gebhart/patrepeval huggingface dataset:
Label-Free Detection of Differential Protein Expression by LC/MALDI Mass Spectrometry (2008)

Protein abundance changes during disease or experimental perturbation are increasingly analyzed by label-free LC/MS approaches. Here we demonstrate the use of LC/MALDI MS for label-free detection of protein expression differences using Escherichia coli cultures grown on arabinose, fructose or glucose as a carbon source. The advantages of MALDI, such as detection of only singly charged ions, and MALDI plate archiving to facilitate retrospective MS/MS data collection are illustrated. MALDI spectra from RP chromatography of tryptic digests of the E. coli lysates were aligned and quantitated using the Rosetta Elucidator system. Approximately 5000 peptide signals were detected in all LC/MALDI runs spanning over 3 orders of magnitude of signal intensity. The average coefficients of variation for all signals across the entire intensity range in all technical replicates were found to be <25%. Pearson correlation coefficients from 0.93 to 0.98 for pairwise comparisons illustrate high replicate reproducibility. Expression differences determined by Analysis of Variance highlighted over 500 isotope clusters ( p < 0.01), which represented candidates for targeted peptide identification using MS/MS. Biologically interpretable protein identifications that could be derived underpin the general utility of this label-free LC/MALDI strategy.
Injury-induced BMP signaling negatively regulates Drosophila midgut homeostasis (2013)

Although much is known about injury-induced signals that increase rates of Drosophila melanogaster midgut intestinal stem cell (ISC) proliferation, it is largely unknown how ISC activity returns to quiescence after injury. In this paper, we show that the bone morphogenetic protein (BMP) signaling pathway has dual functions during midgut homeostasis. Constitutive BMP signaling pathway activation in the middle midgut mediated regional specification by promoting copper cell differentiation. In the anterior and posterior midgut, injury-induced BMP signaling acted autonomously in ISCs to limit proliferation and stem cell number after injury. Loss of BMP signaling pathway members in the midgut epithelium or loss of the BMP signaling ligand decapentaplegic from visceral muscle resulted in phenotypes similar to those described for juvenile polyposis syndrome, a human intestinal tumor caused by mutations in BMP signaling pathway components. Our data establish a new link between injury and hyperplasia and may provide insight into how BMP signaling mutations drive formation of human intestinal cancers.
CD4 T Cells and Their Role in Antitumor Immune Responses (1999)

The specificity and power of the cellular arm of the immune system may provide new therapeutic approaches to cancer. With the assumption that T cells might be able to recognize and eliminate cancer cells with the same efficiency as virus-infected cells, investigators have searched many years for ways to trigger or amplify the patient's inadequate immune response to tumors. Much attention has been given to the role of CD8+ CTLs because most tumors are MHC class I positive, but negative for MHC class II. Moreover, CD8+ CTLs are able to lyse tumor cells directly upon recognition of peptide–MHC class I complexes expressed by the tumor, and their ability to eradicate large tumor masses in vivo has been demonstrated. The focus in cancer immunology on CD8+ T cell responses is also exemplified by an increasing list of tumor antigens identified by tumor-reactive CD8+ CTLs. CD4+ Th cells have received far less attention, which is remarkable given the pivotal role of these cells in regulating most antigen-specific immune responses. Until now, only a few Th epitopes derived from human tumor antigens recognized by CD4+ Th cells have been identified (1, 2). Three studies published in this issue describe the identification of melanoma antigens that are recognized by CD4+ T cells in the context of MHC class II molecules (3–5). Charting the Th response against human melanoma as well as other tumors is important for the development of optimal anticancer vaccines and for the design of other T cell–related therapeutic modalities in cancer.
Genetically directed syntheses of new polymeric materials. Expression of artificial genes encoding proteins with repeating -(AlaGly)3ProGluGly- elements (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGenetically directed syntheses of new polymeric materials. Expression of artificial genes encoding proteins with repeating -(AlaGly)3ProGluGly- elementsKevin P. McGrath, Maurille J. Fournier, Thomas L. Mason, and David A. TirrellCite this: J. Am. Chem. Soc. 1992, 114, 2, 727–733Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/ja00028a048https://doi.org/10.1021/ja00028a048research-articleACS PublicationsRequest reuse permissionsArticle Views616Altmetric-Citations165LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Adiabatic and Multimode Interference Couplers on Silicon-on-Insulator (2006)

