gebhart/patrepeval huggingface dataset:
Functional and molecular characterization of tumor-infiltrating lymphocytes transduced with tumor necrosis factor-alpha cDNA for the gene therapy of cancer in humans (1993)

TNF is effective in causing the regression of selected murine tumors when administered at high concentrations. Therapeutic levels in humans cannot be obtained systemically, however, because of dose-limiting toxicity. The development of immunotherapy with IL-2 and tumor-infiltrating lymphocytes (TIL), which can accumulate at tumor sites in some patients, and of efficient retroviral techniques for gene transfer into eukaryotic cells has allowed new therapeutic approaches using TNF. We have retrovirally transduced human TIL with the gene for TNF in an attempt to deliver high concentrations of TNF to the tumor site without dose-limiting systemic toxicity. Successful gene insertion was confirmed by Southern hybridization in 16 of 16 transduced and selected TIL cultures from 15 different patients, with an estimated 28 to 93% transduced cells within each culture. Transduced selected TIL cultures produced greater amounts of TNF, compared with nontransduced controls, in 11 of 16 cultures evaluated. However, overall production of TNF was > 30-fold lower, compared with a transduced and highly selected tumor cell line control (MEL-TNF). In addition, steady state levels of vector-derived transcript in nine of 10 transduced selected TIL cultures were < 14% of the amount seen in the MEL-TNF control line. In an attempt to increase TNF production, TIL were transduced with a mutated form of TNF containing the IFN-gamma signal peptide in place of the transmembranous region, to enhance secretion into the endoplasmic reticulum. By using this vector, TNF production increased by an average of fivefold. These studies demonstrate that TIL can be genetically modified to express and secrete a protein for use in targeted cancer therapy but that partial expression blockades exist that prevent maximal cytokine production by introduced genes in TIL.
Functional expression in primate cells of cloned DNA coding for the hemagglutinin surface glycoprotein of influenza virus. (1981)

We have used simian virus 40 (SV40) DNA as a vector for expression of functional activity of a cloned influenza viral DNA segment in primate cells. Cloned full-length DNA sequences coding for the hemagglutinin of influenza A virus (Udorn/72/[H3N2]) were inserted into the late region of a viable deletion mutant of SV40, and the hybrid DNA was propagated in the presence of an early SV40 mutant (tsA28) helper. Infection of primate cells with the hybrid virus produced a polypeptide similar in molecular size to the hemagglutinin of influenza virus, as shown by immunoprecipitation and gel electrophoresis. The polypeptide was glycosylated, as shown by incorporation of radioactive sugars. The putative hemagglutinin exhibited functional activity, as shown by agglutination of erythrocytes. In addition, an indirect immunofluorescence assay showed that the hemagglutinin polypeptide of the hybrid virus could be detected on the surface of infected cells.
Real-time expression profiling of microRNA precursors in human cancer cell lines (2005)

Our previous study described a real-time PCR method to quantify microRNA (miRNA) precursors using SYBR green detection [T. D. Schmittgen, J. Jiang, Q. Liu and L. Yang (2004) Nucleic Acids Res., 32, e43]. The present study adapted the assay to a 384-well format and expanded it to include primers to 222 human miRNA precursors. TaqMan minor groove binder probes were used to discriminate nearly identical members of the let-7 family of miRNA isoforms. The miRNA precursor expression was profiled in 32 human cell lines from lung, breast, colorectal, hematologic, prostate, pancreatic, and head and neck cancers. Some miRNA precursors were expressed at similar levels in many of the cell lines, while others were differentially expressed. Clustering analysis of the miRNA precursor expression data revealed that most of the cell lines clustered into their respective tissues from which each cell line was ostensibly derived. miRNA precursor expression by PCR paralleled the mature miRNA expression by northern blotting for most of the conditions studied. Our study provides PCR primer sequences to all of the known human miRNA precursors as of December 2004 and provides a database of the miRNA precursor expression in many commonly used human cancer cell lines.
Reduced Incidence of Gastroduodenal Ulcers With Celecoxib, A Novel Cyclooxygenase-2 Inhibitor, Compared To Naproxen in Patients With Arthritis (2001)

As compared to naproxen (500 mg b.i.d.), use of celecoxib (200 mg b.i.d.), a COX-2 specific agent, at the recommended RA dose and twice the most frequently prescribed OA dose, was associated with lower rates of gastric, duodenal, and gastroduodenal ulcers but had comparable efficacy, in patients with OA and RA.
Niemann-Pick C1 Is Essential for Ebola Virus Infection and a Target of Small Molecule Inhibitors (2012)

