bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abnormalities of the TITF-1 Lineage-Specific Oncogene in NSCLC: Implications in Lung Cancer Pathogenesis and Prognosis
Authors: Tang Ximing , Kadara Humam , Behrens Carmen , Liu Diane D , Xiao Yun , Rice David , Gazdar Adi F. , Fujimoto Junya , Moran Cesar , Varella-Garcia Marileila , Lee J Jack , Hong Waun Ki , Wistuba Ignacio I. 
Published: January 2011

Abstract
Purpose: Emerging evidence suggests that aberrant expression of oncogenes contributes to development of lung malignancy. The thyroid transcription factor 1 (TITF-1) gene functions as a lineage survival gene abnormally expressed in a significant fraction of non–small cell lung cancers (NSCLC), in particular lung adenocarcinomas.
Experimental Design: To better characterize TITF-1 abnormality patterns in NSCLC, we studied TITF-1's gene copy number using FISH and quantitative PCR, as well as its protein expression by immunohistochemistry analysis in a tissue microarray comprising surgically resected NSCLC (N = 321) including 204 adenocarcinomas and 117 squamous cell carcinomas (SCC). TITF-1 copy number and protein expression were correlated with patients' clinicopathologic characteristics, and in a subset of adenocarcinomas with EGFR and KRAS mutation status.
Results: We found that increased TITF-1 protein expression was prevalent in lung adenocarcinomas only and was significantly associated with female gender (P &lt; 0.001), never-smokers (P = 0.004), presence of EGFR mutations (P = 0.05), and better overall survival (all stages, P = 0.0478; stages I and II, P = 0.002). TITF-1 copy number gain(CNG) was detected by FISH analysis in both adenocarcinomas (18.9%; high CNG, 8.3%) and SCCs (20.1%; high CNG, 3.0%), and correlated significantly with the protein product (P = 0.004) and presence of KRAS mutations (P = 0.008) in lung adenocarcinomas. Moreover, multivariate analysis revealed that TITF-1 copy number gain was an independent predictor of poor survival of NSCLC (P = 0.039).
Conclusions: Our integrative study demonstrates that the protein versus genomic patterns of TITF-1 have opposing roles in lung cancer prognosis and may occur preferentially in different subsets of NSCLC patients with distinct oncogene mutations. Clin Cancer Res; 17(8); 2434–43. ©2011 AACR.
The Memory Function of Noradrenergic Activity in Non-REM Sleep
Authors: Gais Steffen , Rasch Björn , Dahmen Johannes C. , Sara Susan , Born Jan 
Published: January 2011

AbstractThere is a long-standing assumption that low noradrenergic activity during sleep reflects mainly the low arousal during this brain state. Nevertheless, recent research has demonstrated that the locus coeruleus, which is the main source of cortical noradrenaline, displays discrete periods of intense firing during non-REM sleep, without any signs of awakening. This transient locus coeruleus activation during sleep seems to occur in response to preceding learning-related episodes. In the present study, we manipulate noradrenergic activity during sleep in humans with either the α2-autoreceptor agonist clonidine or the noradrenaline reuptake inhibitor reboxetine. We show that reducing noradrenergic activity during sleep, but not during wakefulness, impairs subsequent memory performance in an odor recognition task. Increasing noradrenergic availability during sleep, in contrast, enhances memory retention. We conclude that noradrenergic activity during non-REM sleep interacts with other sleep-related mechanisms to functionally contribute to off-line memory consolidation.
Forecasting Post-Extratropical Transition Outcomes for Tropical Cyclones Using Support Vector Machine Classifiers
Authors: Felker Steven R. , LaCasse Brian , Tyo J. Scott , Ritchie Elizabeth A. 
Published: January 2011

