gebhart/patrepeval huggingface dataset:
Specific interactions of neuronal focal adhesion kinase isoforms with Src kinases and amphiphysin (2003)

Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that activates Src family kinases via SH2- and SH3-mediated interactions. Specific FAK isoforms (FAK+), responsive to depolarization and neurotransmitters, are enriched in neurons. We analyzed the interactions of endogenous FAK+ and recombinant FAK+ isoforms containing amino acid insertions (boxes 6,7,28) with an array of SH3 domains and the c-Src SH2/SH3 domain tandem. Endogenous FAK+ bound specifically to the SH3 domains of c-Src (but not n-Src), Fyn, Yes, phosphtidylinositol-3 kinase, amphiphysin II, amphiphysin I, phospholipase Cgamma and NH2-terminal Grb2. The inclusion of boxes 6,7 was associated with a significant decrease in the binding of FAK+ to the c-Src and Fyn SH3 domains, and a significant increase in the binding to the Src SH2 domain, as a consequence of the higher phosphorylation of Tyr-397. The novel interaction with the amphiphysin SH3 domain, involving the COOH-terminal proline-rich region of FAK, was confirmed by coimmunoprecipitation of the two proteins and a closely similar response to stimuli affecting the actin cytoskeleton. Moreover, an impairment of endocytosis was observed in synaptosomes after internalization of a proline-rich peptide corresponding to the site of interaction. The data account for the different subcellular distribution of FAK and Src kinases and the specific regulation of the transduction pathways linked to FAK activation in the brain and implicate FAK in the regulation of membrane trafficking in nerve terminals.
The Effect of Irreversible Electroporation on Blood Vessels (2007)

We present a pilot study on the long term effects of irreversible electroporation (IRE) on a large blood vessel. The study was motivated by the anticipated use of IRE for treatment of cancer tumors abutting large blood vessels. A sequence of 10 direct current IRE pulses of 3800 V/cm, 100 micros each, at a frequency of 10 pulses per second, were applied directly to the carotid artery in six rats. Measuring tissue conductivity during the procedure showed, as predicted, an increase in conductivity during the application of the pulse, which suggests that this measurement can be used to control the application of IRE. All the animals survived the procedure and showed no side effects. Histology performed 28 days after the procedure showed that the connective matrix of the blood vessels remained intact and the number of vascular smooth muscle cells (VSMC) in the arterial wall decreased with no evidence of aneurysm, thrombus formation or necrosis. Average VSMC density was significantly lower following IRE ablation compared with control (24 +/- 11 vs. 139 +/- 14, P<0.001), with no apparent damage to extra cellular matrix components and structure. In addition to the relevance of this study to treatment of cancer near large blood vessels these findings tentatively suggest that IRE has possible applications to treatment of pathological processes in which it is desired to reduce the proliferation of VSMC population, such as restenosis and for attenuating atherosclerotic processes in clinical important locations such as coronary, carotid and renal arteries.
Ion Exchange. (1949)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIon Exchange.Robert KuninCite this: Anal. Chem. 1949, 21, 1, 87–96Publication Date (Print):January 17, 1949Publication History Published online1 May 2002Published inissue 17 January 1949https://pubs.acs.org/doi/10.1021/ac60025a019https://doi.org/10.1021/ac60025a019research-articleACS PublicationsRequest reuse permissionsArticle Views167Altmetric-Citations37LEARN 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
Functional Characterization of a P2X Receptor from Schistosoma mansoni (2004)