Ebolavirus (EboV) is a highly pathogenic enveloped virus that causes outbreaks of zoonotic infection in Africa. The clinical symptoms are manifestations of the massive production of pro-inflammatory cytokines in response to infection and in many outbreaks, case fatality rate exceeds 75%. The unpredictable onset, ease of transmission, rapid progression of disease, high mortality and lack of effective vaccine or therapy have created a high level of public concern about EboV. Here we report the properties of a benzylpiperazine adamantane diamide-derived compound identified in a screen for inhibitors of EboV infection. We found that the inhibitor is specific, reversible, and that the target(s) for inhibition are present in cells and not in virus particles. The compound is not an inhibitor of acid pH-dependent endosome protease activity, which is required for EboV infection. Treatment of cells with this compound causes accumulation of cholesterol in late endosomes and lysosomes (LE/LY), suggesting it inhibits one or more proteins involved in regulation of cholesterol uptake into cells. Using mutant cell lines and informative derivatives of the inhibitor, we found the inhibitor target is the endosomal membrane protein Niemann-Pick C1 (NPC1). NPC1 is a polytopic LE/LY membrane protein that mediates uptake of lipoprotein-derived cholesterol into cells. We find that NPC1 is essential for EboV infection, that NPC1 binds to the protease-cleaved GP1 subunit of the EboV glycoprotein, and that the anti-viral compound inhibits infection by targeting NPC1 and interfering with binding to GP1. Furthermore, analysis of viral variants resistant to the anti-viral compound revealed that the residues which confer resistance are located on the surface of the receptor binding domain of GP1. Combined with the results of previous studies of GP structure and function, our findings support a model of EboV infection in which cleavage of the GP1 subunit by endosomal cathepsin proteases removes heavily glycosylated domains to expose the N-terminal domain, which is a ligand for NPC1 and regulates membrane fusion by the GP2 subunit. Thus, NPC1 is essential for EboV entry and a target for anti-viral therapy.
Ultrasound Radiation Force Modulates Ligand Availability on Targeted Contrast Agents (2006)

Radiation force produced by low-amplitude ultrasound at clinically relevant frequencies remotely translates freely flowing microbubble ultrasound contrast agents over distances up to centimeters from the luminal space to the vessel wall in order to enhance ligand-receptor contact in targeting applications. The question arises as to how the microbubble shell might be designed at the molecular level to fully take advantage of such physical forces in targeted adhesion for molecular imaging and controlled therapeutic release. Herein, we report on a novel surface architecture in which the tethered ligand is buried in a polymeric overbrush. Our results, with biotin-avidin as the model ligand-receptor pair, show that the overbrush conceals the ligand, thereby reducing immune cell binding and increasing circulation persistence. Targeted adhesion is achieved through application of ultrasound radiation force to instantly reveal the ligand within a well-defined focal zone and simultaneously bind the ligand and receptor. Our data illustrate how the adhesive properties of the contrast agent surface can be reversibly changed, from stealth to sticky, through the physical effects of ultrasound. This technique can be combined with any ligand-receptor pair to optimize targeted adhesion for ultrasonic molecular imaging.
Regulation of mitogen-activated protein kinase cascade in adult rat heart preparations in vitro. (1994)

The regulation of mitogen-activated protein kinase (MAPK) and MAPK kinase (MEK) was studied in freshly isolated adult rat heart preparations. In contrast to the situation in ventricular myocytes cultured from neonatal rat hearts, stimulation of MAPK activity by 1 mumol/L phorbol 12-myristate 13-acetate (PMA) was not consistently detectable in crude extracts. After fast protein liquid chromatography, MAPK isoforms p42MAPK and p44MAPK and two peaks of MEK were shown to be activated > 10-fold in perfused hearts or ventricular myocytes exposed to 1 mumol/L PMA for 5 minutes. The identities of MAPK or MEK were confirmed by immunoblotting and, for MAPK, by the "in-gel" myelin basic protein phosphorylation assay. In retrogradely perfused hearts, high coronary perfusion pressure (120 mm Hg for 5 minutes), norepinephrine (50 mumol/L for 5 minutes), or isoproterenol (50 mumol/L for 5 minutes) stimulated MAPK and MEK approximately 2- to 5-fold. In isolated myocytes, endothelin 1 (100 nmol/L for 5 minutes) also stimulated MAPK, but stimulation by norepinephrine or isoproterenol was difficult to detect. Immunoblotting showed that the relative abundances of MAPK and MEK protein in ventricles declined to < 20% of their postpartal abundances after 50 days. This may explain the difficulties encountered in assaying the activity of MAPK in crude extracts from adult hearts. We conclude that potentially hypertrophic agonists and interventions stimulate the MAPK cascade in adult rats and suggest that the MAPK cascade may be an important intracellular signaling pathway in this response.
Inter and Intrastrand Vibrational Coupling in DNA Studied with Heterodyned 2D-IR Spectroscopy (2003)

