gebhart/patrepeval huggingface dataset:
The Protein-tyrosine Phosphatase TCPTP Regulates Epidermal Growth Factor Receptor-mediated and Phosphatidylinositol 3-Kinase-dependent Signaling (1999)

In this study we have investigated the down-regulation of epidermal growth factor (EGF) receptor signaling by protein-tyrosine phosphatases (PTPs) in COS1 cells. The 45-kDa variant of the PTP TCPTP (TC45) exits the nucleus upon EGF receptor activation and recognizes the EGF receptor as a cellular substrate. We report that TC45 inhibits the EGF-dependent activation of the c-Jun N-terminal kinase, but does not alter the activation of extracellular signal-regulated kinase 2. These data demonstrate that TC45 can regulate selectively mitogen-activated protein kinase signaling pathways emanating from the EGF receptor. In EGF receptor-mediated signaling, the protein kinase PKB/Akt and the mitogen-activated protein kinase c-Jun N-terminal kinase, but not extracellular signal-regulated kinase 2, function downstream of phosphatidylinositol 3-kinase (PI 3-kinase). We have found that TC45 and the TC45-D182A mutant, which is capable of forming stable complexes with TC45 substrates, inhibit almost completely the EGF-dependent activation of PI 3-kinase and PKB/Akt. TC45 and TC45-D182A act upstream of PI 3-kinase, most likely by inhibiting the recruitment of the p85 regulatory subunit of PI 3-kinase by the EGF receptor. Recent studies have indicated that the EGF receptor can be activated in the absence of EGF following integrin ligation. We find that the integrin-mediated activation of PKB/Akt in COS1 cells is abrogated by the specific EGF receptor protein-tyrosine kinase inhibitor tyrphostin AG1478, and that TC45 and TC45-D182A can inhibit activation of PKB/Akt following the attachment of COS1 cells to fibronectin. Thus, TC45 may serve as a negative regulator of growth factor or integrin-induced, EGF receptor-mediated PI 3-kinase signaling.
Regulation of BN115, a Low-Temperature-Responsive Gene from Winter Brassica napus (1994)

The genomic clone for BN115, a low-temperature-responsive gene, was isolated from winter Brassica napus and its sequence was determined. A 1.2-kb fragment of the 5' regulatory region (from bp -1107 to +100) was fused to the beta-glucuronidase (GUS) reporter gene and BN115-promoted GUS expression was observed in green tissues of transgenic B. napus plants only after incubation at 2 degrees C. No expression was observed after incubation at 22 degrees C, either in the presence or the absence of ABA. Microprojectile bombardment of winter B. napus leaves with a BN115 promoter/GUS construct yielded similar results and was used to analyze a series of deletions from the 5' end of the promoter. Results obtained from transient expression studies showed that the low-temperature regulation of BN115 expression involves a possible enhancer region between bp -1107 and -802 and a second positive regulatory region located between bp -302 and -274. Deletion analyses and results from replacement with a truncated cauliflower mosaic virus 35S promoter suggest that the minimal size required for any maintenance of low-temperature GUS expression is a -300-bp fragment. Within this fragment are two 8-bp elements with the sequence TGGCCGAC, which are identical to those present in the positive regulatory region of the promoter of the homologous Arabidopsis cor15a gene and to a 5-bp core sequence in the low-temperature- and dehydration-responsive elements identified in the promoter regions of several cold-responsive Arabidopsis thaliana genes.
Cystic fibrosis gene therapy (1995)

Cystic fibrosis is a common severe autosomal recessive genetic disease which is caused by dysfunction of an epithelial cell surface cAMP activated Cl- channel. The effects of this dysfunction are pleoitropic but the human morbidity results from the effects in the respiratory epithelium. Gene therapy is an attractive possible treatment, the gene required is well characterised and only low-level expression is required. The cellular target is accessible and the clinical effects of treatment should be readily assayable. This chapter reviews current proposals for suitable gene delivery mechanisms and vectors and discusses the clinical trials, the results from the first of which are now becoming available.
A Randomized Trial of Bevacizumab, an Anti–Vascular Endothelial Growth Factor Antibody, for Metastatic Renal Cancer (2003)

Bevacizumab can significantly prolong the time to progression of disease in patients with metastatic renal-cell cancer.
Model studies of metalloenzymes involving metal ions as Lewis acid catalysts (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTModel studies of metalloenzymes involving metal ions as Lewis acid catalystsJunghun SuhCite this: Acc. Chem. Res. 1992, 25, 7, 273–279Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/ar00019a001https://doi.org/10.1021/ar00019a001research-articleACS PublicationsRequest reuse permissionsArticle Views1109Altmetric-Citations196LEARN 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
Collagenase Production by Rheumatoid Synovial Cells: Stimulation by a Human Lymphocyte Factor (1977)

