gebhart/patrepeval huggingface dataset:
The Human Interferon Receptor:  NMR-Based Modeling, Mapping of the IFN-α2 Binding Site, and Observed Ligand-Induced Tightening, (2002)

The human interferon receptor (IFNAR) mediates the antiviral and antiproliferative activities of type I interferons (IFNs). This receptor is comprised of subunits IFNAR1 and IFNAR2, the latter exhibiting nanomolar affinity for IFNs. Here the extracellular domain of IFNAR2 (IFNAR2-EC), a soluble 25 kDa IFN-binding polypeptide, and its complex with IFN-alpha 2 were studied using multidimensional NMR. IFNAR2-EC is comprised of two fibronectin-III (FN-III) domains connected by a helical hinge region. The deduced global fold was utilized to improve the alignment of IFNAR2-EC against structurally related receptors and to model its structure. A striking feature of IFNAR2-EC is the limited and localized deviations in chemical shifts exhibited upon ligand binding, observed for only 15% of its backbone (1)H and (15)N nuclei. Analysis of these deviations maps the IFN-alpha 2 binding site upon IFNAR2-EC to a contiguous surface on the N-terminal domain, including the S3-S4 loop (residues 44-53), the S5-S6 loop and S6 beta-strand (residues 74-82), and the S7 beta-strand and the hinge region (residues 95-105). The C-terminal domain contributes only marginally to ligand binding, and no change in the hypothesized interdomain interface is observed. The proposed binding domain encompasses all residues implicated by mutagenesis studies in IFN binding, and suggests adjacent residues cooperate in forming the binding surface. D(2)O-exchange experiments indicate that binding of IFN-alpha2 induces tightening of the N-terminal domain of IFNAR2-EC. This increase in receptor rigidity may play an important role in initiating the intracellular stage of the IFN signaling cascade.
Interleaved 3D‐CNNs for joint segmentation of small‐volume structures in head and neckCTimages (2018)

An accurate and automatic segmentation method has been proposed for small tissues in head and neck CT images, which is important for the planning of radiotherapy.
Recombinant Protein Production in Yeasts (2011)

Recombinant protein production is a multibillion-dollar market. The development of a new product begins with the choice of a production host. While one single perfect host for every protein does not exist, several expression systems ranging from bacterial hosts to mammalian cells have been established. Among them, yeast cell factories combine the advantages of being single cells, such as fast growth and easy genetic manipulation, as well as eukaryotic features including a secretory pathway leading to correct protein processing and post-translational modifications. In this respect, especially the engineering of yeast glycosylation to produce glycoproteins of human-like glycan structures is of great interest. Additionally, different attempts of cellular engineering as well as the design of different production processes that are leading to improved productivities are presented. With the advent of cheaper next-generation sequencing techniques, systems biotechnology approaches focusing on genome scale analyses will advance and accelerate yeast cell factories and thus recombinant protein production processes in the near future. In this review we summarize advantages and limitations of the main and most promising yeast hosts, including Saccharomyces cerevisiae, Pichia pastoris, and Hansenula polymorpha as those presently used in large scale production of heterologous proteins.
Abstract 4767: C6 ceramide sensitizes multiple aggressive pancreatic cancer cell lines to gemcitabine, paclitaxel and cetuximab mediated anti tumor effects in vivo and in vitro (2011)