The cloning and characterization of a P2X receptor (schP2X) from the parasitic blood fluke Schistosoma mansoni provides the first example of a non-vertebrate ATP-gated ion channel. A number of functionally important amino acid residues conserved throughout vertebrate P2X receptors, including 10 extracellular cysteines, aromatic and positively charged residues involved in ATP recognition, and a consensus protein kinase C site in the amino-terminal tail, are also present in schP2X. Overall, the amino acid sequence identity of schP2X with human P2X(1-7) receptors ranges from 25.8 to 36.6%. ATP evoked concentration-dependent currents at schP2X channels expressed in Xenopus oocytes with an EC(50) of 22.1 microM. 2',3'-O-(4-Benzoylbenzoyl)adenosine 5'-triphosphate (Bz-ATP) was a partial agonist (maximum response 75.4 +/- 4.4% that of ATP) with a higher potency (EC(50) of 3.6 microM) than ATP. Suramin and pyridoxal-phosphate-6-azophenyl-2',4'-disulfonic acid blocked schP2X responses to 100 microm ATP with IC(50) values of 9.6 and 0.5 microM, respectively. Ivermectin (10 microM) potentiated currents to both ATP and Bz-ATP by approximately 60% with a minimal effect on potency (EC(50) of 18.2 and 1.6 microM, respectively). The relative permeability of schP2X expressed in HEK293 cells to various cations was determined under bi-ionic conditions. schP2X has a relatively high calcium permeability (P(Ca)/P(Na) = 3.80 +/- 0.29) and an estimated minimum pore diameter similar to that of vertebrate P2X receptors. SchP2X provides a useful comparative model for the better understanding of human P2X receptor function and may also provide an alternative drug target for treatment of schistosomiasis.
Purification of the cystatin C-like inhibitors from urine of nephropathic rats. (1988)

Two cysteine proteinase inhibitors of the cystatin C type have been purified from urine of sodium chromate-treated rats. Both strongly inhibit papain as well as rat liver cathepsin L (Ki less than 10(-11) M) whereas rat liver cathepsins B and H are inhibited to a lesser extent. They differ by their apparent molecular mass of 17 kDa and 22 kDa and by their isoelectric point greater than or equal to 9.5 and 7.7 respectively. These two molecules share complete immunochemical identity and are precipitated by antibodies directed against human cystatin C but not by anti rat thiostatin and anti rat H-kininogen antibodies. They are also found in large amounts in seminal vesicles where they represent most of the cysteine proteinase inhibitory capacity.
Regulation of the Histone Demethylase JMJD1A by Hypoxia-Inducible Factor 1α Enhances Hypoxic Gene Expression and Tumor Growth (2009)

The hypoxia-inducible transcription factors (HIFs) directly and indirectly mediate cellular adaptation to reduced oxygen tensions. Recent studies have shown that the histone demethylase genes JMJD1A, JMJD2B, and JARID1B are HIF targets, suggesting that HIFs indirectly influence gene expression at the level of histone methylation under hypoxia. In this study, we identify a subset of hypoxia-inducible genes that are dependent on JMJD1A in both renal cell and colon carcinoma cell lines. JMJD1A regulates the expression of adrenomedullin (ADM) and growth and differentiation factor 15 (GDF15) under hypoxia by decreasing promoter histone methylation. In addition, we demonstrate that loss of JMJD1A is sufficient to reduce tumor growth in vivo, demonstrating that histone demethylation plays a significant role in modulating growth within the tumor microenvironment. Thus, hypoxic regulation of JMJD1A acts as a signal amplifier to facilitate hypoxic gene expression, ultimately enhancing tumor growth.
Application of Guidelines for Designing User Interface Software (1985)

A survey was conducted of people who had received a report on guidelines for designing user interface software. Analysis of questionnaire responses indicates that design guidelines are generally considered useful, but that there are significant problems in the practical application of guidelines. For effective application, generally stated guidelines must be translated into system-specific design rules.
Characterization of a human macrophage-like cell line stimulated in vitro: a model of macrophage functions. (1980)

When cells of human macrophage-like cell line U937 are cultured in the presence of medium conditioned by mixed lymphocyte culture (MLC), PHA- or Con A-stimulated lymphocytes they demonstrate morphologic and functional characteristics of stimulation. The cells become larger, their surface more villous, and the cytoplasm has increased numbers of lysosomes and phagosomes. There is a marked (at least 10-fold) increase in antibody-dependent cellular cytotoxicity (ADCC) against both erythroid and tumor targets accompanied by increased expression of Fc receptors (FcR). There is also an augmentation of antibody-dependent phagocytosis. Medium conditioned by unstimulated lymphocytes, a B lymphoblastoid cell line or a fibroblast cell line produce very little stimulation of U937 cells. U937 cells gradually lose their increased ADCC capacity if they are washed free of conditioned medium (CM) but can be maintained in a stimulated state for long periods of time by culturing them in medium supplemented with PHA-CM at a concentration of 2%. Stimulation of macrophage-like cell line U937 may provide a useful model for further study of mechanisms of macrophage cytotoxicity and its modulation by products of activated lymphocytes.
Handbook of Aqueous Solubility Data (2003)

