bluuebunny/crossref_metadata_2025_split huggingface dataset:
MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets
Authors: Xia Jianguo , Sinelnikov Igor V. , Wishart David S. 
Published: June 2011

Abstract
Summary: Time-series and multifactor studies have become increasingly common in metabolomic studies. Common tasks for analyzing data from these relatively complex experiments include identification of major variations associated with each experimental factor, comparison of temporal profiles across different biological conditions, as well as detection and validation of the presence of interactions. Here we introduce MetATT, a web-based tool for time-series and two-factor metabolomic data analysis. MetATT offers a number of complementary approaches including 3D interactive principal component analysis, two-way heatmap visualization, two-way ANOVA, ANOVA-simultaneous component analysis and multivariate empirical Bayes time-series analysis. These procedures are presented through an intuitive web interface. At the end of each session, a detailed analysis report is generated to facilitate understanding of the results.
Availability: Freely available at http://metatt.metabolomics.ca
Contact: jianguox@ualberta.ca
Volatile Anesthetics Protect Cancer Cells against Tumor Necrosis Factor-related Apoptosis-inducing Ligand-induced Apoptosis via Caveolins
Authors: Kawaraguchi Yoshitaka , Horikawa Yousuke T. , Murphy Anne N. , Murray Fiona , Miyanohara Atsushi , Ali Sameh S. , Head Brian P. , Patel Piyush M. , Roth David M. , Patel Hemal H. 
Published: June 2011

Background
Volatile anesthetics have a dual effect on cell survival dependent on caveolin expression. The effect of volatile anesthetics on cancer cell survival and death after anesthetic exposure has not been well investigated. The authors examined the effects of isoflurane exposure on apoptosis and its regulation by caveolin-1 (Cav-1).

Methods
The authors exposed human colon cancer cell lines to isoflurane and proapoptotic stimuli and assessed what role Cav-1 plays in cell protection. They evaluated apoptosis using assays for nucleosomal fragmentation, cleaved caspase 3 expression, and caspase activity assays. To test the mechanism, they used pharmacologic inhibitors (i.e., pertussis toxin) and assessed changes in glycolysis.

Results
Apoptosis as measured by nucleosomal fragmentation was enhanced by isoflurane (1.2% in air) in HT29 (by 64% relative to control, P < 0.001) and decreased in HCT116 (by 23% relative to control, P < 0.001) cells. Knockdown of Cav-1 in HCT116 cells increased the sensitivity to apoptotic stimuli but not with scrambled small interfering RNA (siRNA) treatment (19.7 ± 0.4 vs. 20.0 ± 0.6, P = 0.7786 and 19.7 ± 0.5 vs. 16.3 ± 0.4, P = 0.0012, isoflurane vs. control in Cav-1 small interfering RNA vs. scrambled small interfering RNA treated cells, respectively). The protective effect of isoflurane with various exposure times on apoptosis was enhanced in HT29 cells overexpressing Cav-1 (P < 0.001 by two-way ANOVA). Pertussis toxin effectively blocked the antiapoptotic effect of isoflurane exhibited by Cav-1 in all cell lines. Cav-1 cells had increased glycolysis with isoflurane exposure; however, in the presence of tumor necrosis factor-related apoptosis-inducing ligand, this increase in glycolysis was maintained in HT29-Cav-1 but not control cells.

Conclusion
Brief isoflurane exposure leads to resistance against apoptosis via a Cav-1-dependent mechanism.
Thermostablility of phycobiliproteins and antioxidant activity from four thermotolerant cyanobacteria
Authors: Pumas Chayakorn , Vacharapiyasophon Panmuk , Peerapornpisal Yuwadee , Leelapornpisid Pimporn , Boonchum Walailuck , Ishii Masaharu , Khanongnuch Chartchai 
Published: June 2011

SUMMARYFour cyanobacterial strains including Cyanosarcina sp. SK40, Phormidium sp. PD40‐1, Scytonema sp. TP40 and Leptolyngbya sp. KC45 were selected and investigated for the phycobiliprotein (PBP) content and thermostable antioxidant activity of their cell‐free extracts. The highest content of 181.63 mg/g dry weight phycobiliprotein was found in Leptolyngbya sp. KC45 with phycoerythrin (PE) as the main phycobiliprotein. Among the PBPs of four thermotolerant cyanobacteria, PE from Leptolyngbya sp. KC45 exhibited the highest thermal stability as 80% of the original level remained after being heated at 60°C for 30 min. Antioxidant activities were detected in the cell‐free extracts of all cyanobacteria and that of Leptolyngbya sp. KC45 was also found in the highest value of 7.44 ± 0.14 and 3.89 ± 0.08 mg gallic acid equivalent (GAE) g−1 dry weights determined by 2,2‐diphenyl‐1‐picrylhydrazyl radical (DPPH) and reducing power assay, respectively. This also corresponded to the phenolic compound content. Based on DPPH and reducing power assay, antioxidant activities of all cyanobacterial extracts showed the high thermostability as approximately 80% remained after being heated at 80°C for 30 min. However, it clearly indicated that the thermostability of antioxidant activity from the hot spring cyanobacterial cell‐free extract was not contributed only by the PE, but also came from phenolic compounds and other oxidative substances.
Chlamydomonas neoplanoconvexa nom. nov. and its unique phylogenetic position within Volvocales (Chlorophyceae)
Authors: Nakada Takashi , Tomita Masaru 
Published: June 2011

