bluuebunny/crossref_metadata_2025_split huggingface dataset:
PAX2 is activated by estradiol in breast cancer cells of the luminal subgroup selectively, to confer a low invasive phenotype
Authors: Beauchemin David , Lacombe Catherine , Van Themsche Céline 
Published: December 2011

AbstractBackgroundMetastasis is the leading cause of death among breast cancer patients. Identifying key cellular factors controlling invasion and metastasis of breast cancer cells should pave the way to new therapeutic strategies efficiently interfering with the metastatic process. PAX2 (paired box 2) transcription factor is expressed by breast cancer cellsin vivoand recently, it was shown to negatively regulate the expression of ERBB2 (erythroblastic leukemia viral oncogene homolog 2, HER-2/neu), a well-documented pro-invasive and pro-metastastic gene, in luminal/ERalpha-positive (ERα+) breast cancer cells. The objective of the present study was to investigate a putative role for PAX2 in the control of luminal breast cancer cells invasion, and to begin to characterize its regulation.ResultsPAX2 activity was higher in cell lines from luminal compared to non-luminal subtype, and activation of PAX2 by estradiol was selectively achieved in breast cancer cell lines of the luminal subtype. This process was blocked by ICI 182780 and could be antagonized by IGF-1. Knockdown of PAX2 in luminal MCF-7 cells completely abrogated estradiol-induced downregulation of ERBB2 and decrease of cell invasion, whereas overexpression of PAX2 in these cells enhanced estradiol effects on ERBB2 levels and cell invasion.ConclusionsThe study demonstrates that PAX2 activation by estradiol is selectively achieved in breast cancer cells of the luminal subtype, via ERα, and identifies IGF-1 as a negative regulator of PAX2 activity in these cells. Further, it reveals a new role for PAX2 in the maintenance of a low invasive behavior in luminal breast cancer cells upon exposure to estradiol, and shows that overexpression and activation of PAX2 in these cells is sufficient to reduce their invasive ability.
Liver fatty acid composition in mice with or without nonalcoholic fatty liver disease
Authors: Wang Xin , Cao Yuzhen , Fu Yunwei , Guo Guifang , Zhang Xiuying 
Published: December 2011

Abstract

Background
Nonalcoholic fatty liver disease (NAFLD) is one of the most frequent causes of abnormal liver function. Because fatty acids can damage biological membranes, fatty acid accumulation in the liver may be partially responsible for the functional and morphological changes that are observed in nonalcoholic liver disease. The aim of this study was to use gas chromatography-mass spectrometry to evaluate the fatty acid composition of an experimental mouse model of NAFLD induced by high-fat feed and CCl4 and to assess the association between liver fatty acid accumulation and NAFLD. C57BL/6J mice were given high-fat feed for six consecutive weeks to develop experimental NAFLD. Meanwhile, these mice were given subcutaneous injections of a 40% CCl4-vegetable oil mixture twice per week.

Results
A pathological examination found that NAFLD had developed in the C57BL/6J mice. High-fat feed and CCl4 led to significant increases in C14:0, C16:0, C18:0 and C20:3 (P < 0.01), and decreases in C15:0, C18:1, C18:2 and C18:3 (P < 0.01) in the mouse liver. The treatment also led to an increase in SFA and decreases in other fatty acids (UFA, PUFA and MUFA). An increase in the ratio of product/precursor n-6 (C20:4/C18:2) and n-3 ([C20:5+C22:6]/C18:3) and a decrease in the ratio of n-6/n-3 (C20:4/[C20:5+C22:6]) were also observed.

Conclusion
These data are consistent with the hypothesis that fatty acids are deranged in mice with non-alcoholic fatty liver injury induced by high-fat feed and CCl4, which may be involved in its pathogenesis and/or progression via an unclear mechanism.
Cathodoluminescence spectra of gallium nitride nanorods
Authors: Tsai Chia-Chang , Li Guan-Hua , Lin Yuan-Ting , Chang Ching-Wen , Wadekar Paritosh , Chen Quark Yung-Sung , Rigutti Lorenzo , Tchernycheva Maria , Julien François Henri , Tu Li-Wei 
Published: December 2011

