bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global analysis of DNA methylation in early-stage liver fibrosis
Authors: Komatsu Yoko , Waku Tsuyoshi , Iwasaki Naoya , Ono Wakana , Yamaguchi Chie , Yanagisawa Junn 
Published: January 2012

Abstract

Background
Liver fibrosis is caused by chemicals or viral infection. The progression of liver fibrosis results in hepatocellular carcinogenesis in later stages. Recent studies have revealed the importance of DNA hypermethylation in the progression of liver fibrosis to hepatocellular carcinoma (HCC). However, the importance of DNA methylation in the early-stage liver fibrosis remains unclear.

Methods
To address this issue, we used a pathological mouse model of early-stage liver fibrosis that was induced by treatment with carbon tetrachloride (CCl4) for 2 weeks and performed a genome-wide analysis of DNA methylation status. This global analysis of DNA methylation was performed using a combination of methyl-binding protein (MBP)-based high throughput sequencing (MBP-seq) and bioinformatic tools, IPA and Oncomine. To confirm functional aspect of MBP-seq data, we complementary used biochemical methods, such as bisulfite modification and in-vitro-methylation assays.

Results
The genome-wide analysis revealed that DNA methylation status was reduced throughout the genome because of CCl4 treatment in the early-stage liver fibrosis. Bioinformatic and biochemical analyses revealed that a gene associated with fibrosis, secreted phosphoprotein 1 (Spp1), which induces inflammation, was hypomethylated and its expression was up-regulated. These results suggest that DNA hypomethylation of the genes responsible for fibrosis may precede the onset of liver fibrosis. Moreover, Spp1 is also known to enhance tumor development. Using the web-based database, we revealed that Spp1 expression is increased in HCC.

Conclusions
Our study suggests that hypomethylation is crucial for the onset of and in the progression of liver fibrosis to HCC. The elucidation of this change in methylation status from the onset of fibrosis and subsequent progression to HCC may lead to a new clinical diagnosis.
Identification of unique expression signatures and therapeutic targets in esophageal squamous cell carcinoma
Authors: Yan Wusheng , Shih Joanna H , Rodriguez-Canales Jaime , Tangrea Michael A , Ylaya Kris , Hipp Jason , Player Audrey , Hu Nan , Goldstein Alisa M , Taylor Philip R , Emmert-Buck Michael R , Erickson Heidi S 
Published: January 2012

Abstract

Background
Esophageal squamous cell carcinoma (ESCC), the predominant histological subtype of esophageal cancer, is characterized by high mortality. Previous work identified important mRNA expression differences between normal and tumor cells; however, to date there are limited ex vivo studies examining expression changes occurring during normal esophageal squamous cell differentiation versus those associated with tumorigenesis. In this study, we used a unique tissue microdissection strategy and microarrays to measure gene expression profiles associated with cell differentiation versus tumorigenesis in twelve cases of patient-matched normal basal squamous epithelial cells (NB), normal differentiated squamous epithelium (ND), and squamous cell cancer. Class comparison and pathway analysis were used to compare NB versus tumor in a search for unique therapeutic targets.

Results
As a first step towards this goal, gene expression profiles and pathways were evaluated. Overall, ND expression patterns were markedly different from NB and tumor; whereas, tumor and NB were more closely related. Tumor showed a general decrease in differentially expressed genes relative to NB as opposed to ND that exhibited the opposite trend. FSH and IgG networks were most highly dysregulated in normal differentiation and tumorigenesis, respectively. DNA repair pathways were generally elevated in NB and tumor relative to ND indicating involvement in both normal and pathological growth. PDGF signaling pathway and 12 individual genes unique to the tumor/NB comparison were identified as therapeutic targets, and 10 associated ESCC gene-drug pairs were identified. We further examined the protein expression level and the distribution patterns of four genes: ODC1, POSTN, ASPA and IGF2BP3. Ultimately, three genes (ODC1, POSTN, ASPA) were verified to be dysregulated in the same pattern at both the mRNA and protein levels.