SUMMARY Chlamydomonas Ehrenb. is a unicellular volvocalean genus consisting of 400–600 species, most of which are known solely based on microscopy. In this study, a newly isolated strain of Chlamydomonas neoplanoconvexa (M. O. P. Iyengar) Nakada nom. nov. (≡Chlamydomonas planoconvexa M. O. P. Iyengar non J. W. G. Lund) was examined using light microscopy and combined 18S rRNA, rbcL and psaB gene phylogeny. The C. neoplanoconvexa strain was quite similar to Chlamydomonas perpusilla (Korshikov) Gerloff in terms of its small fusiform vegetative cells (∼10 µm in length), parietal chloroplast containing a single pyrenoid, and nucleus posterior to the pyrenoid. However, C. neoplanoconvexa was distinguished from C. perpusilla based on the morphology of the papillae and pyrenoids. The two species belong to the clade Caudivolvoxa in the order Volvocales, but are distantly related to each other. Chlamydomonas perpusilla was shown to be sister to Chlorogonium Ehrenb. (clade Chlorogonia, within Caudivolvoxa), while C. neoplanoconvexa represented a second basal lineage within Caudivolvoxa, next to the clade Characiosiphonia. Although the morphology of C. neoplanoconvexa was not particularly outstanding, its unique phylogenetic position will encourage further investigation of this species and its uncultivated relatives.
A Gradient‐Based Comparison Measure for Visual analysis of Multifield Data
Authors: Nagaraj Suthambhara , Natarajan Vijay , Nanjundiah Ravi S. 
Published: June 2011

AbstractWe introduce a multifield comparison measure for scalar fields that helps in studying relations between them. The comparison measure is insensitive to noise in the scalar fields and to noise in their gradients. Further, it can be computed robustly and efficiently. Results from the visual analysis of various data sets from climate science and combustion applications demonstrate the effective use of the measure.
A Framework for Exploring Multidimensional Data with 3D Projections
Authors: Poco J. , Etemadpour R. , Paulovich F.V. , Long T.V. , Rosenthal P. , Oliveira M.C.F. , Linsen L. , Minghim R. 
Published: June 2011

AbstractVisualization of high‐dimensional data requires a mapping to a visual space. Whenever the goal is to preserve similarity relations a frequent strategy is to use 2D projections, which afford intuitive interactive exploration, e.g., by users locating and selecting groups and gradually drilling down to individual objects. In this paper, we propose a framework for projecting high‐dimensional data to 3D visual spaces, based on a generalization of the Least‐Square Projection (LSP). We compare projections to 2D and 3D visual spaces both quantitatively and through a user study considering certain exploration tasks. The quantitative analysis confirms that 3D projections outperform 2D projections in terms of precision. The user study indicates that certain tasks can be more reliably and confidently answered with 3D projections. Nonetheless, as 3D projections are displayed on 2D screens, interaction is more difficult. Therefore, we incorporate suitable interaction functionalities into a framework that supports 3D transformations, predefined optimal 2D views, coordinated 2D and 3D views, and hierarchical 3D cluster definition and exploration. For visually encoding data clusters in a 3D setup, we employ color coding of projected data points as well as four types of surface renderings. A second user study evaluates the suitability of these visual encodings. Several examples illustrate the framework's applicability for both visual exploration of multidimensional abstract (non‐spatial) data as well as the feature space of multi‐variate spatial data.
Ursodeoxycholic acid dose‐dependently improves liver injury in rats fed a methionine‐ and choline‐deficient diet
Authors: Buko Vyacheslav U. , Kuzmitskaya‐Nikolaeva Irina A. , Naruta Elena E. , Lukivskaya Oksana Y. , Kirko Siarhei N. , Tauschel Horst‐Dietmar 
Published: June 2011