Heterodyned 2D-IR, frequency resolved photon echo, and pump−probe spectroscopies were collected to study the couplings and anharmonicities of cytidine and guanosine bases in DNA. Cytidine and guanosine anharmonicities were measured to be 9 and 14 cm-1, respectively. Strong cross-peaks were observed between the guanosine (G) and cytosine (C) carbonyl stretches in the 2D-IR spectra of the self-complementary oligonucleotide dG5C5 (5‘-GGGGGCCCCC-3‘). The spectra are interpreted in terms of inter- and intrastrand couplings between the carbonyl modes, and an excitonic Hamiltonian, based on transition dipole coupling, was used to fit the 2D-IR spectra. The accuracy of this model is discussed in light of observed couplings to the ring modes.
Host-specific differentiation in the anther smut fungus Microbotryum violaceum as revealed by microsatellites (2000)

Abstract The anther smut fungus Microbotryum violaceum ( = Ustilago violacea) is a parasite of many species of the Caryophyllaceae. Its host specificity has been debated since early this century, when cross-inoculation experiments indicated the existence of host-specific lineages. Recently, on the basis of spore ultrastructure, all presumed host races were lumped within M. violaceum. To measure gene flow among natural populations of anther smuts from different host species, we used microsatellite variation at 5 loci among samples from 8 Silene, 2 Saponaria, 2 Dianthus and 1 Gypsophila species. Most of the 326 M. violaceum samples investigated originated from the Swiss Alps and close surroundings. Microsatellite variation revealed almost perfect isolation among anther smut fungi from different host species. In addition, differentiation was supported by the nonrandom distribution of null alleles among samples from different host species and host genera. Null alleles were most abundant in anther smut samples from non-Silene hosts. The resolution of genetic differentiation among anther smuts from different host species was highest in those from Silene species. Genetic relationships among samples as indicated by Neighbour-Joining analysis based on genetic distances are discussed with respect to host phylogeny and host ecology. One sample was identified as Ustilago gausseni because it had verrucose instead of reticulate spores and was collected from Silene italica. Neighbour-Joining analysis revealed that this sample was similar to the M. violaceum samples from other Silene host species. Therefore, our data question spore morphology as a reliable character for anther smut systematics.
Antioxidant Capacity Manipulation in Transgenic Potato Tuber by Changes in Phenolic Compounds Content (2004)

The main goal of this study was to generate potato tubers with increased levels of flavonoids and thus modified antioxidant capacities. To accomplish this, the vector carrying multigene construct was prepared and several transgenic plants were generated, all overexpressing key biosynthesis pathway enzymes. The single-gene overexpression or simultaneous expression of genes encoding chalcone synthase (CHS), chalcone isomerase (CHI), and dihydroflavonol reductase (DFR) resulted in a significant increase of measured phenolic acids and anthocyanins. The increase in phenolic compounds synthesis is accompanied by decreases in starch and glucose levels in transgenic plants. The flavonoids-enriched plants showed improved antioxidant capacity; however, there is a complex relationship between antioxidant capacity and flavonoids content, suggesting the great participation of other compounds in the antioxidant potential of the plants. These other compounds are not yet recognized.
Cutting Edge: Contact-Mediated Suppression by CD4+CD25+ Regulatory Cells Involves a Granzyme B-Dependent, Perforin-Independent Mechanism (2005)