Abstract
Gallium nitride [GaN] nanorods grown on a Si(111) substrate at 720°C via plasma-assisted molecular beam epitaxy were studied by field-emission electron microscopy and cathodoluminescence [CL]. The surface topography and optical properties of the GaN nanorod cluster and single GaN nanorod were measured and discussed. The defect-related CL spectra of GaN nanorods and their dependence on temperature were investigated. The CL spectra along the length of the individual GaN nanorod were also studied. The results reveal that the 3.2-eV peak comes from the structural defect at the interface between the GaN nanorod and Si substrate. The surface state emission of the single GaN nanorod is stronger as the diameter of the GaN nanorod becomes smaller due to an increased surface-to-volume ratio.
Swine influenza virus infection in different age groups of pigs in farrow-to-finish farms in Thailand
Authors: Takemae Nobuhiro , Parchariyanon Sujira , Ruttanapumma Ruttapong , Hiromoto Yasuaki , Hayashi Tsuyoshi , Uchida Yuko , Saito Takehiko 
Published: December 2011

Abstract

Background
Understanding swine influenza virus (SIV) ecology has become more and more important from both the pig industry and public health points of views. However, the mechanism whereby SIV occurs in pig farms is not well understood. The purpose of this study was to develop a proper strategy for SIV surveillance.

Findings
We conducted longitudinal monitoring in 6 farrow-to-finish farms in the central region of Thailand from 2008 to 2009. Nasal swabs and serum samples were collected periodically from clinically healthy pigs consisting of sows, fattening pigs, weaned piglets and pigs transferred from other farms. A total of 731 nasal swabs were subjected to virus isolation and 641 serum samples were subjected to detection of SIV antibodies against H1 and H3 subtypes using the hemagglutination inhibition test and ELISA. Twelve SIVs were isolated in this study and eleven were from piglets aged 4 and 8 weeks. Phylogenetical analysis revealed that SIVs isolated from different farms shared a common ancestor. Antibodies against SIVs were detected in fattening pigs on farms with no SIV isolation in the respective periods studied. These observations suggested that piglets aged 8 weeks or younger could be a main target for SIV isolation. Farm-to-farm transmission was suggested for farms where pigs from other farms are introduced periodically. In addition, antibodies against SIVs detected in fattening pigs could be a marker for SIV infection in a farm.

Conclusions
The present study provided important information on SIV surveillance that will enable better understanding of SIV ecology in farrow-to-finish farms.
Subcellular Targeting Domains of Sphingomyelin Synthase 1 and 2
Authors: Yeang Calvin , Ding Tingbo , Chirico William J , Jiang Xian-Cheng 
Published: December 2011

AbstractSphingomyelin synthase (SMS) sits at the crossroads of sphingomyelin (SM), ceramide, diacylglycerol (DAG) metabolism. It utilizes ceramide and phosphatidylcholine as substrates to produce SM and DAG, thereby regulating lipid messengers which play a role in cell survival and apoptosis. Furthermore, its product SM has been implicated in atherogenic processes such as retention of lipoproteins in the blood vessel intima. There are two mammalian sphingomyelin synthases: SMS1 and SMS2. SMS1 is found exclusively in the Golgi at steady state, whereas SMS2 exists in the Golgi and plasma membrane. Conventional motifs responsible for protein targeting to the plasma membrane or Golgi are either not present in, or unique to, SMS1 and SMS2. In this study, we examined how SMS1 and SMS2 achieve their respective subcellular localization patterns. Brefeldin A treatment prevented SMS1 and SMS2 from exiting the ER, demonstrating that they transit through the classical secretory pathway. We created truncations and chimeras of SMS1 and SMS2 to define their targeting signals. We found that SMS1 contains a C-terminal Golgi targeting signal and that SMS2 contains a C-terminal plasma membrane targeting signal.
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates
Authors: Xia Li C , Steele Joshua A , Cram Jacob A , Cardon Zoe G , Simmons Sheri L , Vallino Joseph J , Fuhrman Jed A , Sun Fengzhu 
Published: December 2011

Abstract

Background
The increasing availability of time series microbial community data from metagenomics and other molecular biological studies has enabled the analysis of large-scale microbial co-occurrence and association networks. Among the many analytical techniques available, the Local Similarity Analysis (LSA) method is unique in that it captures local and potentially time-delayed co-occurrence and association patterns in time series data that cannot otherwise be identified by ordinary correlation analysis. However LSA, as originally developed, does not consider time series data with replicates, which hinders the full exploitation of available information. With replicates, it is possible to understand the variability of local similarity (LS) score and to obtain its confidence interval.