Aim:  The data on the beneficial effect of ursodeoxycholic acid (UDCA) in non‐alcoholic steatohepatitis (NASH) are controversial. The difference of opinion is connected with UDCA dosage to be used. Therefore, we evaluated the dose‐dependent efficacy of UDCA in experimental NASH.Methods:  Male Wistar rats were fed the methionine‐ and choline‐deficient (MCD) diet for 10 weeks. Rats were administrated UDCA (10, 20, 40 and 80 mg/kg bodyweight intragastrically) after 6 weeks of the MCD diet.Results:  Animals fed the MCD diet developed severe steatohepatitis. Treatment with UDCA dose‐dependently decreased liver damage, but only high‐dose UDCA (80 mg/kg) significantly diminished ultrastructural changes in addition to preventing steatosis, ballooning and inflammatory changes in the liver. The activities of serum marker enzymes and the content of liver triglyceride and blood glucose were increased in MCD diet‐fed rats, but decreased in all the UDCA‐treated groups. Serum insulin concentration was decreased whereas the quantitative insulin sensitivity check index did not changed in MCD diet‐fed groups. Serum tumor necrosis factor‐α content was strongly increased after MCD diet and normalized in the UDCA‐treated rats, with the most pronounced effect in the highest dose groups, 40 and 80 mg/kg. The contents of endogenous ethanol in blood and intestinal mucus were increased in MCD diet‐fed rats which were significantly lowered by UDCA (40 and 80 mg/kg per day).Conclusion:  The present data demonstrate a beneficial effect of UDCA that manifested by the decrease of liver steatosis, inflammatory signs and serum tumor necrosis factor‐α content especially of the highest 40 and 80 mg/kg day doses.
The Human Cytomegalovirus Protein pUL38 Suppresses Endoplasmic Reticulum Stress-Mediated Cell Death Independently of Its Ability To Induce mTORC1 Activation
Authors: Qian Zhikang , Xuan Baoqin , Gualberto Nathaniel , Yu Dong 
Published: June 2011

ABSTRACT

As obligate intracellular parasites, viruses not only hijack cellular machinery, they also deregulate host stress responses for their infection. Human cytomegalovirus (HCMV) modulates the endoplasmic reticulum (ER) stress response, due at least in part to the viral protein pUL38, and one of the consequences is to maintain the viability of infected cells. Consequently, pUL38-deficient virus induces premature cell death during infection. In addition, pUL38 activates mammalian target of rapamycin complex 1 (mTORC1), which may also antagonize other detrimental cellular stresses (N. J. Moorman et al., Cell Host Microbe 3:253–262, 2008). It remains elusive how pUL38 inhibition of cell death is related to mTORC1 activation. In this study, we defined the interplay of the two pUL38 activities. We constructed a series of pUL38 truncation mutants based on the secondary structure prediction and evolutionary conservation of its sequence. We found that the N-terminal 239 residues of pUL38 were necessary and sufficient to block cell death induced by pUL38-deficient virus or by the ER stress inducer tunicamycin. However, this pUL38 domain was unable to activate mTORC1 when expressed alone. Importantly, small-molecule inhibitors of mTORC1, rapamycin or torin 1, did not compromise pUL38 activity to block cell death in isolation or in virus infection. Expression of a constitutively active variant of an mTORC1 activator, Rheb (
R
as
h
omolog
e
nriched in
b
rain), could not prevent cell death induced by pUL38-deficient virus. Collectively, we provide genetic and biochemical evidence that pUL38 prevents ER stress-induced cell death independent of its role in mTORC1 activation.
Structure and Function of the
d
-Galactose Network in Enterobacteria
Authors: Csiszovszki Zsolt , Krishna Sandeep , Orosz László , Adhya Sankar , Semsey Szabolcs 
Published: June 2011

ABSTRACT

Galactose is important for the survival and virulence of bacteria. In
Escherichia coli
, galactose is utilized by the Leloir pathway, which is controlled by a complex network. To shed light on the potential functions the galactose network could perform, we performed bioinformatical analysis of reference genome sequences belonging to the
Enterobacteriaceae
family. We found that several genomes have reduced numbers of components compared to the
E. coli
galactose system, suggesting that the network can be optimized for different environments. Typically, genes are removed by deletions; however, in
Yersinia pestis
, the galactose mutarotase (
galM
) gene is inactivated by a single-base-pair deletion. Lack of GalM activity indicates that the two anomers of
d
-galactose are used for different purposes, α-
d
-galactose as a carbon source and β-
d
-galactose for induction of UDP-galactose synthesis for biosynthetic glycosylation. We demonstrate that activity of the
galM
gene can be restored by different single-base-pair insertions. During the evolution of
Y. pestis
to become a vector-transmitted systemic pathogen, many genes were converted to pseudogenes. It is not clear whether pseudogenes are present to maintain meiotrophism or are in the process of elimination. Our results suggest that the
galM
pseudogene has not been deleted because its reactivation may be beneficial in certain environments.