Adiabatic and multimode interference (MMI) 3-dB couplers based on silicon-on-insulator rib waveguides were fabricated and measured. For testing purposes, pairs of identical couplers were cascaded to form Mach-Zehnder interferometers. The adiabatic couplers showed excess on-chip loss of ~0.5 dB, extinction ratio (ER) of 15-20 dB, and a wide spectral range. The MMI couplers processed on the same wafer showed similar loss per coupler, higher ER, and limited spectral characteristics
Codeine Intoxication Associated with Ultrarapid CYP2D6 Metabolism (2004)

Life-threatening opioid intoxication developed in a patient after he was given small doses of codeine for the treatment of a cough associated with bilateral pneumonia. Codeine is bioactivated by CYP2D6 into morphine, which then undergoes further glucuronidation. CYP2D6 genotyping showed that the patient had three or more functional alleles, a finding consistent with ultrarapid metabolism of codeine. We attribute the toxicity to this genotype, in combination with inhibition of CYP3A4 activity by other medications and a transient reduction in renal function.
β-Catenin Expression in the Bone Marrow Microenvironment Is Required for Long-Term Maintenance of Primitive Hematopoietic Cells (2009)

Hematopoiesis is dependent upon the bone marrow microenvironment, which is comprised of multiple mesenchymal cell types, including fibroblasts, endothelial cells, osteoblasts, and stroma progenitors. The canonical Wnt signaling pathway, which relies on the beta-catenin protein to mediate its signal, is necessary for the normal development of mesenchymal tissue. We hypothesized that canonical Wnt signaling regulates the cellular composition and function of the bone marrow microenvironment. We observed that a beta-catenin-deficient bone marrow microenvironment maintained hematopoietic stem cells but exhibited a decreased capacity to support primitive hematopoietic cells. These results correlated with decreased numbers of osteoblasts and with decreased production of basic fibroblast growth factor, stem cell factor, and vascular cell adhesion molecule-1. From these data, we propose a model in which beta-catenin in the microenvironment is required noncell autonomously for long-term maintenance of hematopoietic progenitors.
Molecular Cloning and Characterization of a Novel Retinoic Acid-inducible Gene That Encodes a Putative G Protein-coupled Receptor (1998)

The effects of retinoids such as all-trans-retinoic acid (ATRA) on cell growth, differentiation, and apoptosis are thought to be mediated by nuclear retinoid receptors, which are involved in ligand-dependent transcriptional activation of target genes. Using differential display, we identified the cDNA of a novel gene, designated retinoic acid-inducible gene 1 (RAIG1), which was induced by ATRA in the squamous carcinoma cell line UMSCC-22B. Two RAIG1 transcripts of 2.4 and 6.8 kilobase pairs, respectively, have the same ORF that encodes a 357-amino acid polypeptide. RAIG1 mRNA is expressed at high level in fetal and adult lung tissues. Induction of RAIG1 expression by ATRA is rapid (within 2 h) and dose-dependent in the range between 1 nM to 1 microM. The constitutive RAIG1 mRNA levels, which were low in three of five head and neck and four of six lung cancer cell lines, increased after ATRA treatment in most cell lines. The deduced RAIG1 protein sequence contains seven transmembrane domains, characteristic of G protein-coupled receptors. A fusion protein of RAIG1 and the green fluorescent protein was localized in the cell surface membrane and perinuclear vesicles in transiently transfected cells. RAIG1 was mapped to chromosome 12p12. 3-p13. Our results provide novel evidence for a possible interaction between retinoid and G protein signaling pathways.
Catalyst-free aldol condensation of ketones and isatins under mild reaction conditions in DMF with molecular sieves 4 Å as additive (2009)