Over the years researchers have reported solubility data in the chemical, pharmaceutical, engineering, and environmental literature for several thousand organic compounds. Until now, this information has been scattered throughout the literature. Containing over 16,000 solubility data points for more than 4,000 organic compounds, Handbook of Aqueous
Carbohydrate Recognition on MUC1‐Expressing Targets Enhances Cytotoxicity of a T Cell Subpopulation (1997)

The influence of the epithelial mucin MUC1 on T cell-mediated lysis was analysed using lymph node lymphocytes (LNL) from patients with colorectal carcinoma. LNL were stimulated with allogeneic, MUC1-transfected B cells and the bulk cultures were cloned. Alloreactive cytotoxic T cell clones were obtained which preferentially lysed MUC1-expressing targets. The majority was CD4+ and MHC-class II-restricted, and a minor group was CD8+ and MHC-class I-restricted. All the clones expressed CD3 and TCR alpha beta, and were CD56-. The capacity to preferentially kill MUC1-expressing targets was stable in several clones for up to 6 months in culture. The enhancing effect of MUC1 on the lysis was investigated in more detail. It was only seen after inhibition of O-linked glycosylation in the targets. Furthermore, this effect was completely abrogated by the monoclonal antibody 3C9, directed against the Thomsen-Friedenreich antigen (T-antigen, Gal beta 1-3GalNAc bound alpha 1-3 to Ser/Thr) as well as by the soluble disaccharide Gal beta 1-3GalNAc, but not by other similar disaccharides. The authors conclude that in their system the preferential killing of MUC1-expressing targets is due to the recognition of an internal carbohydrate epitope accessible on under-glycosylated MUC1, possibly T-antigen, by an auxiliary receptor molecule on T cells.
Real-Time Quantitative Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) for the Measurement of Prostate-Specific Antigen mRNA in the Peripheral Blood of Patients with Prostate Carcinoma Using the TaqManTM Detection System (2001)

Circulating prostate cells can be detected in peripheral blood of patients with clinically localized or advanced prostate carcinoma. Traditionally, nested reverse transcriptase-polymerase chain reaction (RT-PCR) is used for this as a sensitive, but qualitative only, detection system. We developed a quantitative real-time RT-PCR method for measuring prostate-specific antigen (PSA) mRNA in peripheral blood of prostate cancer patients. A quantitative assay was developed using an external standard reference curve generated with RNA from the human prostate cell line LNCaP. Basal blood samples were collected from 44 patients without evidence of distant metastases and from 30 healthy controls. In 29 patients surgically treated with radical prostatectomy, the measurement of PSA mRNA was performed in blood samples collected before, at the end and 6 days after surgery. In 14 patients treated with radiotherapy, the measurements were repeated at 3-month intervals to evaluate time-related changes during therapy. The measurements were also performed for one year at 3-month intervals in one patient treated with anti-androgen therapy. We found detectable PSA mRNA in 14/44 (32%) basal blood samples. A wide range of values were observed in these patients, ranging from 0.5 to 1724 pg of total LNCaP RNA/ml blood. In patients undergoing radical prostatectomy, circulating PSA mRNA was detectable in eight patients in basal samples, and in seven of them also in blood specimens collected at the end of surgery, showing an increase in only two patients. In blood samples collected 6 days later, PSA mRNA was dramatically reduced in all patients, but still present in seven of them. In four patients, whose basal samples were negative, PSA mRNA was detectable in samples collected at the end of surgery and three of them were negative after 6 days. In patients who did not receive surgical treatment, a rapid decrease in PSA mRNA was demonstrated in five patients treated with radiotherapy and in one patient undergoing androgen deprivation. No detectable PSA mRNA was found in healthy controls. The levels of PSA mRNA in peripheral blood from patients with prostate carcinoma can be easily measured by this sensitive, quantitative and reliable procedure. This assay is a promising tool for the detection and follow-up of these patients.
Infection of HLA-DR1 Transgenic Mice with a Human Isolate of Influenza A Virus (H1N1) Primes a Diverse CD4 T-Cell Repertoire That Includes CD4 T Cells with Heterosubtypic Cross-Reactivity to Avian (H5N1) Influenza Virus (2009)