IMPORTANCE
Evolution of bacteria to populate a new environment necessarily involves reengineering of their molecular network. Members of the
Enterobacteriaceae
family of bacteria have diverse lifestyles and can function in a wide range of environments. In this study we performed bioinformatical analysis of 34 reference genome sequences belonging to the
Enterobacteriaceae
family to gain insight into the natural diversity of the
d
-galactose utilization network. Our bioinformatical analysis shows that in several species, some genes of the network are completely missing or are inactivated by large deletions. The only exception is the galactose mutarotase (
galM
) gene of
Yersinia pestis
, which is converted to a pseudogene by a single-base-pair deletion. In this paper, we discuss the possible consequences of
galM
inactivation on network function. We suggest that
galM
was converted to a pseudogene rather than being deleted in evolution because its reactivation can be beneficial in certain environments.
Gene Expression Profiling of Fixed Tissues Identified Hypoxia-Inducible Factor-1α, VEGF, and Matrix Metalloproteinase-2 as Biomarkers of Lymph Node Metastasis in Hepatocellular Carcinoma
Authors: Xiang Zuo-Lin , Zeng Zhao-Chong , Fan Jia , Tang Zhao-You , Zeng Hai-Ying , Gao Dong-Mei 
Published: June 2011

Abstract
Purpose: Hepatocellular carcinoma (HCC) most often develops in patients infected with hepatitis B or hepatitis C virus. Differential gene expression profiling is useful for investigating genes associated with lymph node metastasis (LNM). We screened genes to identify potential biomarkers for LNM in HCC.
Experimental Design: RNA was extracted from formalin-fixed specimens of paired intratumoral and peritumoral tissues of patients with lymph node–positive (n = 36) or negative (n = 36) HCC. A cDNA-mediated annealing, selection, extension, and ligation assay was done with an array of 502 known cancer-related genes to identify differentially expressed genes in 20 pairs of patients with or without LNM. Candidate biomarkers were evaluated by using immunohistochemistry and tissue microarrays in an independent cohort of 309 HCC patients who had undergone hepatectomy. Of the 309 patients, 235 (76.1%) patients were infected with hepatitis B.
Results: Compared with lymph node–negative patients, lymph node–positive patients had 17 overexpressed genes and 19 underexpressed genes in intratumoral tissues, and 25 overexpressed genes and 22 underexpressed genes in peritumoral tissues. Hypoxia-inducible factor (HIF)-1α, VEGF, and matrix metalloproteinase (MMP)-2 were selected for analysis in the cohort of 309 HCC patients. We found that intratumoral protein levels of HIF-1α, VEGF, and MMP-2 were independent risk factors for developing LNM.
Conclusion: We identified 83 cancer genes that were differentially expressed in lymph node–positive and lymph node–negative HCC. Our findings show that the combination of intratumoral HIF-1α, VEGF, and MMP-2 may be useful as a molecular prediction model for LNM. Clin Cancer Res; 17(16); 5463–72. ©2011 AACR.
Compensatory Pathways Induced by MEK Inhibition Are Effective Drug Targets for Combination Therapy against Castration-Resistant Prostate Cancer
Authors: Gioeli Daniel , Wunderlich Winfried , Sebolt-Leopold Judith , Bekiranov Stefan , Wulfkuhle Julia D. , Petricoin Emanuel F. , Conaway Mark , Weber Michael J. 
Published: June 2011

Abstract
Targeted therapies have often given disappointing results when used as single agents in solid tumors, suggesting the importance of devising rational combinations of targeted drugs. We hypothesized that construction of such combinations could be guided by identification of growth and survival pathways whose activity or expression become upregulated in response to single-agent drug treatment. We mapped alterations in signaling pathways assessed by gene array and protein phosphorylation to identify compensatory signal transduction pathways in prostate cancer xenografts treated with a MAP/ERK kinase (MEK) inhibitor PD325901. In addition to numerous components of the extracellular signal–regulated kinase (ERK) signaling pathway, components of the IKK, hedgehog, and phosphoinositide 3-kinase/Akt/mTOR pathways were upregulated following treatment with PD325901. Combinations of PD325901 with inhibitors of any one of these upregulated pathways provided synergistically greater growth inhibition of in vitro cell growth and survival than the individual drugs alone. Thus, the identification of compensatory signal transduction pathways paves the way for rational combinatorial therapies for the effective treatment of prostate cancer. Mol Cancer Ther; 10(9); 1581–90. ©2011 AACR.
Novel Therapeutic Options in Anaplastic Large Cell Lymphoma: Molecular Targets and Immunological Tools
Authors: Merkel Olaf , Hamacher Frank , Sifft Eveline , Kenner Lukas , Greil Richard 
Published: June 2011