In the presence of molecular sieve (MS) 4 Å in DMF, a catalyst-free aldol condensation of a variety of aromatic and aliphatic ketones with isatins under mild reaction conditions has been developed. This approach may provide access to a wide range of 3-substituted-3-hydroxyindolin-2-ones in good to excellent yields.
Following TRAIL’s path in the immune system (2009)

The members of the tumour necrosis factor (TNF) superfamily of cytokines play important roles in the regulation of various immune-cell functions. Likewise, induction of cell death by apoptosis is indispensable for the normal functioning of the immune system. There are two major pathways of apoptosis induction. The intrinsic, or mitochondrial, pathway is regulated by the activation and interaction of members of the Bcl-2 family. The extrinsic, or death receptor, pathway is triggered by certain TNF family members when they engage their respective cognate receptors on the surface of the target cell. Hence, cell-to-cell-mediated death signals are induced by activation of these death receptor-ligand systems. Besides TNF itself and the CD95 (Fas/APO-1) ligand (FasL/Apo1L), the TNF-related apoptosis-inducing ligand (TRAIL/Apo2L) belongs to the subfamily of ligands that is responsible for extrinsic induction of cell death. Depending on their status of stimulation, TRAIL can be expressed by various cells of the immune system, amongst them natural killer (NK) cells, T cells, natural killer T cells (NKT cells), dendritic cells and macrophages. TRAIL has been implicated in immunosuppressive, immunoregulatory and immune-effector functions. With respect to pathological challenges, TRAIL and its receptors have been shown to play important roles in the immune response to viral infections and in immune surveillance of tumours and metastases. In this review we summarize the current knowledge on the role of TRAIL and its receptors in the immune system and, based on this, we discuss future directions of research into the diverse functions of this fascinating receptor-ligand system.
Roles of Disulfide Bonds in Bacterial Alkaline Phosphatase (1997)

Alkaline phosphatase of Escherichia coli (a homodimeric protein found in the periplasmic space) contains two intramolecular disulfide bonds (Cys-168-Cys-178 and Cys-286-Cys-336) that are formed after export to the periplasmic space. The location-specific folding character of this enzyme allowed its wide usage as a reporter of protein localization in prokaryotic cells. To study the roles of disulfide bonds in alkaline phosphatase, we eliminated each of them by Cys to Ser mutations. Intracellular stability of alkaline phosphatase decreased in the absence of either one or both of the disulfide bonds. The mutant proteins were stabilized in a DegP protease-deficient strain, allowing accumulation at significant levels and subsequent characterization. A mutant protein that lacked the N-terminally located disulfide bond (Cys-168-Cys-178) was found to have Cys-286 and Cys-336 residues disulfide-bonded, to have a dimeric structure, and to have almost full enzymatic activity. Nevertheless, the mutant protein lost the trypsin-resistant conformation that is characteristically observed for the wild-type enzyme. In contrast, mutants lacking Cys-286 and Cys-336 were monomeric and inactive. These results indicate that the Cys-286-Cys-336 disulfide bond is required and is sufficient for correctly positioning the active site region of this enzyme, but such an active conformation is still insufficient for the conformational stability of the enzyme. Thus, a fully active state of this enzyme can be formed without full protein stability, and the two disulfide bonds differentially contribute to these properties.
Adapting Content for Mobile Devices in Heterogeneous Collaboration Environments. (2003)

The portability of new miniaturized devices, together with their ability to connect conveniently to networks in different places, makes mobile computing possible. Recent advances that have led to increasing bandwidths, for wireless communications, enable mobile users to utilize a vast range of sophisticated services such as real-time collaborative services. Garnet Collaborative system is a universal accessible collaborative environment supporting synchronous communication and universal accessibility from a wide range of devices. Garnet Message System Micro Edition (GMSME) is developed to integrate heterogeneous mobile devices into the Garnet collaborative system. Garnet integrates desktop in traditional LAN environments, wireless LAN based mobile devices, and pervasive 3G communication technology seamlessly. In this paper, we describe the process of adapting content in GMSME. GMSME provides application-aware transcoding, to tune the shared resources, for different collaborative models. Also, it optimizes shared resources for each heterogeneous client environments.
Super-hydrophobicity fundamentals: implications to biofouling prevention (2006)