Human peripheral blood lymphocytes incubated in culture for 1 to 3 days at 37 degree C, but not at 4 degree C, release a soluble factor which can stimulate, up to 400-fold, collagenase production by isolated, adherent, rheumatoid synovial cells. Production of lymphocyte factor is enhanced by phytohemagglutinin or concanavalin A. By gel filtration the factor has an apparent molecular weight of about 12,000.
A Novel Human Stem Cell Coculture System that Maintains the Survival and Function of Culture Islet-Like Cell Clusters (2008)

Islet-like cell clusters (ICCs) have been suggested to be a source of insulin-producing tissue for xenotransplantation in type 1 diabetes. We designed an approach to maintain the cultured rat pancreatic ICC survival and function, when cocultured with human umbilical cord mesenchymal stem cells (HUMSCs). HUMSCs in coculture have the ability to maintain ICC survival and function, for which number and insulin secretion of ICCs are increasing and lasting for 3 months, while ICCs gradually crash, which results in cell death after a period of 12 days of culture without HUMSCs. Cytokine protein array showed it has more than a twofold increase in levels of several cytokines (interleukin-6, tissue inhibitor of metalloproteinases-1, tissue inhibitor of metalloproteinases-2, monocyte chemoattractant protein-1, growth related oncogene, hepatocyte growth factor, insulin-like growth factor binding proteins 4, and interleukin-8) on coculture medium, implying an important role of these cytokines in this coculture system. These findings suggest that coculture with HUMSCs may have a significant potential to protect ICCs from damage during culture, and may be employed in a novel culture approach to maintain islet cell survival and function before transplantation.
Task Loss Estimation for Sequence Prediction (2015)

Often, the performance on a supervised machine learning task is evaluated with a emph{task loss} function that cannot be optimized directly. Examples of such loss functions include the classification error, the edit distance and the BLEU score. A common workaround for this problem is to instead optimize a emph{surrogate loss} function, such as for instance cross-entropy or hinge loss. In order for this remedy to be effective, it is important to ensure that minimization of the surrogate loss results in minimization of the task loss, a condition that we call emph{consistency with the task loss}. In this work, we propose another method for deriving differentiable surrogate losses that provably meet this requirement. We focus on the broad class of models that define a score for every input-output pair. Our idea is that this score can be interpreted as an estimate of the task loss, and that the estimation error may be used as a consistent surrogate loss. A distinct feature of such an approach is that it defines the desirable value of the score for every input-output pair. We use this property to design specialized surrogate losses for Encoder-Decoder models often used for sequence prediction tasks. In our experiment, we benchmark on the task of speech recognition. Using a new surrogate loss instead of cross-entropy to train an Encoder-Decoder speech recognizer brings a significant ~13% relative improvement in terms of Character Error Rate (CER) in the case when no extra corpora are used for language modeling.
The allylic protection method in solid-phase oligonucleotide synthesis. An efficient preparation of solid-anchored DNA oligomers (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe allylic protection method in solid-phase oligonucleotide synthesis. An efficient preparation of solid-anchored DNA oligomersYoshihiro Hayakawa, Shigeharu Wakabayashi, Hisatoyo Kato, and Ryoji NoyoriCite this: J. Am. Chem. Soc. 1990, 112, 5, 1691–1696Publication Date (Print):February 1, 1990Publication History Published online1 May 2002Published inissue 1 February 1990https://pubs.acs.org/doi/10.1021/ja00161a006https://doi.org/10.1021/ja00161a006research-articleACS PublicationsRequest reuse permissionsArticle Views1798Altmetric-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
Dominant Epitopes of the C6 Diagnostic Peptide ofBorrelia burgdorferiAre Largely Inaccessible to Antibody on the Parent VlsE Molecule (2007)

Lyme borreliosis (LB) is a disease for which antibody-based detection assays are often required for diagnosis. The variable surface molecule VlsE and IR6, one of its invariable regions, are commonly targeted by the antibody response in infected individuals. A series of enzyme-linked immunosorbent assays was performed to comparatively examine the antibody responses of North American LB patients (n = 37) to VlsE and invariable segments of this molecule. Both immunoglobulin M (IgM) and IgG responses to full-length VlsE and to peptides reproducing invariable regions 2, 4, and 6, as well as the invariable domains at the amino and carboxyl termini of VlsE, were assessed. The proportions and specificities of reactivity to the invariable segments were tested by using cognate peptides as competitors for VlsE binding by patient serum antibodies. IR6 epitopes (by the C6 peptide) were found to dominate the response to invariable segments. IR6 (C6)-specific antibodies were detected in 78% of the serum specimens, whereas <40% of patients generated antibodies that bound the N- or C-terminal domain and <12% of patients responded to either IR2 or IR4. Interestingly, 15 of 37 patients generated IgG antibodies that reacted with C6 but not with VlsE. Conversely, IgM responses were frequent for VlsE but not for invariable segments. A representative number of the serum specimens (n = 8) that contained IgG antibodies reacting with both C6 and VlsE was assessed in competition experiments, using C6 as a competitor. Only half of these specimens contained IgG antibodies whose binding to VlsE could be inhibited >50% by competition with the added C6 peptide. The median percent inhibition was 45.5%. These findings indicate that IR6 epitopes are largely concealed from the VlsE molecular surface and that full-length VlsE-based diagnosis likely detects antibodies to conformational and/or variable region epitopes.
The American College of Rheumatology criteria for the classification and reporting of osteoarthritis of the hand (1990)