Conclusions
These data reveal insight into genes and molecular pathways mediating ESCC development and provide information potentially useful in designing novel therapeutic interventions for this tumor type.
Synthesis and Solid-State Polymerization of Butadiyne Derivatives with Trialkoxyphenylurethane Groups
Authors: Takahashi Rintaro , Nunokawa Tatsuya , Shibuya Tadahiro , Tomita Ryohei , Tatewaki Yoko , Okada Shuji , Kimura Tatsumi , Shimada Satoru , Matsuda Hiro 
Published: January 2012

Abstract
3,4,5-Trialkoxyphenyl isocyanate derivatives, in which alkoxy was dodecyloxy or methoxy, reacted with 4,6-decadiyn-1,10-diol and 5,7-dodecadiyn-1,12-diol, and four butadiyne derivatives with (N-trialkoxyphenyl)urethane groups were successfully synthesized. Their solid-state polymerization stimulated by UV or γ-ray irradiation was investigated. All monomers in crystals were found to be polymerizable. However, conversion was different depending on the compounds. The derivatives from 5,7-dodecadiyn-1,12-diol showed better conversion, suggesting that they have more favorable monomer arrangement for the solid-state polymerization. Polymers of dodecyloxy derivatives could be partially dissolved in chloroform and they showed solvatochromism when hexane was added to the solution. As was expected from the structure of tridodecyloxyphenyl groups introduced, dodecyloxy derivatives gave organogels in various organic solvents in the concentration less than 2 wt %. However, these gels could not be polymerized by UV irradiation, and the monomer alignment was found to be different between crystalline and gel states.
Subphthalocyanine Derivatives Having a Phosphorus Group as an Axial Substituent
Authors: Yamasaki Yasuhiro , Mori Tomohiro 
Published: January 2012

Abstract
The synthesis and properties of novel subphthalocyanines having a phosphorus group as an axial substituent are reported. The excellent solubility of these materials may provide a good production method for optical films without impairing the excellent properties peculiar to the original subphthalocyanines.
HF–Pyridine: A Versatile Promoter for Monoacylation/Sulfonylation of Phenolic Diols and for Direct Conversion of t-Butyldimethylsilyl Ethers to the Corresponding Acetates
Authors: Michigami Kyosuke , Yoshimoto Kazuya , Hayashi Masahiko 
Published: January 2012

Abstract
Monoacylation and trifluoromethanesulfonylation of phenolic diols were achieved by the aid of HF–pyridine, whereas diacylation occurred with pyridine alone. Furthermore, HF–pyridine was found to promote the direct conversion of t-butyldimethylsilyl ethers to the corresponding acetates.
Fluorescence Quenching of Two Conjugated Polyelectrolytes by Natural Amino Acids and Hemeproteins
Authors: Sun Qinfang , Lu Rong , Yu Anchi 
Published: January 2012

Abstract
We found that none of twenty natural amino acids quenches the fluorescence of anionic PTP, but phenylalanine, tryptophan, and tyrosine do quench obviously the fluorescence of cationic PFP. The overlaps between the Q-band absorption spectrum of myoglobin, cytochrome c, and horseradish peroxidase and the fluorescence emission spectrum of PTP indicate that the fluorescence quenching of PTP by hemeproteins is via fluorescence resonance energy transfer, not via photoinduced electron transfer.
Nickel-catalyzed Diastereoselective Reductive Coupling Reaction of Norbornene with Aldehydes in the Presence of Triethylborane
Authors: Ogata Kenichi , Toh Ayumi , Shimada Daisuke , Fukuzawa Shin-ichi 
Published: January 2012

Abstract
Highly diastereoselective reductive coupling reaction was achieved between an aldehyde and a norbornene to afford an alcohol compound using a nickel/phosphine catalyst system in the presence of a reducing agent. The combination of a PCy3 ligand and triethylborane as the reducing agent proved effective for the reaction. A wide range of aldehydes were found to participate in the reaction with high diastereoselectivities.
Optimization study of the catalytic activity of DNAzymes based on telomeric G-quadruplexes
Authors: Kosman Joanna , Juskowiak Bernard 
Published: January 2012

Abstract
Optimization studies of the procedure for peroxidase activity measurements with DNAzymes based on telomeric sequences and colorimetric indicator reactions are reported. Effect of metal cation, nature and concentration of surfactant, as well as thermal treatment of G-quadruplex sample are investigated. Nature of metal cation exhibited modest influence on the system performance. Great improvement of enzymatic activity of the telomeric quadruplexes in the presence of Brij 58 surfactant was observed. Further improvement of catalytic activity of the system based on human telomeric sequence was attained by applying a thermal treatment (heating/rapid cooling) procedure to prepare G-quadruplex/hemin complexes.
Using 2-D electrophoresis followed by nano HPLC in nuclear protein analysis of MCF-7 breast cancer cell line by MALDI-TOF/TOF
Authors: Tkáčiková Soňa , Talian Ivan , Petrovič Marián , Sabo Ján 
Published: January 2012

