bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonlinear Cascades of Surface Oceanic Geostrophic Kinetic Energy in the Frequency Domain*
Authors: Arbic Brian K. , Scott Robert B. , Flierl Glenn R. , Morten Andrew J. , Richman James G. , Shriver Jay F. 
Published: April 2012

Abstract
Motivated by the ubiquity of time series in oceanic data, the relative lack of studies of geostrophic turbulence in the frequency domain, and the interest in quantifying the contributions of intrinsic nonlinearities to oceanic frequency spectra, this paper examines the spectra and spectral fluxes of surface oceanic geostrophic flows in the frequency domain. Spectra and spectral fluxes are computed from idealized two-layer quasigeostrophic (QG) turbulence models and realistic ocean general circulation models, as well as from gridded satellite altimeter data. The frequency spectra of the variance of streamfunction (akin to sea surface height) and of geostrophic velocity are qualitatively similar in all of these, with substantial variance extending out to low frequencies. The spectral flux Π(ω) of kinetic energy in the frequency ω domain for the QG model documents a tendency for nonlinearity to drive energy toward longer periods, in like manner to the inverse cascade toward larger length scales documented in calculations of the spectral flux Π(k) in the wavenumber k domain. Computations of Π(ω) in the realistic model also display an “inverse temporal cascade.” In satellite altimeter data, some regions are dominated by an inverse temporal cascade, whereas others exhibit a forward temporal cascade. However, calculations performed with temporally and/or spatially filtered output from the models demonstrate that Π(ω) values are highly susceptible to the smoothing inherent in the construction of gridded altimeter products. Therefore, at present it is difficult to say whether the forward temporal cascades seen in some regions in altimeter data represent physics that is missing in the models studied here or merely sampling artifacts.
Exploring the relevance of autonomy and relatedness for mental health in healthy and depressed women from two different cultures: When does culture matter?
Authors: Balkir Nazli , Arens Elisabeth A , Barnow Sven 
Published: April 2012

Background: It is well known that the absence of both autonomy and social support (relatedness) are two important etiologic pathways to major depressive disorder (MDD). However, cross-cultural researchers state that the implications of autonomy and relatedness for mental health vary across cultures. Aim: To test these assumptions, the current study investigated the relevance of autonomy and relatedness for mental health in healthy and depressed women from two different cultures (Germans and Turkish immigrants in Germany). Methods: One hundred and eight (108) women were evaluated for their levels of autonomy/relatedness satisfaction, for overall psychopathological complaints including depression, for affectivity and for perceived loneliness through self-report measures. Results: Among healthy groups, relatedness satisfaction predicted better mental health in Turkish women, whereas in German women, autonomy satisfaction was the better mental health predictor. Within depressed groups however, cultural differences in mental health outcomes regarding autonomy were no longer evident. Autonomy was associated with higher levels of mental health in Turkish as well as in German patients. Conclusions: Our findings indicate that the relationship between autonomy and mental health is culture-specific in healthy women, but disappears in depressed women. These findings are discussed with consideration of clinical implications and an outlook regarding further research.
Cytotoxicity of different sized TiO2 nanoparticles in mouse macrophages
Authors: Zhang Jinyang , Song Wenhua , Guo Jing , Zhang Jinhua , Sun Zengtian , Li Liying , Ding Feng , Gao Minling 
Published: April 2012

With large-scale production and wide application of nano-titanium oxide (TiO2), its health hazard has attracted extensive attention worldwide. In this study, mouse macrophages (Ana-1 and MH-S cells) were used to evaluate the cytotoxicity of different sized TiO2 nanoparticles. The results showed that TiO2 nanoparticles caused low toxicity, especially in MH-S cells. There was a difference in the cytotoxicity induced by different sized TiO2 particles. The 25 nm anatase particles induced the strongest cytotoxicity and oxidative stress, followed by 5 and 100 nm anatase particles; in contrast, 100 nm rutile particles induced the lowest toxicity. Although TiO2 nanoparticles induced high levels of intracellular reactive oxygen species (ROS), the determination of ROS demonstrated that the inherent oxidative capacity of TiO2 nanoparticles was lower in the absence of photoactivation. Therefore, the generation of intracellular ROS could not completely depend on inherent oxidative capacity of TiO2 nanoparticles. Toxicity of TiO2 nanoparticles could mainly depend on the structural characteristics.
Acute demyelinating lesions with restricted diffusion in multiple sclerosis
Authors: Balashov Konstantin E , Lindzen Eric 
Published: April 2012