Abstract Clinical criteria for the classification of symptomatic idiopathic (primary) osteoarthritis (OA) of the hands were developed from data collected in a multi‐center study. Patients with OA were compared with a group of patients who had hand symptoms from other causes, such as rheumatoid arthritis and the spondylar‐thropathies. Variables from the medical history, physical examination, laboratory tests, and radiographs were analyzed. All patients had pain, aching, or stiffness in the hands. Patients were classified as having clinical OA if on examination there was hard tissue enlargement involving at least 2 of 10 selected joints, swelling of fewer than 3 metacarpophalangeal joints, and hard tissue enlargement of at least 2 distal interphalangeal (DIP) joints. If the patient had fewer than 2 enlarged DIP joints, then deformity of at least 1 of the 10 selected joints was necessary in order to classify the symptoms as being due to OA. The 10 selected joints were the second and third DIP, the second and third proximal interphalangeal, and the trapeziometacarpal (base of the thumb) joints of both hands. Criteria derived using the “classification tree” method were 92% sensitive and 98% specific. The “traditional format” classification method required that at least 3 of these 4 criteria be present to classify a patient as having OA of the hand. The latter sensitivity was 94% and the specificity was 87%. Radiography was of less value than clinical examination in the classification of symptomatic OA of the hands.
Parameterization studies for the SAM and HMMER methods of hidden Markov model generation. (1996)

Multiple sequence alignment of distantly related viral proteins remains a challenge to all currently available alignment methods. The hidden Markov model approach offers a new, flexible method for the generation of multiple sequence alignments. The results of studies attempting to infer appropriate parameter constraints for the generation of de novo HMMs for globin, kinase, aspartic acid protease, and ribonuclease H sequences by both the SAM and HMMER methods are described.
Inferring the Location of Twitter Messages Based on User Relationships (2011)

Abstract User interaction in social networks, such as Twitter and Facebook, is increasingly becoming a source of useful information on daily events. The online monitoring of short messages posted in such networks often provides insight on the repercussions of events of several different natures, such as (in the recent past) the earthquake and tsunami in Japan, the royal wedding in Britain and the death of Osama bin Laden. Studying the origins and the propagation of messages regarding such topics helps social scientists in their quest for improving the current understanding of human relationships and interactions. However, the actual location associated to a tweet or to a Facebook message can be rather uncertain. Some tweets are posted with an automatically determined location (from an IP address), or with a user‐informed location, both in text form, usually the name of a city. We observe that most Twitter users opt not to publish their location, and many do so in a cryptic way, mentioning non‐existing places or providing less specific place names (such as “Brazil”). In this article, we focus on the problem of enriching the location of tweets using alternative data, particularly the social relationships between Twitter users. Our strategy involves recursively expanding the network of locatable users using following‐follower relationships. Verification is achieved using cross‐validation techniques, in which the location of a fraction of the users with known locations is used to determine the location of the others, thus allowing us to compare the actual location to the inferred one and verify the quality of the estimation. With an estimate of the precision of the method, it can then be applied to locationless tweets. Our intention is to infer the location of as many users as possible, in order to increase the number of tweets that can be used in spatial analyses of social phenomena. The article demonstrates the feasibility of our approach using a dataset comprising tweets that mention keywords related to dengue fever, increasing by 45% the number of locatable tweets.
Nocturnal acid breakthrough (2004)