Abstract
Anaplastic large cell lymphoma (ALCL) is a CD30-positive, aggressive T-cell lymphoma, and about half of the patients with this disease harbor the t(2;5)(p21;q35) translocation. This chromosomal aberration leads to fusion of the NPM gene with the ALK tyrosine kinase, leading to its constitutive activation. To date, treatment options include polychemotherapy (e.g., cyclophosphamide, doxorubicin, vincristine, and prednisone), which is sometimes combined with radiation in the case of bulky disease, leading to remission rates of ∼80%. However, the remaining patients do not respond to therapy, and some patients experience chemo-resistant relapses, making the identification of new and better treatments imperative. The recent discovery of deregulated ALK in common cancers such as non–small cell lung cancer and neuroblastoma has reinvigorated industry interest in the development of ALK inhibitors. Moreover, it has been shown that the ALK protein is an ideal antigen for vaccination strategies due to its low expression in normal tissue. The characterization of microRNAs that are deregulated in ALCL will yield new insights into the biology of ALCL and open new avenues for therapeutic approaches in the future. Also, CD30 antibodies that have been tested in ALCL for quite a while will probably find a place in forthcoming treatment strategies. Mol Cancer Ther; 10(7); 1127–36. ©2011 AACR.
Periodic mixed convection of a nanofluid in a cavity with top lid sinusoidal motion
Authors: Karimipour A , Nezhad A H , Behzadmehr A , Alikhani S , Abedini E 
Published: June 2011

The periodic mixed convection of a water–copper nanofluid inside a rectangular cavity with aspect ratio of 3 is investigated numerically. The temperature of the bottom wall of the cavity is assumed greater than the temperature of the top lid which oscillates horizontally with the velocity defined as u = u0 sin ( ωt). The effects of Richardson number, Ri, and volume fraction of nanoparticles on the flow and thermal behaviour of the nanofluid are investigated. Velocity, temperature profiles, and streamlines are presented. It is observed that when Ri < 1, heat transfer rate is much greater than when Ri > 1. The higher value of Ri corresponds to a lower value of the amplitude of the oscillation of Nu m in the steady periodic state. Moreover, increasing the volume fraction of the nanoparticles increases the heat transfer rate.
The avidity of anti-β2-glycoprotein I antibodies in patients with or without antiphospholipid syndrome: a collaborative study in the frame of the European forum on antiphospholipid antibodies
Authors: Čučnik S , Kveder T , Ulcova GZ , Swadzba J , Musial J , Valesini G , Avčin T , Rozman B , Božič B 
Published: June 2011

Objective. The objective of this study was to extend the findings of the preliminary study by measuring the avidity of IgG anti-β2-glycoprotein I antibodies (anti-β2-GPI) on a larger group of patients with primary or secondary antiphospholipid syndrome (APS) and anti-β2-GPI positive patients without APS in the frame of the European Forum on antiphospholipid antibodies (aPL). Methods. Serum from 137 patients with primary APS, APS associated with autoimmune diseases, and patients with autoimmune diseases other than APS from five EU rheumatology centres were tested for anti-β2-GPI antibodies. The 109 patients who were sera positive for anti-β2-GPI by the in-house anti-β2-GPI enzyme-linked immunosorbent assay (ELISA) at the Immunology Laboratory, UMC Ljubljana were selected for further testing on avidity with chaotropic anti-β2-GPI ELISA. Results. High, low and heterogeneous avidity IgG anti-β2-GPI was found in 32/109, 17/109 and 60/109 patients respectively. Significantly more patients with APS were in the high avidity than in the low avidity anti-β2-GPI group, while the opposite was observed for non-APS (both p < 0.001). The most common clinical feature among patients with high avidity anti-β2-GPI was thrombosis, mainly due to venous thrombosis ( p < 0.01 and p < 0.001, versus low avidity anti-β2-GPI group). Conclusion. Patients with or without APS had anti-β2-GPI of high, low or heterogeneous avidity. High avidity anti-β2-GPI was associated with thrombosis and APS, while in the low avidity anti-β2-GPI group non-APS (predominantly SLE) patients prevailed. Determination of anti-β2-GPI avidity should be considered in the analytical strategies for further differentiation of patients with anti-β2-GPI antibodies.