Background and objectives: It is widely accepted that typical acute demyelinating lesions in relapsing–remitting multiple sclerosis (RRMS) exhibit vasogenic edema with increased diffusion, as demonstrated by an increased apparent diffusion coefficient on MRI. In contrast, acute ischemic lesions demonstrate cytotoxic edema with restricted diffusion. Recent reports have documented selected cases of acute demyelinating lesions exhibiting restricted diffusion (ADLRD) in MS. We aimed to assess the morphologies, distributions, signal characteristics and changes over time of nine ADLRD. An additional goal was to obtain clinical correlations and relate our findings to all previously published case reports describing ADLRD. Methods: A retrospective case series study was performed at two academic centers. MRI characteristics of nine ADLRD found in six RRMS patients were compared with typical active symptomatic contrast-enhancing lesions with increased or normal diffusion in control RRMS patients. Results: The average size of ADLRD was not significantly different from typical lesions. A periventricular location and faint signal on T2-weighted images were significantly more common for ADLRD compared with typical lesions. Two patients with ADLRD on initial MRI exhibited new ADLRD on their follow up scans. Conclusion: Our results and review of prior published cases suggest that ADLRD represent a new variant of MS lesion. The restricted diffusion that is a characteristic of ADLRD on MRI is a new challenge in the differential diagnosis of stroke in young adults. The pathogenesis of ADLRD remains to be understood.
Definitions, methodological and statistical issues for phase 3 clinical trials in chronic myeloid leukemia: a proposal by the European LeukemiaNet
Authors: Guilhot Joëlle , Baccarani Michele , Clark Richard E. , Cervantes Francisco , Guilhot François , Hochhaus Andreas , Kulikov Sergei , Mayer Jiri , Petzer Andreas L. , Rosti Gianantonio , Rousselot Philippe , Saglio Giuseppe , Saussele Susanne , Simonsson Bengt , Steegmann Juan-Luis , Zaritskey Andrey , Hehlmann Rüdiger 
Published: April 2012

Abstract
The treatment policy of chronic myeloid leukemia (CML), particularly with tyrosine kinase inhibitors, has been influenced by several recent studies that were well designed and rapidly performed, but their interpretation is of some concern because different end points and methodologies were used. To understand and compare the results of the previous and future studies and to translate their conclusion into clinical practice, there is a need for common definitions and methods for analyses of CML studies. A panel of experts was appointed by the European LeukemiaNet with the aim of developing a set of definitions and recommendations to be used in design, analyses, and reporting of phase 3 clinical trials in this disease. This paper summarizes the consensus of the panel on events and major end points of interest in CML. It also focuses on specific issues concerning the intention-to-treat principle and longitudinal data analyses in the context of long-term follow-up. The panel proposes that future clinical trials follow these recommendations.
BactQuant: An enhanced broad-coverage bacterial quantitative real-time PCR assay
Authors: Liu Cindy M , Aziz Maliha , Kachur Sergey , Hsueh Po-Ren , Huang Yu-Tsung , Keim Paul , Price Lance B 
Published: April 2012

Abstract

Background
Bacterial load quantification is a critical component of bacterial community analysis, but a culture-independent method capable of detecting and quantifying diverse bacteria is needed. Based on our analysis of a diverse collection of 16 S rRNA gene sequences, we designed a broad-coverage quantitative real-time PCR (qPCR) assay—BactQuant—for quantifying 16 S rRNA gene copy number and estimating bacterial load. We further utilized in silico evaluation to complement laboratory-based qPCR characterization to validate BactQuant.

Methods
The aligned core set of 4,938 16 S rRNA gene sequences in the Greengenes database were analyzed for assay design. Cloned plasmid standards were generated and quantified using a qPCR-based approach. Coverage analysis was performed computationally using >670,000 sequences and further evaluated following the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines.

Results
A bacterial TaqMan® qPCR assay targeting a 466 bp region in V3-V4 was designed. Coverage analysis showed that 91% of the phyla, 96% of the genera, and >80% of the 89,537 species analyzed contained at least one perfect sequence match to the BactQuant assay. Of the 106 bacterial species evaluated, amplification efficiencies ranged from 81 to 120%, with r

2
-value of >0.99, including species with sequence mismatches. Inter- and intra-run coefficient of variance was <3% and <16% for Ct and copy number, respectively.