Abstract
Intensity changes following the multistage process of extratropical transition have proven to be especially difficult to forecast because of the extremely similar storm evolutions prior to and during the first stages of the transformation from a warm-cored axisymmetric tropical storm to a cold-cored asymmetrical extratropical low pressure system. In this study, differences in surrounding synoptic environments between dissipating and reintensifying extratropical transitioning tropical cyclones are used to develop a predictive technique for extratropical transition intensity change that can be used to enhance the standard numerical guidance. Using a set of all historical transitioning storms between 2000 and 2008 in the western North Pacific, common differences between 850-hPa potential temperature fields surrounding extratropical transition intensifiers and extratropical transition dissipaters, respectively, were identified. These features were then used as inputs into a support vector machine classification system in the hopes of creating a robust prediction system. Once the system was trained on a random subset of the data (80%), performance was tested on the remaining test set (20%). Overall, it was found that the prediction system was able to correctly predict extratropical transition intensity outcome in &gt;75% of the test cases at 72 h prior to extratropical transition. This paper discusses the feature selection and classification system used, as well as the performance results, in detail.
Response of the Antarctic Stratosphere to Two Types of El Niño Events
Authors: Hurwitz M. M. , Newman P. A. , Oman L. D. , Molod A. M. 
Published: January 2011

Abstract
This study is the first to identify a robust El Niño–Southern Oscillation (ENSO) signal in the Antarctic stratosphere. El Niño events between 1979 and 2009 are classified as either conventional “cold tongue” events (positive SST anomalies in the Niño-3 region) or “warm pool” events (positive SST anomalies in the Niño-4 region). The 40-yr ECMWF Re-Analysis (ERA-40), NCEP, and Modern Era Retrospective–Analysis for Research and Applications (MERRA) meteorological reanalyses are used to show that the Southern Hemisphere stratosphere responds differently to these two types of El Niño events. Consistent with previous studies, cold tongue events do not impact temperatures in the Antarctic stratosphere. During warm pool El Niño events, the poleward extension and increased strength of the South Pacific convergence zone favor an enhancement of planetary wave activity during September–November. On average, these conditions lead to higher polar stratospheric temperatures and a weakening of the Antarctic polar jet in November and December, as compared with neutral ENSO years. The phase of the quasi-biennial oscillation (QBO) modulates the stratospheric response to warm pool El Niño events; the strongest planetary wave driving events are coincident with the easterly phase of the QBO.
Revisiting Vacillations in Shallow-Water Models of the Stratosphere Using Potential-Vorticity-Based Numerical Algorithms
Authors: MirRokni Seyed Majid , Mohebalhojeh Ali R. , Dritschel David G. 
Published: January 2011

Abstract
Polar vortex vacillations are investigated using long-term simulations of potential-vorticity (PV)-based shallow-water (SW) models for the stratosphere. In the models examined, mechanical forcing is applied through a time-independent topography mimicking tropospheric excitation of the stratosphere. Thermal forcing is applied through a linear relaxation of the mass field to a time-independent equilibrium state mimicking the radiative relaxation taking place in the stratosphere. The SW equations in the PV, velocity divergence, and acceleration divergence representation are solved for a range of resolutions using the “diabatic contour-advective semi-Lagrangian” (DCASL) algorithm and a standard pure semi-Lagrangian (SL) algorithm. Using very different numerical algorithms enables the determination of the degree of numerical sensitivity and the properties of the vacillations with much greater accuracy than in previous related studies.
The focus here is on the Lagrangian or material evolution of the polar vortex. The authors examine quasi-Lagrangian diagnostics based on equivalent latitude, the mass enclosed by PV contours, and the terms involved in its time evolution. The PV field forms the basis for calculating quasi-Lagrangian diagnostics. Variations in the mass enclosed by a PV contour are associated with nonconservative processes such as diabatic heating, friction, and irreversible small-scale mixing. Generally, the mass of the polar vortex increases under the action of diabatic mass fluxes, whereas it decreases under the action of dissipative mass fluxes.
The results herein differ from previous results reported at T42 resolution by Rong and Waugh in which a spectral transform algorithm is used to solve the SW equations in a vorticity–divergence–mass representation, and in which dissipation is provided by explicitly damping vorticity using hyperdiffusion. Except for the first large-amplitude oscillation, there is little sign of a clear, systematic phase shift between the dissipative and diabatic mass fluxes across the edge of the polar vortex, as proposed by Rong and Waugh as the main mechanism responsible for the vacillations. Concomitant with the absence of a phase shift, the vacillations tend to decay and occur intermittently. Rather than a phase shift, inherent fluctuations in both the diabatic and mass fluxes across the edge of the polar vortex appear to be responsible for the vacillations.
The Effect of Satellite Rainfall Error Modeling on Soil Moisture Prediction Uncertainty
Authors: Maggioni Viviana , Reichle Rolf H. , Anagnostou Emmanouil N. 
Published: January 2011