Abstract Introduction: Pancreatic adenocarcinoma continues to be a highly lethal malignancy (5 yr survival 5%) poorly responsive to all chemo radiation therapies, with only modest improvement with Gemcitabine the current “main line” drug. We have previously demonstrated the C6 Ceramide chemo enhancement of Gemcitabine and other pancreatic chemo agents. The current study explores the mechanism of C6 Ceramide effects on pancreatic chemo resistance pathways – pro-survival and ras-signaling in pancreatic cancer cells. Methods: In vivo: 2-3 month SCID male mice with pancreatic (pan) tumor implants (2 × 106 L3.6 cells) received intraperitoneal (I.P.) injections (3x/wk) of Paclitaxel (Pax) (3.0mg/gm), Gemcitabine (Gem, 10mg/gm) with/without C6 ceramide (10mg/ml) and were observed 6 weeks and tumor response/survival recorded. In vitro: Drug dose Pax 3 ug/ml, Gem 3 ug/ml, C6 Ceramide 10 ug/ml. The MTT anti tumor response was measured in 3 pancreatic lines L3.6, PANC-1, and MIA (Kras mutated). Signaling activation by Western blot utilized antibodies: LY294002, and Wortmannin to block PI3K/AKT pathway, U0126 and PD 98059 to block ERK pathway and Rapamycin to block mTORC1 pathway. Results: Combined therapy with C6 Ceramide induced significant inhibition of exponential tumor growth and prolonged survival by Gem and Pax. Administration of Gem or Pax with C6 Ceramide induced a significant increase in cell death and apoptosis in pancreatic cancer cells (L3.6, PANC-1 and MIA PaCa-2) which were associated with inhibiting perturbations of cell signaling pathways including pro-survival PI3K/Akt/mTOR, and ERK/MAPK, Ras signaling pathways. Pharmacological inhibition with specific signaling pathway inhibitors enhanced cytotoxicity by Gem or Pax, suggesting that survival pathway inhibition might be the key mechanism contributing to C6 Ceramide synergism of Pax or Gem anti-tumor effects. We also showed C6 ceramide potentiation of Cetuximab anti tumor effects on Kras mutant MIA cells thus overcoming (EGFR mAb) resistance by inhibiting pro-survival PI3K/AKT/mTOR pathways and bypassing K-RAS mutant Ras-ERK pathways. Conclusion: C6 Ceramide an apoptosis signal potentiates the anti tumor effects of chemo agents Gemcitabine and Paclitaxel and the biologic EGFR Inhibitor Cetuximab against 3 aggressive pancreatic cancer cell lines by apparent inhibition of the pro-survival PI3K/AKT/mTOR pathways and the Kras mutated ERK/MAPK pathway. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4767. doi:10.1158/1538-7445.AM2011-4767
Optimal selection of speech data for automatic speech recognition systems (2002)

\n Contains fulltext :\n 75067.pdf (author's version ) (Open Access)\n
Sustained transgene expression despite T lymphocyte responses in a clinical trial of rAAV1-AAT gene therapy (2009)

Alpha-1 antitrypsin (AAT) deficiency is well-suited as a target for human gene transfer. We performed a phase 1, open-label, dose-escalation clinical trial of a recombinant adeno-associated virus (rAAV) vector expressing normal (M) AAT packaged into serotype 1 AAV capsids delivered by i.m. injection. Nine AAT-deficient subjects were enrolled sequentially in cohorts of 3 each at doses of 6.9 x 10(12), 2.2 x 10(13), and 6.0 x 10(13) vector genome particles per patient. Four subjects receiving AAT protein augmentation discontinued therapy 28 or 56 days before vector administration. Vector administration was well tolerated, with only mild local reactions and 1 unrelated serious adverse event (bacterial epididymitis). There were no changes in hematology or clinical chemistry parameters. M-specific AAT was expressed above background in all subjects in cohorts 2 and 3 and was sustained at levels 0.1% of normal for at least 1 year in the highest dosage level cohort, despite development of neutralizing antibody and IFN-gamma enzyme-linked immunospot responses to AAV1 capsid at day 14 in all subjects. These findings suggest that immune responses to AAV capsid that develop after i.m. injection of a serotype 1 rAAV vector expressing AAT do not completely eliminate transduced cells in this context.
Fluid program built around hole cleaning, protecting formation (1990)