Abstract
The biomarker identification is an important tool in early cancer detection. The MCF-7 breast cancer cell line was chosen as a model system. The nuclear proteins were extracted utilizing a commercially manufactured kit and separated on two dimensional (2-D) sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE). The first dimension was performed on isoelectric focusing strips with pH range 4–7. Afterwards the proteins were tryptic digested and identification was performed by matrix assisted laser desorption technique with time of flight mass analyzer (MALDI-TOF/TOF). For unambiguous identification proteins with too low concentration or spots contains protein mixture the nano high performance liquid chromatography (HPLC) was used. The 2-D gel electrophoresis (2-DGE) seems to be a good tool to separate large amount of proteins using relatively simple procedure and its hyphenation with HPLC can create the perfect analytical solution for proteome identification. About 150 nuclei protein spots were visualized and the most abundant of them were identified.
Parametric optimization of neutral linear system with two delays with P-controller
Authors: Duda Józef 
Published: January 2012

Parametric optimization of neutral linear system with two delays with P-controller
In the paper the problem of parametric optimization of a linear neutral system with two delays accomplished with respect to the integral quadratic performance index is formulated and solved. A method of computing the value of performance index relies on determining such a Lyapunov functional defined on the state space that its value for the initial state is equal to that of performance index. In the paper the form of Lyapunov functional is assumed and a method of computing its coefficients is given. An example illustrating the application of the theory discussed is presented. It concerns a system with the P-controller designed to control a plant with two delays both retarded and neutral type. For such a system the value of the considered performance index is determined.
Validation of a program for supercritical power plant calculations
Authors: Kotowicz Janusz , Łukowicz Henryk , Bartela Łukasz , Michalski Sebastian 
Published: January 2012

Validation of a program for supercritical power plant calculations
This article describes the validation of a supercritical steam cycle. The cycle model was created with the commercial program GateCycle and validated using in-house code of the Institute of Power Engineering and Turbomachinery. The Institute's in-house code has been used extensively for industrial power plants calculations with good results. In the first step of the validation process, assumptions were made about the live steam temperature and pressure, net power, characteristic quantities for high- and low-pressure regenerative heat exchangers and pressure losses in heat exchangers. These assumptions were then used to develop a steam cycle model in Gate-Cycle and a model based on the code developed in-house at the Institute of Power Engineering and Turbomachinery. Properties, such as thermodynamic parameters at characteristic points of the steam cycle, net power values and efficiencies, heat provided to the steam cycle and heat taken from the steam cycle, were compared. The last step of the analysis was calculation of relative errors of compared values. The method used for relative error calculations is presented in the paper. The assigned relative errors are very slight, generally not exceeding 0.1%. Based on our analysis, it can be concluded that using the GateCycle software for calculations of supercritical power plants is possible.
Le « Dieu vivant » romantique
Authors: Rétat Claude 
Published: January 2012

L’expression « Dieu vivant » provient de la Bible (nombreuses occurrences dans l’ancien et dans le nouveau Testament). Elle figure en bonne place dans les dictionnaires du XIX e siècle, portant la notion d’un « vrai » Dieu (par opposition aux « idoles ») et d’un Dieu « personnel » (par opposition aux idées abstraites), conçu comme principe de toute vie. Cette étude part d’un constat : la fréquence de réemploi en contexte romantique, la richesse des potentialités de réutilisation. « Dieu vivant » se constitue en formule-bascule, pour réinvestir des représentations théologiques et déboucher sur un nouvel imaginaire du vivant . La formule est pour ainsi dire active en romantisme : ainsi, chez Hugo, est-elle la formule même qui parle au vivant et le met en branle (« Le cèdre »). Il s’agit donc ici de tracer les cadres de ce ré-emploi romantique. Est analysé l’investissement massif de la formule, autour de 1830, par la littérature saint-simonienne, au service d’une pensée de l’organique, du lien, du « corps social », et plus encore d’une pratique vivante de la réflexion sur le vivant. Son application à une pensée totalisante de l’histoire, de l’humanité et de la nature (« Dieu vivant » permettant de théologiser la pensée de la vie universelle, du vivant mû par le même moteur) ressort de l’œuvre d’Edgar Quinet. Michelet apporte une vue du Dieu vivant, pièce maîtresse d’un système d’auto-création du sujet par lui-même, qui déplace peut-être la perspective du vivant à celle de la vitalité .
Le corps des rois des rois dans la ville : Ménélik II et Haylé Sellasé à Addis Abeba
Authors: Sohier Estelle 
Published: January 2012