Conclusions
The BactQuant assay offers significantly broader coverage than a previously reported universal bacterial quantification assay BactQuant in vitro performance was better than the in silico predictions.
Cost-effectiveness analysis of neonatal hearing screening program in china: should universal screening be prioritized?
Authors: Huang Li-Hui , Zhang Luo , Tobe Ruo-Yan Gai , Qi Fang-Hua , Sun Long , Teng Yue , Ke Qing-Lin , Mai Fei , Zhang Xue-Feng , Zhang Mei , Yang Ru-Lan , Tu Lin , Li Hong-Hui , Gu Yan-Qing , Xu Sai-Nan , Yue Xiao-Yan , Li Xiao-Dong , Qi Bei-Er , Cheng Xiao-Huan , Tang Wei , Xu Ling-Zhong , Han De-Min 
Published: April 2012

Abstract

Background
Neonatal hearing screening (NHS) has been routinely offered as a vital component of early childhood care in developed countries, whereas such a screening program is still at the pilot or preliminary stage as regards its nationwide implementation in developing countries. To provide significant evidence for health policy making in China, this study aims to determine the cost-effectiveness of NHS program implementation in case of eight provinces of China.

Methods
A cost-effectiveness model was conducted and all neonates annually born from 2007 to 2009 in eight provinces of China were simulated in this model. The model parameters were estimated from the established databases in the general hospitals or maternal and child health hospitals of these eight provinces, supplemented from the published literature. The model estimated changes in program implementation costs, disability-adjusted life years (DALYs), average cost-effectiveness ratio (ACER), and incremental cost-effectiveness ratio (ICER) for universal screening compared to targeted screening in eight provinces.

Results and discussion
A multivariate sensitivity analysis was performed to determine uncertainty in health effect estimates and cost-effectiveness ratios using a probabilistic modeling technique. Targeted strategy trended to be cost-effective in Guangxi, Jiangxi, Henan, Guangdong, Zhejiang, Hebei, Shandong, and Beijing from the level of 9%, 9%, 8%, 4%, 3%, 7%, 5%, and 2%, respectively; while universal strategy trended to be cost-effective in those provinces from the level of 70%, 70%, 48%, 10%, 8%, 28%, 15%, 4%, respectively. This study showed although there was a huge disparity in the implementation of the NHS program in the surveyed provinces, both universal strategy and targeted strategy showed cost-effectiveness in those relatively developed provinces, while neither of the screening strategy showed cost-effectiveness in those relatively developing provinces. This study also showed that both strategies especially universal strategy achieve a good economic effect in the long term costs.

Conclusions
Universal screening might be considered as the prioritized implementation goal especially in those relatively developed provinces of China as it provides the best health and economic effects, while targeted screening might be temporarily more realistic than universal screening in those relatively developing provinces of China.
Food intake profiles of children aged 12, 24 and 48 months from the 2004 Pelotas (Brazil) birth cohort: an exploratory analysis using principal components
Authors: Gatica Giovanna , Barros Aluisio J D , Madruga Samanta , Matijasevich Alicia , Santos Iná S 
Published: April 2012

Abstract

Objectives
To identify food intake profiles of children during their first four years of life and assess its variations according to sociodemographic and behavioral characteristics.

Methods
The Pelotas Birth Cohort Study (Brazil) recruited 4,231 liveborns, who were followed-up at ages 3, 12, 24 and 48 months. Food consumption data of children aged 12, 24 and 48 months was collected using a list of foods consumed during a 24-hour period prior to the interview. The food profiles were identified with the use of principal component analysis (PCA) for each age studied.

Results
Five components were identified at each age, four of them similar in all time points, namely: beverages, milks, staple, and snacks. A meat & vegetables component was identified at 12 and 24 months and a treats component at 48 months. The greatest nutritional differences were found among children from different socioeconomic levels. With regard to the milks component, higher breast milk intake compared to cow's milk was seen among poorer children (12- and 24-month old) and higher milk and chocolate powdered milk drink consumption was seen among more affluent children aged 48 months. Poorer children of less educated mothers showed higher adherence to the treats component (48 months). Regarding to the snack component, poorer children consumed more coffee, bread/cookies while more affluent children consumed proportionately more fruits, yogurt and soft drinks. Child care outside of the home was also a factor influencing food profiles more aligned with a healthier diet.