The specificity of the CD4 T-cell immune response to influenza virus is influenced by the genetic complexity of the virus and periodic encounters with variant subtypes and strains. In order to understand what controls CD4 T-cell reactivity to influenza virus proteins and how the influenza virus-specific memory compartment is shaped over time, it is first necessary to understand the diversity of the primary CD4 T-cell response. In the study reported here, we have used an unbiased approach to evaluate the peptide specificity of CD4 T cells elicited after live influenza virus infection. We have focused on four viral proteins that have distinct intracellular distributions in infected cells, hemagglutinin (HA), neuraminidase (NA), nucleoprotein, and the NS1 protein, which is expressed in infected cells but excluded from virion particles. Our studies revealed an extensive diversity of influenza virus-specific CD4 T cells that includes T cells for each viral protein and for the unexpected immunogenicity of the NS1 protein. Due to the recent concern about pandemic avian influenza virus and because CD4 T cells specific for HA and NA may be particularly useful for promoting the production of neutralizing antibody to influenza virus, we have also evaluated the ability of HA- and NA-specific CD4 T cells elicited by a circulating H1N1 strain to cross-react with related sequences found in an avian H5N1 virus and find substantial cross-reactivity, suggesting that seasonal vaccines may help promote protection against avian influenza virus.
On the significance of very small angle scattered radiation to radiographic imaging at low energies (1983)

We have studied the angular distribution of scattered radiation at low energies for angles between 2 degrees and 15 degrees from the outward normal to the exit surface of several phantoms, with 1 degree resolution. A cryogenically cooled germanium detector was used to measure the spectra of the scattered radiation. The differential scattering fluences, or numbers of photons per unit solid angle per unit surface area, exhibit distinct peaks at angles in the vicinity of 5 degrees, with the angular position being only slightly energy dependent but very material dependent. The scattered spectra show large changes as a function of angle, in some cases actually becoming harder than the exit unscattered beam. The significance of this behavior relative to the imaging of targets in mammography examinations is discussed.
Analysis and correction of gradient nonlinearity and B0 inhomogeneity related scaling errors in two‐dimensional phase contrast flow measurements (2004)

Phase contrast flow measurements will be increasingly biased at eccentric positions, where nonlinearity of gradients and inhomogeneity of the main field become important. In theory, they scale the result of phase contrast flow values in two ways: incorrect velocity encoding of moving spins and geometric distortion of the vessel cross-sectional area. A flow phantom, consisting of a 3D grid of interconnected tubes, was used to determine the spatial dependence of the associated scaling factors, which demonstrate that scaling errors in flow can be as large as 20% within the examined volume of 336 x 336 x 336 mm(3). The same phantom was also used to determine and minimize concomitant gradient effects. Correction of the off-center flow values with the local scaling factors and the concomitant gradient phase improves the measurement accuracy substantially, both in the flow phantom and in a volunteer study.
Chondrogenic differentiation of mesenchymal stem cells induced by collagen‐based hydrogel: An in vivo study (2009)

Chondrogenic differentiation of mesenchymal stem cells (MSCs) relies on inductive media of chondrogenic environment. With proper design, a cellular microenvironment mimicking chondrogenic environment might be created to induce chondrogenesis of MSCs. In this study, bone marrow mesenchymal cells (BMSCs) were encapsulated in collagen-based hydrogel, and then enclosed in diffusion-chambers which allow the body fluid to permeate and preclude the host cells to invade. Then, the chamber with the hydrogel-BMSCs composite was implanted in the back of rabbits subcutaneously. The specimens in the chamber were harvested for histological, immunohistochemical, and RT-PCR analyses after 8 weeks. The results showed that cells with the characteristic of chondrocytes were homogenously distributed and the extracellular matrix (ECM) of cartilage has been secreted, indicating the chondrogenic differentiation of BMSCs. As control, nothing was obtained with only BMSCs. Moreover, the expression of collagen type II, indicator of cartilage ECM, was less in tissues with collagen-alginate-hydrogel (CAH) than that with collagen-hydrogel (CH). The results showed that both CH and CAH may induce the chondrogenesis and the induction is materials dependent. From in vitro experiments, TGF-beta is a necessary signal molecule for chondrogenesis, and it was suggested that the material may take in vivo growth factors to trigger chondrogenesis. From the studies, the chondrogenic induction of the hydrogel may be ascribed to that the hydrogel may provide a suitable environment and aggregate the signal molecule for chondrogenesis in vivo. The results would lend valuable reference in clinical for selection of appropriate scaffold for cartilage repair.
7-Alkylidenecephalosporin Esters as Inhibitors of Human Leukocyte Elastase (1997)