Ménélik II et Haylé Sellasé, les deux principaux souverains éthiopiens du xxe siècle, ont tous deux connu des fins de règne et de vie troubles, caractérisées par l’absence de funérailles au moment de leur disparition. Différentes sources endogènes et exogènes sont disponibles pour mieux appréhender leur histoire, au nombre desquelles des monuments visibles aujourd’hui dans la capitale éthiopienne. Le croisement des sources et des regards éthiopiens et étrangers permet de démêler l’écheveau des circonstances de la disparition de Ménélik II et les raisons de la dissimulation du corps du roi défunt. Il permet aussi de comprendre comment son successeur, Haylé Sellasé, a géré politiquement le corps – et, partant, la mémoire – de son prédécesseur, en plaçant également au cœur de sa politique symbolique son propre futur lieu de sépulture. Les monuments d’Addis Abeba transmettent nombre d’informations sur l’histoire des funérailles royales en Éthiopie au xxe siècle, mais aussi sur la place du corps des souverains défunts dans le système politico-religieux de la royauté éthiopienne contemporaine.
DNA Double-Strand Breaks Relieve USF-Mediated Repression of Dβ2 Germline Transcription in Developing Thymocytes
Authors: Stone Jennifer L. , McMillan Ruth E. , Skaar David A. , Bradshaw Justin M. , Jirtle Randy L. , Sikes Michael L. 
Published: January 2012

Abstract
Activation of germline promoters is central to V(D)J recombinational accessibility, driving chromatin remodeling, nucleosome repositioning, and transcriptional read-through of associated DNA. We have previously shown that of the two TCRβ locus (Tcrb) D segments, Dβ1 is flanked by an upstream promoter that directs its transcription and recombinational accessibility. In contrast, transcription within the DJβ2 segment cluster is initially restricted to the J segments and only redirected upstream of Dβ2 after D-to-J joining. The repression of upstream promoter activity prior to Tcrb assembly correlates with evidence that suggests DJβ2 recombination is less efficient than that of DJβ1. Because inefficient DJβ2 assembly offers the potential for V-to-DJβ2 recombination to rescue frameshifted V-to-DJβ1 joints, we wished to determine how Dβ2 promoter activity is modulated upon Tcrb recombination. In this study, we show that repression of the otherwise transcriptionally primed 5′Dβ2 promoter requires binding of upstream stimulatory factor (USF)-1 to a noncanonical E-box within the Dβ2 12-recombination signal sequence spacer prior to Tcrb recombination. USF binding is lost from both rearranged and germline Dβ2 sites in DNA-dependent protein kinase, catalytic subunit-competent thymocytes. Finally, genotoxic dsDNA breaks lead to rapid loss of USF binding and gain of transcriptionally primed 5′Dβ2 promoter activity in a DNA-dependent protein kinase, catalytic subunit-dependent manner. Together, these data suggest a mechanism by which V(D)J recombination may feed back to regulate local Dβ2 recombinational accessibility during thymocyte development.
Adjuvant Immunotherapy of Experimental Autoimmune Encephalomyelitis: Immature Myeloid Cells Expressing CXCL10 and CXCL16 Attract CXCR3+CXCR6+ and Myelin-Specific T Cells to the Draining Lymph Nodes Rather Than the Central Nervous System
Authors: O’Connor Richard A. , Li Xujian , Blumerman Seth , Anderton Stephen M. , Noelle Randolph J. , Dalton Dyana K. 
Published: January 2012

Abstract
CFA is a strong adjuvant capable of stimulating cellular immune responses. Paradoxically, adjuvant immunotherapy by prior exposure to CFA or live mycobacteria suppresses the severity of experimental autoimmune encephalomyelitis (EAE) and spontaneous diabetes in rodents. In this study, we investigated immune responses during adjuvant immunotherapy of EAE. Induction of EAE in CFA-pretreated mice resulted in a rapid influx into the draining lymph nodes (dLNs) of large numbers of CD11b+Gr-1+ myeloid cells, consisting of immature cells with ring-shaped nuclei, macrophages, and neutrophils. Concurrently, a population of mycobacteria-specific IFN-γ–producing T cells appeared in the dLNs. Immature myeloid cells in dLNs expressed the chemokines CXCL10 and CXCL16 in an IFN-γ–dependent manner. Subsequently, CD4+ T cells coexpressing the cognate chemokine receptors CXCR3 and CXCR6 and myelin oligodendrocyte glycoprotein (MOG)-specific CD4+ T cells accumulated within the chemokine-expressing dLNs, rather than within the CNS. Migration of CD4+ T cells toward dLN cells was abolished by depleting the CD11b+ cells and was also mediated by the CD11b+ cells alone. In addition to altering the distribution of MOG-specific T cells, adjuvant treatment suppressed development of MOG-specific IL-17. Thus, adjuvant immunotherapy of EAE requires IFN-γ, which suppresses development of the Th17 response, and diverts autoreactive T cells away from the CNS toward immature myeloid cells expressing CXCL10 and CXCL16 in the lymph nodes.
Skewing of the NK Cell Repertoire by MHC Class I via Quantitatively Controlled Enrichment and Contraction of Specific Ly49 Subsets
Authors: Brodin Petter , Lakshmikanth Tadepally , Kärre Klas , Höglund Petter 
Published: January 2012