Results
We extended our LSA technique to time series data with replicates and termed it extended LSA, or eLSA. Simulations showed the capability of eLSA to capture subinterval and time-delayed associations. We implemented the eLSA technique into an easy-to-use analytic software package. The software pipeline integrates data normalization, statistical correlation calculation, statistical significance evaluation, and association network construction steps. We applied the eLSA technique to microbial community and gene expression datasets, where unique time-dependent associations were identified.

Conclusions
The extended LSA analysis technique was demonstrated to reveal statistically significant local and potentially time-delayed association patterns in replicated time series data beyond that of ordinary correlation analysis. These statistically significant associations can provide insights to the real dynamics of biological systems. The newly designed eLSA software efficiently streamlines the analysis and is freely available from the eLSA homepage, which can be accessed at http://meta.usc.edu/softs/lsa.
Cerebral perfusion pressure, microdialysis biochemistry and clinical outcome in patients with traumatic brain injury
Authors: Paraforou Theoniki , Paterakis Konstantinos , Fountas Konstantinos , Paraforos George , Chovas Achilleas , Tasiou Anastasia , Mpakopoulou Maria , Papadopoulos Dimitrios , Karavellis Antonios , Komnos Apostolos 
Published: December 2011

Abstract

Background
Traumatic Brain Injury (TBI) is a major cause of death and disability. It has been postulated that brain metabolic status, intracranial pressure (ICP) and cerebral perfusion pressure (CPP) are related to patients' outcome. The aim of this study was to investigate the relationship between CPP, ICP and microdialysis parameters and clinical outcome in TBIs.

Results
Thirty four individuals with severe brain injury hospitalized in an intensive care unit participated in this study. Microdialysis data were collected, along with ICP and CPP values. Glasgow Outcome Scale (GOS) was used to evaluate patient outcome at 6 months after injury. Fifteen patients with a CPP greater than 75 mmHg, L/P ratio lower than 37 and Glycerol concentration lower than 72 mmol/l had an excellent outcome (GOS 4 or 5), as opposed to the remaining 19 patients. No patient with a favorable outcome had a CPP lower than 75 mmHg or Glycerol concentration and L/P ratio greater than 72 mmol/l and 37 respectively. Data regarding L/P ratio and Glycerol concentration were statistically significant at p = 0.05 when patients with favorable and unfavorable outcome were compared. In a logistic regression model adjusted for age, sex and Glasgow Coma Scale on admission, a CPP greater than 75 mmHg was marginally statistically significantly related to outcome at 6 months after injury.

Conclusions
Patients with favorable outcome had certain common features in terms of microdialysis parameters and CPP values. An individualized approach regarding CPP levels and cut -off points for Glycerol concentration and L/P ratio are proposed.
Agrobacterium tumefaciens-mediated transformation of Aspergillus aculeatus for insertional mutagenesis
Authors: Kunitake Emi , Tani Shuji , Sumitani Jun-ichi , Kawaguchi Takashi 
Published: December 2011

Abstract

Agrobacterium tumefaciens-mediated transformation (AMT) was applied to Aspergillus aculeatus. Transformants carrying the T-DNA from a binary vector pBIG2RHPH2 were sufficiently mitotically stable to allow functional genomic analyses. The AMT technique was optimized by altering the concentration of acetosyringone, the ratio and concentration of A. tumefaciens and A. aculeatus cells, the duration of co-cultivation, and the status of A. aculeatus cells when using conidia, protoplasts, or germlings. On average, 30 transformants per 104 conidia or 217 transformants per 107 conidia were obtained under the optimized conditions when A. tumefaciens co-cultured with fungi using solid or liquid induction media (IM). Although the transformation frequency in liquid IM was 100-fold lower than that on solid IM, the AMT method using liquid IM is better suited for high-throughput insertional mutagenesis because the transformants can be isolated on fewer selection media plates by concentrating the transformed germlings. The production of two albino A. aculeatus mutants by AMT confirmed that the inserted T-DNA disrupted the polyketide synthase gene AapksP, which is involved in pigment production. Considering the efficiency of AMT and the correlation between the phenotypes and genotypes of the transformants, the established AMT technique offers a highly efficient means for characterizing the gene function in A. aculeatus.
Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer
Authors: Staaf Johan , Jönsson Göran , Ringnér Markus , Baldetorp Bo , Borg Åke 
Published: December 2011

