro , Inatsu Masaru 
Published: January 2016

Abstract
A set of short-term experiments using a regional atmospheric model (RAM) were carried out to investigate the response of tropical cyclone (TC) tracks to sea surface temperature (SST) in the western North Pacific. For 10 selected TC cases occurring during 2002–07, a warm and a cold run are performed with 2 and −2 K added to the SSTs uniformly over the model domain, respectively. The cases can be classified into three groups in terms of recurvature: recurved tracks in the warm and cold runs, a recurved track in the warm run and a nonrecurved track in the cold run, and nonrecurved tracks in both runs. Commonly the warm run produced northward movement of the TC faster than the cold run. The rapid northward migration can be mainly explained by the result that cyclonic circulation to the west of the TC is found in the steering flow in the warm run and it is not in the cold run. The beta effect is also activated under the warm SST environment. For the typical TC cases, a linear baroclinic model experiment is performed to examine how the cyclonic circulation is intensified in the warm run. The stationary linear response to diabatic heating obtained from the RAM experiment reveals that the intensified TC by the warm SST excites the cyclonic circulation in the lower troposphere to the west of the forcing position. The vorticity and thermodynamic equation analysis shows the detailed mechanism. The time scale of the linear response and the teleconnection are also discussed.
Taking into Account Atmospheric Uncertainty Improves Sequential Assimilation of SMOS Sea Ice Thickness Data in an Ice–Ocean Model
Authors: Yang Qinghua , Losch Martin , Losa Svetlana N. , Jung Thomas , Nerger Lars 
Published: January 2016

AbstractThe sensitivity of assimilating sea ice thickness data to uncertainty in atmospheric forcing fields is examined using ensemble-based data assimilation experiments with the Massachusetts Institute of Technology General Circulation Model (MITgcm) in the Arctic Ocean during November 2011–January 2012 and the Met Office (UKMO) ensemble atmospheric forecasts. The assimilation system is based on a local singular evolutive interpolated Kalman (LSEIK) filter. It combines sea ice thickness data derived from the European Space Agency’s (ESA) Soil Moisture Ocean Salinity (SMOS) satellite and Special Sensor Microwave Imager/Sounder (SSMIS) sea ice concentration data with the numerical model. The effect of representing atmospheric uncertainty implicit in the ensemble forcing is assessed by three different assimilation experiments. The first two experiments use a single deterministic forcing dataset and a different forgetting factor to inflate the ensemble spread. The third experiment uses 23 members of the UKMO atmospheric ensemble prediction system. It avoids additional ensemble inflation and is hence easier to implement. As expected, the model-data misfits are substantially reduced in all three experiments, but with the ensemble forcing the errors in the forecasts of sea ice concentration and thickness are smaller compared to the experiments with deterministic forcing. This is most likely because the ensemble forcing results in a more plausible spread of the model state ensemble, which represents model uncertainty and produces a better forecast.
The determination of serum and urinary endocan concentrations in patients with bladder cancer
Authors: Laloglu Esra , Aksoy Hulya , Aksoy Yılmaz , Ozkaya Fatih , Akcay Fatih 
Published: January 2016

Background Endocan (endothelial cell-specific molecule-1) is a proteoglycan and plays an important role in angiogenesis and inflammation. The aim of this study was to evaluate of serum and urinary concentrations of endothelial cell-specific molecule-1 in bladder cancer. Methods The study included 50 bladder cancer patients, 50 with urinary tract infection and 51 healthy volunteers. Serum and urinary endothelial cell-specific molecule-1 concentrations were measured with enzyme linked immunosorbent assay. Results In bladder cancer group, serum and urinary endothelial cell-specific molecule-1 concentrations were significantly higher than in the healthy subjects ( P = 0.003 and P < 0.0001). Urinary endothelial cell-specific molecule-1 concentrations in cases with urinary tract infection were higher than in healthy volunteers ( P = 0.002). There were no significant differences between bladder cancer and urinary tract infection groups in terms of serum and urinary endothelial cell-specific molecule-1 concentrations. Urinary endothelial cell-specific molecule-1 concentrations were higher than those of corresponding serum endothelial cell-specific molecule-1 concentrations ( P < 0.0001 for bladder cancer and urinary tract infection groups, P = 0.002 for healthy subjects). In bladder cancer group, there was a positive correlation between serum endothelial cell-specific molecule-1 and urinary endothelial cell-specific molecule-1 concentrations ( r = 0.32, P = 0.002). For serum endothelial cell-specific molecule-1, sensitivity and specificity were 50%, and 77%, and for urinary endothelial cell-specific molecule-1, 62%, and 71%, respectively. Conclusion Serum and urinary endothelial cell-specific molecule-1 concentrations increase in bladder cancer. This parameter also increases in serum and urine of cases with urinary tract infection. That urinary endothelial cell-specific molecule-1 values were higher than serum endothelial cell-specific molecule-1 values in all groups may be attributed to direct exfoliation of epithelial cells in bladder to urine.