AbstractA major task for the immune system is to secure powerful immune reactions while preserving self-tolerance. This process is particularly challenging for NK cells, for which tolerizing inhibitory receptors for self-MHC class I is both cross-reactive and expressed in an overlapping fashion between NK cells. We show in this study that during an education process, self-MHC class I molecules enrich for potentially useful and contract potentially dangerous NK cell subsets. These processes were quantitatively controlled by the expression level of the educating MHC class I allele, correlated with susceptibility to IL-15 and sensitivity to apoptosis in relevant NK cell subsets, and were linked to their functional education. Controlling the size of NK cell subsets with unique compositions of inhibitory receptors may represent one mechanism by which self-MHC class I molecules generate a population of tolerant NK cells optimally suited for efficient missing self-recognition.
Distinct Kinetics of Gag-Specific CD4+ and CD8+ T Cell Responses during Acute HIV-1 Infection
Authors: Riou Catherine , Ganusov Vitaly V. , Campion Suzanne , Mlotshwa Mandla , Liu Michael K. P. , Whale Victoria E. , Goonetilleke Nilu , Borrow Persephone , Ferrari Guido , Betts Michael R. , Haynes Barton F. , McMichael Andrew J. , Gray Clive M. 
Published: January 2012

Abstract
HIV infection is characterized by a gradual deterioration of immune function, mainly in the CD4 compartment. To better understand the dynamics of HIV-specific T cells, we analyzed the kinetics and polyfunctional profiles of Gag-specific CD4+ and CD8+ T cell responses in 12 subtype C-infected individuals with different disease-progression profiles, ranging from acute to chronic HIV infection. The frequencies of Gag-responsive CD4+ and CD8+ T cells showed distinct temporal kinetics. The peak frequency of Gag-responsive IFN-γ+CD4+ T cells was observed at a median of 28 d (interquartile range: 21–81 d) post-Fiebig I/II staging, whereas Gag-specific IFN-γ+CD8+ T cell responses peaked at a median of 253 d (interquartile range: 136–401 d) and showed a significant biphasic expansion. The proportion of TNF-α–expressing cells within the IFN-γ+CD4+ T cell population increased (p = 0.001) over time, whereas TNF-α–expressing cells within IFN-γ+CD8+ T cells declined (p = 0.005). Both Gag-responsive CD4+ and CD8+ T cells showed decreased Ki67 expression within the first 120 d post-Fiebig I/II staging. Prior to the disappearance of Gag-responsive Ki67+CD4+ T cells, these cells positively correlated (p = 0.00038) with viremia, indicating that early Gag-responsive CD4 events are shaped by viral burden. No such associations were observed in the Gag-specific CD8+ T cell compartment. Overall, these observations indicated that circulating Gag-responsive CD4+ and CD8+ T cell frequencies and functions are not synchronous, and properties change rapidly at different tempos during early HIV infection.
Fine-Grained Emotion Detection in Suicide Notes: A Thresholding Approach to Multi-Label Classification
Authors: Luyckx Kim , Vaassen Frederik , Peersman Claudia , Daelemans Walter 
Published: January 2012

We present a system to automatically identify emotion-carrying sentences in suicide notes and to detect the specific fine-grained emotion conveyed. With this system, we competed in Track 2 of the 2011 Medical NLP Challenge, 14 where the task was to distinguish between fifteen emotion labels, from guilt, sorrow, and hopelessness to hopefulness and happiness. Since a sentence can be annotated with multiple emotions, we designed a thresholding approach that enables assigning multiple labels to a single instance. We rely on the probability estimates returned by an SVM classifier and experimentally set thresholds on these probabilities. Emotion labels are assigned only if their probability exceeds a certain threshold and if the probability of the sentence being emotion-free is low enough. We show the advantages of this thresholding approach by comparing it to a naïve system that assigns only the most probable label to each test sentence, and to a system trained on emotion-carrying sentences only.