Conclusions
The study results showed that very early in life children show food profiles that are strongly associated with social (maternal schooling, socioeconomic position and child care) and behavioral characteristics (breast-feeding duration, bottle-feeding and pacifier use).
Novel mouse mammary cell lines for in vivo bioluminescence imaging (BLI) of bone metastasis
Authors: Bolin Celeste , Sutherland Caleb , Tawara Ken , Moselhy Jim , Jorcyk Cheryl L 
Published: April 2012

AbstractBackgroundTumor cell lines that can be trackedin vivoduring tumorigenesis and metastasis provide vital tools for studying the specific cellular mechanisms that mediate these processes as well as investigating therapeutic targets to inhibit them. The goal of this study was to engineer imageable mouse mammary tumor cell lines with discrete propensities to metastasize to bonein vivo. Two novel luciferase expressing cell lines were developed and characterized for use in the study of breast cancer metastasis to bone in a syngeneic mouse model.ResultsThe 4 T1.2 luc3 and 66c14 luc2 cell lines were shown to have high levels of bioluminescence intensityin vitroandin vivoafter orthotopic injection into mouse mammary fat pads. The 4 T1.2 luc3 cell line was found to closely model the sites of metastases seen in human patients including lung, liver, and bone. Specifically, 4 T1.2 luc3 cells demonstrated a high incidence of metastasis to spine, with anex-vivoBLI intensity three orders of magnitude above the commercially available 4 T1 luc2 cells. 66c14 luc2 cells also demonstrated metastasis to spine, which was lower than that of 4 T1.2 luc3 cells but higher than 4 T1 luc2 cells, in addition to previously unreported metastases in the liver. High osteolytic activity of the 4 T1.2 luc3 cellsin vivoin the bone microenvironment was also detected.ConclusionsThe engineered 4 T1.2 luc3 and 66c14 luc2 cell lines described in this study are valuable tools for studying the cellular events moderating the metastasis of breast tumor cells to bone.
Circulating and synovial antibody profiling of juvenile arthritis patients by nucleic acid programmable protein arrays
Authors: Gibson David S , Qiu Ji , Mendoza Eliseo A , Barker Kristi , Rooney Madeleine E , LaBaer Joshua 
Published: April 2012

Abstract
Introduction
Juvenile idiopathic arthritis (JIA) is a heterogeneous disease characterized by chronic joint inflammation of unknown cause in children. JIA is an autoimmune disease and small numbers of autoantibodies have been reported in JIA patients. The identification of antibody markers could improve the existing clinical management of patients.

Methods
A pilot study was performed on the application of a high-throughput platform, the nucleic acid programmable protein array (NAPPA), to assess the levels of antibodies present in the systemic circulation and synovial joint of a small cohort of juvenile arthritis patients. Plasma and synovial fluid from 10 JIA patients was screened for antibodies against 768 proteins on NAPPAs.

Results
Quantitative reproducibility of NAPPAs was demonstrated with > 0.95 intra-array and inter-array correlations. A strong correlation was also observed for the levels of antibodies between plasma and synovial fluid across the study cohort (r = 0.96). Differences in the levels of 18 antibodies were revealed between sample types across all patients. Patients were segregated into two clinical subtypes with distinct antibody signatures by unsupervised hierarchical cluster analysis.

Conclusion
The NAPPAs provide a high-throughput quantitatively reproducible platform to screen for disease-specific autoantibodies at the proteome level on a microscope slide. The strong correlation between the circulating antibody levels and those of the inflamed joint represents a novel finding and provides confidence to use plasma for discovery of autoantibodies in JIA, thus circumventing the challenges associated with joint aspiration. We expect that autoantibody profiling of JIA patients on NAPPAs could yield antibody markers that can act as criteria to stratify patients, predict outcomes and understand disease etiology at the molecular level.
Amplification and high-level expression of heat shock protein 90 marks aggressive phenotypes of human epidermal growth factor receptor 2 negative breast cancer
Authors: Cheng Qing , Chang Jeffrey T , Geradts Joseph , Neckers Leonard M , Haystead Timothy , Spector Neil L , Lyerly H Kim 
Published: April 2012

Abstract
Introduction
Although human epidermal growth factor receptor 2 (HER2) positive or estrogen receptor (ER) positive breast cancers are treated with clinically validated anti-HER2 or anti-estrogen therapies, intrinsic and acquired resistance to these therapies appears in a substantial proportion of breast cancer patients and new therapies are needed. Identification of additional molecular factors, especially those characterized by aggressive behavior and poor prognosis, could prioritize interventional opportunities to improve the diagnosis and treatment of breast cancer.