The theory of wetting on super-hydrophobic surfaces is presented and discussed, within the general framework of equilibrium wetting and contact angles. Emphasis is put on the implications of super-hydrophobicity to the prevention of biofouling. Two main lines of thought are discussed, viz. i) "mirror imaging" of the Lotus effect, namely designing a surface that repels biological entities by being super-hydrophilic, and ii) designing a surface that minimises the water-wetted area when submerged in water (by keeping an air film between the water and the surface), so that the suspended biological entities have a low probability of encountering the solid surface.
PARP inhibition: a novel approach to treat ischaemia/reperfusion and inflammation-related injuries (1999)

No abstract.
Introducción a las Epistemologías Sistémico/Constructivistas (1997)

En el decenio que acompana al fin de siglo no solo presenciamos el derrumbe de algunos estados - nacionales, sistemas politicos y economicos, tambien las bases epistemologicas que sustentaron, durante largo tiempo, nuestros modos de hacer investigacion social han tenido importantes e inesperados vuelcos. A estas alturas no puede asegurarse el tipo de consenso que se alcanzara en el futuro, solo es evidente que estamos en presencia de una pluralidad competitiva de epistemologias con sus correspondientes opciones metodologicas. Estas, en su cierre, se bifurcan en epistemologias tradicionales que tienen por centro lo observado y en las emergentes epistemologias del observador.
Dietary Supplementation of Chardonnay Grape Seed Flour Reduces Plasma Cholesterol Concentration, Hepatic Steatosis, and Abdominal Fat Content in High-Fat Diet-Induced Obese Hamsters (2014)

The mechanisms for the hypocholesterolemic and antiobesity effects of grape seed flours derived from white and red winemaking processing were investigated using male Golden Syrian hamsters fed high-fat (HF) diets supplemented with 10% partially defatted grape seed flours from Chardonnay (ChrSd), Cabernet Sauvignon (CabSd), or Syrah (SyrSd) pomace as compared to a HF control diet for 3 weeks. Hamsters fed the ChrSd diet had significantly lowered plasma total-, VLDL-, and LDL-cholesterol concentrations compared to the CabSd, SyrSd, and control diets. The improved plasma cholesterol after ChrSd was correlated with the up-regulation of hepatic genes related to cholesterol (CYP51) and bile acid (CYP7A1) synthesis as well as LDL-cholesterol uptake (LDLR). A reduction of hepatic lipid content was associated with altered expression of the genes related to lipid metabolism. However, fecal total lipid content was not changed. Expression of ileal apical sodium bile acid transporter (ASBT) was not affected by ChrSd, indicating unchanged ileal bile acid reabsorption. The antiobesity effect of the ChrSd diet appears to be related to expression of adipogenesis- and inflammation-related genes in adipose tissue. These findings suggest that flavonoid-rich Chardonnay grape seed flour induced cholesterol-lowering, antiobesity, and anti-inflammatory health benefits and attenuation of hepatic steatosis via regulation of gene expression related to cholesterol, bile acid, and lipid metabolism in liver and adipose tissue.
SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping (2010)

The user interfaces for functional SNP analyses have been substantially improved and integrated. SNP-RFLPing 2 offers a new and user-friendly interface for RFLP genotyping that can be used in association studies and is freely available at http://bio.kuas.edu.tw/snp-rflping2.
Specific Delivery of Therapeutic RNAs to Cancer Cells via the Dimerization Mechanism of phi29 Motor pRNA (2005)