The potentially severe borehole problems intrinsic with horizontal drilling can be minimized dramatically with the selection of a nondamaging drilling fluid system possessing optimum hole cleaning and lubrication capabilities. Drilling fluids for vertical wells are often chosen primarily for their ability to control the formations surrounding the reservoir. By modifying the fluid properties and dynamics, these same fluids, in many cases, can be used to drill horizontally. This paper describes special considerations that must be made for using these fluids in highly deviated holes. In this regard, the author devotes particular attention to the cleaning, lubrication, and maximum payzone protection capabilities of the fluid system.
Embryonic Lethal Abnormal Vision-Like RNA-Binding Proteins Regulate Neurite Outgrowth and Tau Expression in PC12 Cells (1999)

The embryonic lethal abnormal vision (ELAV)-like proteins are mRNA-binding proteins that regulate mRNA stability. The neuronal members of this family are required for neuronal differentiation. We identified the binding region of purified HuD protein to a target neuronal mRNA encoding for the tau microtubule-associated protein and demonstrated an in vivo interaction between the ELAV-like protein and its target tau mRNA. We show that treatment of neuronal cells with antisense oligodeoxynucleotides directed against HuD blocks the induction of neurite outgrowth and decreases the levels of tau mRNAs, indicating that the ELAV-like proteins are required for neuronal differentiation.
Passive temperature compensation techniquefor fibre Bragg grating displacement sensor (1999)

A novel fibre Bragg grating displacement sensor is presented. Using a uniform density and thickness overlapped dual-isosceles triangular cantilever beam as a strain agent, it is demonstrated both experimentally and theoretically that this sensor is able to automatically compensate for wavelength shifts induced by temperature. The measured sensitivity of this sensor is 0.1051 nm/mm within the working range of –18 – 18 mm.
PENGARUH LEVERAGE, PROFITABILITAS, SIZE, DAN GROWTH OPPORTUNITY TERHADAP NILAI PERUSAHAAN (2016)

The purpose of this research is to examine the influence of leverage, profitability, size, and growth opportunity to the firm value. The population is all manufacturing companies which are listed in Indonesia Stock Exchange in 2011-2015 periods. The sample collection technique has been carried out by using purposive sampling. Purposive sampling is a sample collection method through some certain criteria which has been determined by the researcher. Based on the determined sample criteria, 53 companies have been selected as samples. This research has been done by using 5-year time spans. Therefore the total number of this research samples are 265 companies. This research has been carried out by using secondary data in the form of annual financial statement which have been obtained from Indonesia Stock Exchange. The data analysis technique has been conducted by using multiple linear regressions analysis with its significance level is 5%. The result of Goodness of fit test of models shows that simultaneously leverage, profitability, size, and growth opportunity have an influence to the firm value. the result of partial test shows that leverage variable has negative influence to the firm value whereas profitability, size, and growth opportunity have positive influence to the firm value. Keywords : Leverage, profitability, size, growth opportunity, firm value
Insoluble detergent-resistant aggregates form between pathological and nonpathological lengths of polyglutamine in mammalian cells (1999)

Pathological degeneration of neurons in Huntington's disease and associated neurodegenerative disorders is directly correlated with the expansion of CAG repeats encoding polyglutamines of extended length. The physical properties of extended polyglutamines and the intracellular consequences of expression of polyglutamine expansion have been the object of intensive investigation. We have extended the range of lengths of polyglutamine produced by recombinant DNA methodology by constructing a library of CAG/CAA repeats coding for a range of 25-300 glutamine residues. We have investigated the subcellular localization, interaction with other polyglutamine-containing polypeptides, and the physical properties of aggregated forms of polyglutamine in the cell. Extended polyQ aggregated in the cytoplasm and was only transported to the nucleus when a strong nuclear localization signal was present. Polyglutamine below pathological lengths could be captured in aggregates and transported to ectopic cell locations. The CREB-binding protein (CBP), containing a homopolymeric stretch of 19 glutamines, was likewise found to coaggregate in a polyglutamine-dependent manner, suggesting that pathology in polyglutamine disease may result from cellular depletion of normal proteins containing polyglutamine. We have observed a striking detergent resistance in aggregates produced from polyglutamine of pathological length. This observation has led to the development of a fluorescence-based assay exploiting the detergent resistance of polyglutamine aggregates that should facilitate high-throughput screening for agents that suppress polyglutamine aggregation in cells.
Fluorine‐19 NMR imaging of glucose metabolism (1988)