Abstract
Introduction
Human epidermal growth factor receptor 2 (HER2)-amplified breast cancer represents a clinically well-defined subgroup due to availability of targeted treatment. However, HER2-amplified tumors have been shown to be heterogeneous at the genomic level by genome-wide microarray analyses, pointing towards a need of further investigations for identification of recurrent copy number alterations and delineation of patterns of allelic imbalance.

Methods
High-density whole genome array-based comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) array data from 260 HER2-amplified breast tumors or cell lines, and 346 HER2-negative breast cancers with molecular subtype information were assembled from different repositories. Copy number alteration (CNA), loss-of-heterozygosity (LOH), copy number neutral allelic imbalance (CNN-AI), subclonal CNA and patterns of tumor DNA ploidy were analyzed using bioinformatical methods such as genomic identification of significant targets in cancer (GISTIC) and genome alteration print (GAP). The patterns of tumor ploidy were confirmed in 338 unrelated breast cancers analyzed by DNA flow cytometry with concurrent BAC aCGH and gene expression data.

Results
A core set of 36 genomic regions commonly affected by copy number gain or loss was identified by integrating results with a previous study, together comprising > 400 HER2-amplified tumors. While CNN-AI frequency appeared evenly distributed over chromosomes in HER2-amplified tumors, not targeting specific regions and often < 20% in frequency, the occurrence of LOH was strongly associated with regions of copy number loss. HER2-amplified and HER2-negative tumors stratified by molecular subtypes displayed different patterns of LOH and CNN-AI, with basal-like tumors showing highest frequencies followed by HER2-amplified and luminal B cases. Tumor aneuploidy was strongly associated with increasing levels of LOH, CNN-AI, CNAs and occurrence of subclonal copy number events, irrespective of subtype. Finally, SNP data from individual tumors indicated that genomic amplification in general appears as monoallelic, that is, it preferentially targets one parental chromosome in HER2-amplified tumors.

Conclusions
We have delineated the genomic landscape of CNAs, amplifications, LOH, and CNN-AI in HER2-amplified breast cancer, but also demonstrated a strong association between different types of genomic aberrations and tumor aneuploidy irrespective of molecular subtype.
Soluble urokinase-type plasminogen activator receptor levels in patients with burn injuries and inhalation trauma requiring mechanical ventilation: an observational cohort study
Authors: Backes Yara , van der Sluijs Koenraad F , Tuip de Boer Anita M , Hofstra Jorrit Jan , Vlaar Alexander PJ , Determann Rogier M , Knape Paul , Mackie David P , Schultz Marcus J 
Published: December 2011

Abstract
Introduction
Soluble urokinase-type plasminogen activator receptor (suPAR) has been proposed as a biologic marker of fibrinolysis and inflammation. The aim of this study was to investigate the diagnostic and prognostic value of systemic and pulmonary levels of suPAR in burn patients with inhalation trauma who need mechanical ventilation.

Methods
suPAR was measured in plasma and nondirected lung-lavage fluid of mechanically ventilated burn patients with inhalation trauma. The samples were obtained on the day of inhalation trauma and on alternate days thereafter until patients were completely weaned from the mechanical ventilator. Mechanically ventilated patients without burns and without pulmonary disease served as controls.

Results
Systemic levels of suPAR in burn patients with inhalation trauma were not different from those in control patients. On admission and follow up, pulmonary levels of suPAR in patients with inhalation trauma were significantly higher compared with controls. Pulmonary levels of suPAR highly correlated with pulmonary levels of interleukin 6, a marker of inflammation, and thrombin-antithrombin complexes, markers of coagulation, but not plasminogen activator activity, a marker of fibrinolysis. Systemic levels of suPAR were predictive of the duration of mechanical ventilation and length of intensive care unit (ICU) stay. Duration of mechanical ventilation and length of ICU stay were significantly longer in burn-injury patients with systemic suPAR levels > 9.5 ng/ml.