Abstract
This study assesses the impact of satellite rainfall error structure on soil moisture simulations with the NASA Catchment land surface model. Specifically, the study contrasts a complex satellite rainfall error model (SREM2D) with the standard rainfall error model used to generate ensembles of rainfall fields as part of the Land Data Assimilation System (LDAS) developed at the NASA Global Modeling and Assimilation Office. The study is conducted in the Oklahoma region, which offers good coverage by weather radars and in situ meteorological and soil moisture measurement stations. The authors used high-resolution (25 km, 3-hourly) satellite rainfall fields derived from the NOAA/Climate Prediction Center morphing (CMORPH) global satellite product and rain gauge–calibrated radar rainfall fields (considered as the reference rainfall). The LDAS simulations are evaluated in terms of rainfall and soil moisture error. Comparisons of rainfall ensembles generated by SREM2D and LDAS against reference rainfall show that both rainfall error models preserve the satellite rainfall error characteristics across a range of spatial scales. The error structure in SREM2D is shown to generate rainfall replicates with higher variability that better envelop the reference rainfall than those generated by the LDAS error model. Likewise, the SREM2D-generated soil moisture ensemble shows slightly higher spread than the LDAS-generated ensemble and thus better encapsulates the reference soil moisture. Soil moisture errors, however, are less sensitive than precipitation errors to the complexity of the precipitation error modeling approach because soil moisture dynamics are dissipative and nonlinear.
Processing Turbulence Data Collected on board the Helicopter Observation Platform (HOP) with the Empirical Mode Decomposition (EMD) Method
Authors: Holder Heidi E. , Bolch M. Adam , Avissar Roni 
Published: January 2011

Abstract
The Duke University Helicopter Observation Platform (HOP) has previously been shown to be a useful instrument for the measurement of turbulent atmospheric fluxes. As with all such measurements, especially those made from moving platforms, spurious signals, such as instrument noise and mesoscale atmospheric motions, are superposed on the desired signal. Empirical mode decomposition (EMD) is applied in a novel way to identify and separate out different signals represented by intrinsic mode functions (IMFs) in the HOP data and is shown to be an effective tool for the task. The method produces a basis that is adaptive, unique, and orthogonal, all of which are required for this type of data processing, and none of which are present in more traditional techniques. The results of applying EMD are shown to be nonlinear, and occasionally the removal of the correct number of IMFs increases the observed value of energy and fluxes calculated with the eddy correlation technique.
Reconstruction of Aircraft Trajectories from AMDAR Weather Reports
Authors: Drüe Clemens 
Published: January 2011

Abstract
It is well known that aircraft-based meteorological measurements exhibit systematic errors depending on various flight dynamic parameters. It is also widely assumed that operational Aircraft Meteorological Data Relay (AMDAR) weather reports by commercial aircraft are affected in a similar way. However, so far, it is not possible to study such systematic errors, because datasets that contain both AMDAR reports and flight dynamic variables are not available. To overcome this deficiency, a method was developed to reconstruct the flight trajectories of aircraft using just the aircraft type and operational AMDAR reports. Because AMDAR reports do not contain information on the flight plan, origin, destination, or the motion vector of the airplane, it is not possible to employ a trajectory solver as used by air traffic control. Instead, the method uses groups of trajectory templates that are fitted to AMDAR data taken during approach or departure. This algorithm allows estimation of the heading, true airspeed, aircraft mass, roll state, pitch angle, and angle of attack of the reporting aircraft for each AMDAR report. For verification, the algorithm was applied to navigation data gathered from two Airbus-manufactured aircraft, of which one is in commercial service and one is used for aviation research. From a total of 48 profiles, a very good agreement of reconstructed and measured values was found.
Oxidative stress, antioxidant status and lipid profile in the saliva of type 2 diabetics
Authors: Al-Rawi Natheer H 
Published: January 2011