Metabolic imaging reflecting glucose metabolism in the glycolytic and aldose reductase sorbitol (ARS) pathways was performed noninvasively in rat using fluorinated glucose analogs, 2-fluoro-2-deoxy-D-glucose (2-FDG) or 3-fluoro-3-deoxy-D-glucose (3-FDG), and fluorine-19 (19F) nuclear magnetic resonance (NMR) imaging. 19F images of 2-FDG-6-phosphate, a main metabolite of 2-FDG in the glycolytic pathway, showed high glucose utilization in the brain, spinal cord, and heart. Images of 3-fluoro-3-deoxy-D-sorbitol (3-FDSL), a main metabolite of 3-FDG in the ARS pathway, demonstrated the heterogeneous nature of the spatial distribution of aldose reductase activities, being highest in the brain and lens. The extremely low toxicity of 3-FDG indicates promise for clinical application of 3-FDG NMR imaging.
Mechanical Reinforcement of Polymers Using Carbon Nanotubes (2006)

Abstract Owing to their unique mechanical properties, carbon nanotubes are considered to be ideal candidates for polymer reinforcement. However, a large amount of work must be done in order to realize their full potential. Effective processing of nanotubes and polymers to fabricate new ultra‐strong composite materials is still a great challenge. This Review explores the progress that has already been made in the area of mechanical reinforcement of polymers using carbon nanotubes. First, the mechanical properties of carbon nanotubes and the system requirements to maximize reinforcement are discussed. Then, main methods described in the literature to produce and process polymer–nanotube composites are considered and analyzed. After that, mechanical properties of various nanotube–polymer composites prepared by different techniques are critically analyzed and compared. Finally, remaining problems, the achievements so far, and the research that needs to be done in the future are discussed.
Automated synthesis of peptide C-terminal aldehydes (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAutomated synthesis of peptide C-terminal aldehydesAileen M. Murphy, Raymond Dagnino Jr., Pureza L. Vallar, Anthony J. Trippe, Shannon L. Sherman, Richard H. Lumpkin, Susan Y. Tamura, and Thomas R. WebbCite this: J. Am. Chem. Soc. 1992, 114, 8, 3156–3157Publication Date (Print):April 1, 1992Publication History Published online1 May 2002Published inissue 1 April 1992https://pubs.acs.org/doi/10.1021/ja00034a082https://doi.org/10.1021/ja00034a082research-articleACS PublicationsRequest reuse permissionsArticle Views625Altmetric-Citations104LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Two Classes of PDGF Receptor Eecognize Different Isoforms of PDGF (1988)

Previous studies involving platelet-derived growth factor (PDGF) have been based on the premise that a single cell-surface receptor binds all three isoforms of PDGF (AA, BB, and AB). It is now shown that two populations of PDGF receptor exist and can be distinguished by their ligand binding specificity. The B receptor binds only the BB dimer, whereas the A/B receptor binds AA, BB, and AB dimers. Human dermal fibroblasts appear to express seven times as much B receptor as A/B receptor. The B receptor is responsible for most PDGF receptor phosphorylation.
Interleukin-6 and interleukin-6 soluble receptor regulate proliferation of normal, human papillomavirus-immortalized, and carcinoma-derived cervical cells in vitro. (1995)