Conclusions
Pulmonary levels of suPAR are elevated in burn patients with inhalation trauma, and they correlate with pulmonary inflammation and coagulation. Although pulmonary levels of suPAR may have diagnostic value in burn-injury patients, systemic levels of suPAR have prognostic value.
Taperin (c9orf75), a mutated gene in nonsyndromic deafness, encodes a vertebrate specific, nuclear localized protein phosphatase one alpha (PP1α) docking protein
Authors: Ferrar Tony , Chamousset Delphine , De Wever Veerle , Nimick Mhairi , Andersen Jens , Trinkle-Mulcahy Laura , Moorhead Greg B. G. 
Published: December 2011

Summary
The promiscuous activity of protein phosphatase one (PP1) is controlled in the cell by associated proteins termed regulatory or targeting subunits. Using biochemical and proteomic approaches we demonstrate that the autosomal recessive nonsyndromic hearing loss gene, taperin (C9orf75), encodes a protein that preferentially docks the alpha isoform of PP1. Taperin associates with PP1 through a classic ‘RVxF’ motif and suppresses the general phosphatase activity of the enzyme. The steady-state localization of taperin is predominantly nuclear, however we demonstrate here that the protein can shuttle between the nucleus and cytoplasm and that it is found complexed to PP1 in both of these cellular compartments. Although originally identified as a hearing loss gene, Western blot analyses with taperin-specific antibodies revealed that the protein is widely expressed across mammalian tissues as multiple splice variants. Taperin is a recent proteome addition appearing during the vertebrate lineage with the PP1 binding site embedded within the most conserved region of the protein. Taperin also shares an ancestral relationship with the cytosolic actin binding protein phostensin, another PP1 interacting partner. Quantitative Stable Isotope Labeling by Amino acids in Culture (SILAC)-based mass spectrometry was employed to uncover additional taperin binding partners, and revealed an interaction with the DNA damage response proteins Ku70, Ku80, PARP and topoisomerases I and IIα. Consistent with this, we demonstrate the active recruitment of taperin to sites of DNA damage. This makes taperin a new addition to the family of PP1 targeting subunits involved in the DNA damage repair pathway.
Gas-Temperature Imaging in a Microwave-Plasma Nanoparticle-Synthesis Reactor Using Multi-Line NO-LIF Thermometry
Authors: Hecht C. , Abdali A. , Dreier T. , Schulz C. 
Published: December 2011

Abstract
Multi-line NO-LIF thermometry is used to determine the two-dimensional temperature distribution inside a low-pressure plasma reactor. The applicability of multi-line temperature measurements to non-equilibrium plasma environments was evaluated. Temperatures between 300 and 3000 K have been observed, while microwave power, and pressure show a strong effect on the temperature distribution. Metal-organic precursors added for particle synthesis additionally influence the temperature through the heat release during particle formation and the oxidation of organic ligands.
Identification of Tetrahydrofuran Reaction Pathways in Premixed Flames
Authors: Kasper Tina , Lucassen Arnas , Jasper Ahren W. , Li Wenjun , Westmoreland Philip R. , Kohse-Höinghaus Katharina , Yang Bin , Wang Juan , Cool Terrill A. , Hansen Nils 
Published: December 2011

Abstract
Premixed low-pressure tetrahydrofuran/oxygen/argon flames are investigated by photoionization molecular-beam mass spectrometry using vacuum-ultraviolet synchrotron radiation. For two equivalence ratios (φ = 1.00 and 1.75), mole fractions are measured as a function of distance from the burner for almost 60 intermediates with molar masses ranging from 2 (H2) to 88 (C4H6O2), providing a broad database for flame modeling studies. The isomeric composition is resolved by comparisons between experimental photoionization efficiency data and theoretical simulations, based on calculated ionization energies and Franck-Condon factors. Special emphasis is put on the resolution of the first reaction steps in the fuel destruction. The photoionization experiments are complemented by electron-ionization molecular-beam mass-spectrometry measurements that provide data with high mass resolution. For three additional flames with intermediate equivalence ratios (φ = 1.20, 1.40 and 1.60), mole fractions of major species and photoionization efficiency spectra of intermediate species are reported, extending the database for the development of chemical kinetic models.