Background: The aim of this study was to assess the salivary content of lipid peroxidation and antioxidants in patients with type 2 diabetes. Method: We studied 25 patients with type 2 diabetes and other 25 age- and sex-matched health control. To evaluate the oxidative status we measured the levels of malondialdehyde (MDA) in the saliva and serum of all participants. Lipid profile was also estimated through measuring total cholesterol, triglycerides, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and very low-density lipoprotein cholesterol (VLDL-C) levels. Antioxidant levels were also assessed through measuring the salivary and serum concentration of uric acid, superoxide dismutase and reduced glutathione (GSH). Results: The high concentration of lipid fractions in saliva usually follows that recorded in serum. Salivary MDA levels, a product of lipid peroxidation, were significantly increased among diabetics together with uric acid. However, GSH levels were similar to those of the control group. Conclusion: Lipid peroxidation and antioxidant parameters assessed in saliva of diabetic patients may be of great importance in evaluating the disease activity and severity. The increase in lipid peroxidation and the tendency of antioxidants to rise in diabetes is probably due to an adaptive response to the pro-oxidant status of diabetes.
Comparative analysis of risk factors for acute graft-versus-host disease and for chronic graft-versus-host disease according to National Institutes of Health consensus criteria
Authors: Flowers Mary E. D. , Inamoto Yoshihiro , Carpenter Paul A. , Lee Stephanie J. , Kiem Hans-Peter , Petersdorf Effie W. , Pereira Shalini E. , Nash Richard A. , Mielcarek Marco , Fero Matthew L. , Warren Edus H. , Sanders Jean E. , Storb Rainer F. , Appelbaum Frederick R. , Storer Barry E. , Martin Paul J. 
Published: January 2011

Abstract
Risk factors for grades 2-4 acute graft-versus-host disease (GVHD) and for chronic GVHD as defined by National Institutes of Health consensus criteria were evaluated and compared in 2941 recipients of first allogeneic hematopoietic cell transplantation at our center. In multivariate analyses, the profiles of risk factors for acute and chronic GVHD were similar, with some notable differences. Recipient human leukocyte antigen (HLA) mismatching and the use of unrelated donors had a greater effect on the risk of acute GVHD than on chronic GVHD, whereas the use of female donors for male recipients had a greater effect on the risk of chronic GVHD than on acute GVHD. Total body irradiation was strongly associated with acute GVHD, but had no statistically significant association with chronic GVHD, whereas grafting with mobilized blood cells was strongly associated with chronic GVHD but not with acute GVHD. Older patient age was associated with chronic GVHD, but had no effect on acute GVHD. For all risk factors associated with chronic GVHD, point estimates and confidence intervals were not significantly changed after adjustment for prior acute GVHD. These results suggest that the mechanisms involved in acute and chronic GVHD are not entirely congruent and that chronic GVHD is not simply the end stage of acute GVHD.
Enhanced Near-Infrared Luminescence of Yb(III) Complexes with Phosphine Oxide and Hexafluoroacetylacetonate Ligands
Authors: Kishimoto Shin-ichiro , Nakagawa Tetsuya , Kawai Tsuyoshi , Hasegawa Yasuchika 
Published: January 2011

Abstract
Near-infrared (NIR) luminescent Yb(III) complexes composed of low-vibrational frequency (LVF) fluorinated acetylacetonate and phosphine oxide ligands are reported. Their structures are determined using X-ray single-crystal analyses and categorized as eight-coordinated square antiprism. The radiative rate constants (kr), the nonradiative rate constants (knr), and the 4f–4f emission quantum efficiency (ΦEm) are estimated using their absorption spectra of magnetic dipole transition in Yb(III) complexes (2F5/2 → 2F7/2) and the observed emission lifetimes. Characteristic NIR luminescence properties of Yb(III) complexes with LVF phosphine oxide and fluorinated acetylacetonate ligands are elucidated in terms of the radiative and nonradiative rate constants.
Design of Functional Nucleic Acid Systems for Biomolecular Analysis
Authors: Sando Shinsuke 
Published: January 2011