A series of 7-alkylidenecephalosporins and 7-vinylidenecephalosporins, as their benzhydryl esters, have been tested as inhibitors of both porcine pancreatic elastase and human leukocyte elastase. Selected 7-alkylidenecephalosporin esters are found to be potent inhibitors of HLE. One category of new inhibitors is the 7-(haloalkylidene)cephalosporins. In contrast to previously reported cephalosporin-based elastase inhibitors, these haloalkylidene cephems show optimum inhibitory activity as sulfides, rather than as sulfones. They are efficient and irreversible inhibitors. A second class of active compounds is represented by the benzhydryl ester 7-(cyanomethylidene)cephalosporin sulfone. In contrast to the activity of these new inhibitors, the benzhydryl ester of the mechanism-based beta-lactamase inhibitor, 7-[(2'-pyridyl)methylidene]-cephalosporin sulfone showed little inhibitory activity as an elastase inhibitor. 7-Vinylidenecephalosporins were also relatively poor inhibitors, although the terminally unsubstituted allene sulfide showed activity as an inhibitor of PPE. A modeling analysis suggests the 7-alkylidene substituents can be readily accommodated in the S1 pocket. A potential mechanism of inhibition is proposed.
Implementation of a discretionary access control model for script-based systems (2002)

Powerful applications can be implemented using command scripts. A command script is a program written by one user, called a writer, and made available to another user, called the reader, who executes the script. For instance, command scripts could be used by Mosaic, the popular World-wide Web browsing tool, to provide fancy interfaces to services, such as banking, shopping, etc. However, the use of command scripts presents a serious security problem. A command script is run with the reader's access rights, so a writer can use a command script to gain unauthorized access to the reader's data and applications. Existing solutions to the problem either severely restrict I/O capability of scripts, limiting the range of applications that can be supported, or permit all I/O to scripts, potentially compromising the security of the reader's data. We define a discretionary access control model that permits users to flexibly limit the access rights of the processes that execute a command script. We use this model in a prototype system that safely executes command scripts available from Mosaic.
Tertiary structure of bacterial selenocysteine tRNA (2013)

Selenocysteine (Sec) is translationally incorporated into proteins in response to the UGA codon. The tRNA specific to Sec (tRNA(Sec)) is first ligated with serine by seryl-tRNA synthetase (SerRS). In the present study, we determined the 3.1 Å crystal structure of the tRNA(Sec) from the bacterium Aquifex aeolicus, in complex with the heterologous SerRS from the archaeon Methanopyrus kandleri. The bacterial tRNA(Sec) assumes the L-shaped structure, from which the long extra arm protrudes. Although the D-arm conformation and the extra-arm orientation are similar to those of eukaryal/archaeal tRNA(Sec)s, A. aeolicus tRNA(Sec) has unique base triples, G14:C21:U8 and C15:G20a:G48, which occupy the positions corresponding to the U8:A14 and R15:Y48 tertiary base pairs of canonical tRNAs. Methanopyrus kandleri SerRS exhibited serine ligation activity toward A. aeolicus tRNA(Sec) in vitro. The SerRS N-terminal domain interacts with the extra-arm stem and the outer corner of tRNA(Sec). Similar interactions exist in the reported tRNA(Ser) and SerRS complex structure from the bacterium Thermus thermophilus. Although the catalytic C-terminal domain of M. kandleri SerRS lacks interactions with A. aeolicus tRNA(Sec) in the present complex structure, the conformational flexibility of SerRS is likely to allow the CCA terminal region of tRNA(Sec) to enter the SerRS catalytic site.