The application of small RNA in therapy has been hindered by the lack of an efficient and safe delivery system to target specific cells. Packaging RNA (pRNA), part of the DNA-packaging motor of bacteriophage phi29(Phi29), was manipulated by RNA nanotechnology to make chimeric RNAs that form dimers via interlocking right- and left-hand loops. Fusing pRNA with receptor-binding RNA aptamer, folate, small interfering RNA (siRNA), ribozyme, or another chemical group did not disturb dimer formation or interfere with the function of the inserted moieties. Incubation of cancer cells with the pRNA dimer, one subunit of which harbored the receptor-binding moiety and the other harboring the gene-silencing molecule, resulted in their binding and entry into the cells, and subsequent silencing of anti/proapoptotic genes. The chimeric pRNA complex was found to be processed into functional double-stranded siRNA by Dicer (RNA-specific endonuclease). Animal trials confirmed the suppression of tumorigenicity of cancer cells by ex vivo delivery. It has been reported [Shu, D., Moll, W.-D., Deng, Z., Mao, C., and Guo, P. (2004). Nano Lett. 4:1717-1724] that RNA can be used as a building block for bottom-up assembly in nanotechnology. The assembly of protein-free 25-nm RNA nanoparticles reported here will allow for repeated long-term administration and avoid the problems of short retention time of small molecules and the difficulties in the delivery of particles larger than 100 nm.
Expression of MAGE‐1, MAGE‐2, MAGE‐3/‐6 and MAGE‐4A/‐4B genes in ovarian tumors (1995)

MAGE genes encoding tumor-rejection antigens recognized by cytotoxic T lymphocytes are expressed at the mRNA level in various malignant tumors. We have investigated the expression of genes MAGE-1, -2, -3/-6 and -4a/-4b at the mRNA level in malignant and non-malignant ovarian tumors as well as in normal ovaries by reverse transcription-polymerase chain reaction. MAGE-1, -2, -3/-6 and -4a/-4b were expressed in 12, 5, 11 and 4 of 58 malignant tumors, respectively. The majority of these MAGE-mRNA-positive tumors were histologically surface-epithelial-stromal tumors, in particular serous adenocarcinomas. They mostly consisted of either advanced-stage or recurrent tumors. In contrast, neither benign tumors nor normal ovaries expressed any of the MAGE genes investigated. A 46-kDa MAGE-1 protein was identified in MAGE-1-mRNA-positive serous adenocarcinomas by immunoblot analysis with polyclonal anti-MAGE-1 antibody. These results provide important information for specific immunotherapy of ovarian serous adenocarcinomas with MAGE gene products.
A Surprising Cross-Species Conservation in the Genomic Landscape of Mouse and Human Oral Cancer Identifies a Transcriptional Signature Predicting Metastatic Disease (2014)

These data demonstrate surprising cross-species genomic conservation that has translational relevance for human oral squamous cell cancer. Clin Cancer Res; 20(11); 2873-84. ©2014 AACR.
A Location System with RFID Technology in Building Construction Site (2005)

A Location System with RFID Technology in Building Construction Site Soungho Chae, Naruo Kano Abstract: In this paper, the authors explained the overview of data sampling method for development of a location system for workers using RFID technology. Data is the RSSI (Receive Signal Strength Indication) from RFID tag attached to the worker installing a rolling shutter, and was obtained from antennas and RFID readers set around the construction site. Discriminant analysis was done using RSSI collected and the area where worker is performing a task, and a estimation model of the working area was prepared. The model had a range of the percentage of correctly classified from 3% to 30%. The authors suggested the method to make estimate by using integrated models prepared in respect of RFID readers, and showed the percentage of correctly classified of 43.2%. According to the result, the authors confirmed the possibility of the location system with RFID technology, and mentioned the factors necessary to develop for further practical use. Keywords: Location system, RFID Technology, Building construction site, Discriminant analysis model DOI: https://doi.org/10.22260/ISARC2005/0020 Download fulltext Download BibTex Download Endnote (RIS) TeX Import to Mendeley