Abstract
With the aim of realizing an in situ nucleic acid analysis, we have developed functional nucleic acid probes that can autonomously detect and analyze nucleic acid sequences of interest. Fluorophore-labeled artificial oligonucleotide probes with target-dependent self-ligation or self-digestion functionalities can be used to sense nucleic acids in solution, on solid supports, or even in cells. In addition, we have successfully established a new sensing system using nonmodified nucleic acids as a probe. These probes and sensors are all composed of nonmodified natural-type nucleic acids, and thus can be transcribed directly from dsDNA, giving a high potency for in situ or in-cell application.
Optional screening strategies for cervical cancer using standalone tests and their combinations among low- and medium-income populations in Latin America and Eastern Europe
Authors: Sarian Luis Otavio , Derchain Sophie , Shabalova Irena , Tatti Silvio , Naud Paulo , Longatto-Filho Adhemar , Syrjänen Stina , Syrjänen Kari 
Published: January 2011

Background The performance of cervical cancer (CC) screening can be improved by combining Pap smear with human papillomavirus (HPV) testing or visual methods, addressing local demographic, clinical and economic characteristics. Objectives To examine the performance of standalone and combined screening tools in populations with variable prevalence of cervical intraepithelial neoplasia (CIN) and CC. Methods Merged data-sets from the Latin American Screening Study and New Independent States cohorts provided results for 15,000 women, screened using Pap smear, HPV testing and visual inspection with acetic acid, in Brazil, Argentina, Russia, Belarus and Latvia. Bayesian correction for verification bias was used. Results At CIN2+ cut-off, HPV detection alone was the most sensitive technique. There was an improvement (88.5% to 92.7%) in Hybrid Capture 2 (HC2) sensitivity among women ≥35 years old. Using HPV detection alone was the least specific screening tool, regardless of the age group (69.9% [95% CI 66.5–72.8%] and 86.4% [95% CI 84.6–88.2%], in < or ≥35 years, respectively). Of the test combinations, Pap smear (LSIL threshold) with HC2 had the highest specificity (98.7%; 95% CI 98.3–99.0%). However, in women ≥35 years, the sensitivity of Pap alone was superior to that of the combination. Conclusions The Pap test is a highly specific screening option in populations with medium-range CC prevalence. Combined testing for HPV in this scenario may yield slightly better positive predictive values in women ≥35 years of age with LSIL, but at a high incremental cost.
Is human papillomavirus screening preferable to current policies in vaccinated and unvaccinated women? A cost-effectiveness analysis
Authors: Accetta Gabriele , Biggeri Annibale , Carreras Giulia , Lippi Giuseppe , Carozzi Francesca Maria , Confortini Massimo , Zappa Marco , Paci Eugenio 
Published: January 2011

Objectives Italy was the first European nation to offer free vaccination against human papillomavirus (HPV) types 16 and 18. The vaccination is actively encouraged and is available free of charge to 11-year-old girls. The introduction of new technologies such as HPV DNA testing and HPV vaccination requires cost-effectiveness analysis of cervical cancer strategies in Italy for both vaccinated and unvaccinated women. Methods A calibrated Markov model was developed to describe the natural history of HPV infection and cervical carcinogenesis. We performed a microsimulation generating the life histories of 10 million women. Changes in these life histories occur as consequences of prevention strategies. We estimated costs of screening activities using an activity-based costing analysis. We assessed lifetime risk due to cervical cancer, lifetime costs and quality-adjusted life-expectancy (QALE) for 18 scenarios. Strategies varied by screening interval (three and five years), primary and triage test (Pap test and HPV DNA test), and HPV 16 and 18 vaccination. Results The current screening policy (Pap test every three years) is more costly and less effective than HPV DNA test and Pap test triage every five years. For unvaccinated women an HPV DNA test every five years with a Pap test triage was cost-effective (ICER €5753/QALE). Vaccination followed by the same screening strategy was cost-effective (ICER €23,951/QALE) for women who are eligible to be vaccinated. Conclusions Our findings strongly support changing the Pap screening policy to the use of HPV DNA as a primary test with Pap test triage for both vaccinated and unvaccinated women.