A variety of sexually transmitted diseases frequently accompany infection with human papillomavirus and stimulate inflammation of the cervical mucosa. Inflammation and cell injury cause release of proinflammatory cytokines, which in turn might regulate growth of human papillomavirus-infected cells. This study compared the interaction of the proinflammatory cytokine, interleukin-6 (IL-6), and its soluble receptor with normal ecto- and endocervical cells, human papillomavirus-immortalized ectocervical cells, and squamous carcinoma-derived cell lines. Proliferation of normal cervical cells was enhanced by IL-6 but inhibited by its soluble receptor. However, both IL-6 and its soluble receptor significantly stimulated growth of the three immortal and four cervical carcinoma-derived cell lines analyzed. Stimulation by IL-6 was dose dependent and was blocked by an antibody that neutralized IL-6 activity. IL-6-mediated proliferation was accompanied by increased expression of RNAs encoding transforming growth factor-alpha and amphiregulin, two epidermal growth factor receptor ligands. Furthermore, growth stimulation by IL-6 was significantly inhibited by antibodies that either blocked signal transduction by the epidermal growth factor receptor or that neutralized transforming growth factor-alpha or amphiregulin activity. Thus, IL-6 stimulates proliferation of human papillomavirus-immortalized cervical cells via an epidermal growth factor receptor-dependent pathway involving autocrine stimulation by transforming growth factor-alpha and amphiregulin.
ChemInform Abstract: An Efficient Synthesis of Polysubstituted 3‐Halo‐2(1H)‐pyridinones. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Estrogens and Endometrial Cancer in a Retirement Community (1976)

All cases of endometrial cancer occurring among the residents of an affluent retirement community were compared with controls chosen from a roster of all women in the same community. Evidence of estrogen and other drug use and of selected medical conditions was obtained from three sources: medical records of the principal care facility, interviews, and the records of the local pharmacy. The risk ratio for any estrogen use was estimated from all available evidence to be 8.0 (95 per cent confidence interval, 3.5 to 18.1). and the for conjugated estrogen use to be 5.6 (95 per cent confidence interval, 2.8 to 11.1). Increased risk from estrogens was shown for invasive as well as noninvasive cancer, and a dose-response effect was demonstrated. For an estrogen user, the risk from endometrial cancer appeared to exceed by far the base-line risk from any other single cancer.
Lumbar herniated disk disease and canal stenosis: prospective evaluation by surface coil MR, CT, and myelography (1986)

Sixty patients with suspected lumbar herniated disk and/or canal stenosis were studied prospectively with surface coil MRI, CT, and/or myelography, and the results were compared with the surgically confirmed abnormality. Forty-eight patients had lumbar surgery at 62 levels. There were no negative explorations. Thirty-nine patients had a myelogram and CT. Thirty of the CTs were performed following the injection of metrizamide for myelography. Nine patients had a CT without intrathecal contrast material 1 to several days before the myelogram. Six patients had myelography only, and three patients had CT only. All studies were evaluated for the location and type of disease in a forced choice fashion. Independent of the surgically correlated levels, there was 86.8% agreement between the MR and CT studies in all patients at 151 levels and 87.2% agreement between MR and myelography at 218 levels. At the operative levels, there was 82.6% agreement between MR and surgical findings for both type and location of disease; 83% agreement between CT and surgical findings; and 71.8% agreement between myelography and surgical findings. There was 92.5% agreement when MR and CT were used jointly, and 89.4% agreement when CT and myelography were used jointly. The results of this study indicate that a technically adequate MR examination was equivalent to CT and myelography in the diagnosis of lumbar canal stenosis and herniated disk disease. CT and MR can be complementary studies, and surface coil MR can be viewed as an alternative to myelography.
A Metal-Dependent DNA-Binding Protein Interacts with a Constitutive Element of a Light-Responsive Promoter (1990)

Eric Lam, Yuriko Kano-Murakami, Philip Gilmartin, Bettina Niner, Nam-Hai Chua, A Metal-Dependent DNA-Binding Protein Interacts with a Constitutive Element of a Light-Responsive Promoter, The Plant Cell, Vol. 2, No. 9 (Sep., 1990), pp. 857-866