Methods
We compiled a collection of 4,010 breast tumor gene expression data derived from 23 datasets that have been posted on the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. We performed a genome-scale survival analysis using Cox-regression survival analyses, and validated using Kaplan-Meier Estimates survival and Cox Proportional-Hazards Regression survival analyses. We conducted a genome-scale analysis of chromosome alteration using 481 breast cancer samples obtained from The Cancer Genome Atlas (TCGA), from which combined expression and copy number data were available. We assessed the correlation between somatic copy number alterations and gene expression using analysis of variance (ANOVA).

Results
Increased expression of each of the heat shock protein (HSP) 90 isoforms, as well as HSP transcriptional factor 1 (HSF1), was correlated with poor prognosis in different subtypes of breast cancer. High-level expression of HSP90AA1 and HSP90AB1, two cytoplasmic HSP90 isoforms, was driven by chromosome coding region amplifications and were independent factors that led to death from breast cancer among patients with triple-negative (TNBC) and HER2-/ER+ subtypes, respectively. Furthermore, amplification of HSF1 was correlated with higher HSP90AA1 and HSP90AB1 mRNA expression among the breast cancer cells without amplifications of these two genes. A collection of HSP90AA1, HSP90AB1 and HSF1 amplifications defined a subpopulation of breast cancer with up-regulated HSP90 gene expression, and up-regulated HSP90 expression independently elevated the risk of recurrence of TNBC and poor prognosis of HER2-/ER+ breast cancer.

Conclusions
Up-regulated HSP90 mRNA expression represents a confluence of genomic vulnerability that renders HER2 negative breast cancers more aggressive, resulting in poor prognosis. Targeting breast cancer with up-regulated HSP90 may potentially improve the effectiveness of clinical intervention in this disease.
Validating the Interval to Biochemical Failure for the Identification of Potentially Lethal Prostate Cancer
Authors: Buyyounouski Mark K. , Pickles Tom , Kestin Larry L. , Allison Roger , Williams Scott G. 
Published: April 2012

Purpose To validate the interval to biochemical failure (IBF) as a prognostic factor at the time of biochemical failure for prostate cancer mortality (PCM) following radiotherapy (RT). Patients and Methods From a collaborative data set of men with clinically localized prostate cancer treated with RT from four institutions in three countries, we identified 1,722 men with biochemical failure (BF; prostate-specific antigen nadir + 2 ng/mL). The IBF was defined as the time interval from completion of treatment to the date of BF. The primary outcome measure was discriminatory power in the form of the concordance index (c-index). Results Seventeen percent of men had an IBF ≤ 18 months. Median potential follow-up beyond the time of BF was 67 months. There were 290 deaths from prostate cancer. The IBF was the most discriminating individual prognostic factor overall, with a sensitivity of IBF ≤ 18 months to predict PCM within 10 years of 48.4% (95% CI, 43.3% to 54.1%); the specificity was 86.1% (95% CI, 84.5% to 87.7%), equating to a c-index of 0.611 (95% CI, 0.578 to 0.647). The 5-year cumulative incidence of PCM for IBF more than 18 months versus IBF ≤ 18 months was 9.4% (95% CI, 7.7% to 11.5%) versus 26.3% (95% CI, 21.2% to 31.8%); corresponding 10-year estimates were 26.2% (95% CI, 21.5% to 30.8%) versus 55.9% (95% CI, 48.9% to 63.0%), respectively (P < .001 for both). IBF exhibited minimal change in performance across various follow-up durations. Conclusion IBF is the single most robust prognostic factor for PCM following RT without androgen deprivation therapy. This external validation demonstrates that patients and clinicians can use this information to make decisions about subsequent treatments.