Nocturnal acid breakthrough (NAB) was defined by Peghini et al. in 1998 as the presence of at least 60 continuous minutes of intragastric pH < 4 during the overnight period (22:00-06:00 h) in patients taking a proton pump inhibitor (PPI) twice-daily before meals. NAB was shown to occur in more than 70% of patients on PPI therapy but can be decreased or eliminated by adding a histamine-2 receptor antagonist (H2RA) at bedtime. Helicobacter pylori status influences intragastric acid control on PPI therapy: H. pylori-positive patients having better gastric acid control compared with their H. pylori-negative counterparts. Recent data indicate that NAB might not occur in H. pylori-positive subjects on twice-daily PPI, suggesting there is no need for combined PPI twice-daily and H2RA therapy to control night-time gastric acid secretion in these individuals. The clinical importance of NAB has been debated ever since this concept was introduced. The importance of NAB in healthy subjects and asymptomatic, uncomplicated gastro-oesophageal reflux disease patients on PPI therapy may be low, but ignoring it in patients with poor oesophageal motility and Barrett's oesophagus may result in suboptimal treatment. Further studies are warranted to investigate whether leaving H. pylori to 'assist'acid suppression obtained by PPI twice-daily, adding bedtime H2RAs after successful H. pylori eradication or other approaches to eliminate NAB results in better clinical outcomes.
Effects of multiwalled carbon nanotube on holographic polymer dispersed liquid crystal (2010)

Abstract The morphology and electro‐optical performance of holographic polymer dispersed liquid crystal (HPDLC) were investigated with the addition of multiwalled carbon nanotube (CNT), both pristine and chemically modified one (CNT‐CC). With the addition of CNT, the diffraction efficiency increased and showed a maximum at 0.6% while nucleation was delayed due to the increased mixture viscosity. Film was driven only with CNT due to the induced local electric field of polymer to overcome the threshold resistance. Among the two types of CNT, chemically modified one gave finer CNT dispersion, lower mixture viscosity, larger liquid crystal (LC) droplet, higher diffraction efficiency, and shorter response time while the pristine CNT decreased the driving voltage. Copyright © 2010 John Wiley &amp; Sons, Ltd.
Optical waveguides in crystalline dielectric materials produced by femtosecond‐laser micromachining (2013)

Abstract Femtosecond‐laser micromachining (also known as inscription or writing) has been developed as one of the most efficient techniques for direct three‐dimensional microfabrication of transparent optical materials. In integrated photonics, by using direct writing of femtosecond/ultrafast laser pulses, optical waveguides can be produced in a wide variety of optical materials. With diverse parameters, the formed waveguides may possess different configurations. This paper focuses on crystalline dielectric materials, and is a review of the state‐of‐the‐art in the fabrication, characterization and applications of femtosecond‐laser micromachined waveguiding structures in optical crystals and ceramics. A brief outlook is presented by focusing on a few potential spotlights.
PROTECTION OF PIG KIDNEY (PK15) CELLS FROM THE CYTOTOXIC EFFECT OF ANTI-PIG ANTIBODIES BY α-GALACTOSYL OLIGOSACCHARIDES1 (1994)

Anti-pig antibodies in human and baboon serum are believed to be directed against alpha-galactosyl (alpha Gal) epitopes expressed on various pig cells, including vascular endothelia. We have investigated the effect of human sera on the PK15 pig kidney cell line, which abundantly expresses alpha Gal epitopes. To quantitate cell viability, we have used a staining method that differentiates live cells from dead ones. Various carbohydrates (n = 28) were added individually to serum at concentrations of 0.125-50 mg/ml. Unmodified serum caused approximate 100% PK15 cell death within 60 min. Carbohydrates that were not alpha Gal based did not significantly protect PK15 cells. Of the alpha Gal-based carbohydrates, only B disaccharide protected PK15 cells from both human and baboon serum (76% and 93% protection, respectively, at 1 mg/ml). Three alpha Gal oligosaccharides provided approximately 80-90% protection against both human and baboon sera at a concentration of 10 mg/ml. Three other closely related structures protected only against baboon serum (> 80%) at high concentration (50 mg/ml), suggesting a difference in anti-pig antibody affinity between baboon and man. Specific anti-alpha Gal antibody-depleted serum caused < 10% pig cell death, whereas the antibodies eluted from the alpha Gal columns caused > 70% pig cell death. In conclusion, this study provides further evidence that (1) alpha Gal structures are the targets for human and baboon anti-pig antibodies, and (2) there may be a therapeutic role for the infusion of specific alpha Gal carbohydrates, or for antibody removal using alpha Gal immunoaffinity columns, in order to prevent hyperacute rejection of pig organs in man.
Surface Technology for the 21st Century. Chromium-Free Conversion Coating of Zinc Plating Using Mn(II)-Silicate Solution. (2001)

Chromium-free conversion coating films composed of Mn (II) -silicate were studied by salt spray tests, measurements of polarization resistance and surface analysis. Corrosion resistance of the film was better than the film consisting of each own component. The top of the film was composed with mainly silicate, however, inside of the film was mixture of Mn (II) and silicate. Total amounts of Mn (II) and Si in the film were an important factor for the corrosion resistance.