CD4+CD25+ regulatory T cells (Treg) are potent immunosuppressive cells that are pivotal in the regulation of peripheral tolerance. In this report, we identify granzyme B (GZ-B) as one of the key components of Treg-mediated suppression. Induction of regulatory activity is correlated with the up-regulation of GZ-B expression. Proof of a functional involvement of GZ-B in contact-mediated suppression by Treg is shown by the reduced ability of Treg from GZ-B-/- mice to suppress as efficiently as Treg from WT mice. GZ-B-mediated suppression is perforin independent, because suppression by Treg from perforin-/- and WT is indistinguishable. Additionally, suppression mediated by Treg appears to be mediated, in part, by the induction of apoptosis in the CD4+CD25- effector cell. In summary, GZ-B is one of the key mechanisms through which CD4+CD25+ Treg induce cell contact-mediated suppression.
The Lymphotoxin-β Receptor Is Necessary and Sufficient for LIGHT-mediated Apoptosis of Tumor Cells (2000)

LIGHT is a tumor necrosis factor (TNF) ligand superfamily member, which binds two known cellular receptors, lymphotoxin-beta receptor (LTbetaR) and the herpesvirus entry mediator (HveA). LIGHT is a homotrimer that activates proapoptotic and integrin-inducing pathways. Receptor binding residues via LIGHT were identified by introducing point mutations in the A' --> A" and D --> E loops of LIGHT, which altered binding to LTbetaR and HveA. One mutant of LIGHT exhibits selective binding to HveA and is inactive triggering cell death in HT29.14s cells or induction of ICAM-1 in fibroblasts. Studies with HveA- or LTbetaR-specific antibodies further indicated that HveA does not contribute, either cooperatively or by direct signaling, to the death pathway activated by LIGHT. LTbetaR, not HveA, recruits TNF receptor-associated factor-3 (TRAF3), and LIGHT-induced death is blocked by a dominant negative TRAF3 mutant. Together, these results indicate that TRAF3 recruitment propagates death signals initiated by LIGHT-LTbetaR interaction and implicates a distinct biological role for LIGHT-HveA system.
Disruption of respiratory cilia by proteases including those of Pseudomonas aeruginosa (1986)

Pseudomonad proteases disrupted the function and structure of demembranated cilia (axonemes) extracted from porcine tracheae. Proteolytic degradation by the two pseudomonad proteases elastase and alkaline protease and by trypsin and subtilisin impaired motility of ATP-activated axonemes. In addition, electron microscopic observation of negatively stained axonemes indicated that exposure to proteases caused dissociation into individual doublet or singlet microtubules. Inhibition of motility and axonemal fraying occurred when axonemes were treated with less than 5 U of proteolytic activity of any of the four proteases tested. When the effects of 2 U of each protease were compared, trypsin and subtilisin were able to produce immotility in less time than pseudomonad elastase and alkaline protease, while alkaline protease and subtilisin caused the most axonemal fraying in 10 min. Proteolytic digestion of axonemal proteins was detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. All four proteases cleaved dynein proteins (proteins necessary for motility), though treatment with trypsin resulted in the most extensive solubilization of axonemal proteins. Trypsin and subtilisin both produced more changes in the protein profiles of treated axonemes, using fewer units of proteolytic activity, than the pseudomonad proteases. However, the limited alteration of only a few axonemal proteins by pseudomonad proteases indicates that cleavage need not be extensive to produce dysfunction. Thus, ciliary axonemes are susceptible to proteolytic attack. Degradation of axonemal proteins by pseudomonad proteases, which are released during active infection, may contribute to the impaired ciliary function associated with pseudomonad colonization of the respiratory tract.
The role of elastic restoring forces in right-ventricular filling (2015)

The RV works as a suction pump, exploiting contraction energy to facilitate filling by means of strong elastic recoil. Restoring forces are influenced by the inotropic state and RV conformational changes mediated by direct ventricular interdependence.
Mapping of the Alz 50 epitope in microtubule‐associated proteins tau (1990)

Alz 50 and seven other monoclonal antibodies have been shown to react with both tau and Alzheimer brain proteins of molecular mass 60-70 kDa. The location of some of the epitopes of these antibodies (Alz 50, Tau-2, NP14, Ab 636.7) on the tau molecule is unknown, whereas those of others (Tau 60, Tau 14, Tau-1, Tau 46) have recently been demonstrated in fetal human tau at amino acid residues 60-72, 83-120, 131-140, and 315-352. To determine the location of the unknown epitopes, human tau was digested with chymotrypsin and trypsin, and the bovine microtubule fraction was incubated with chymotrypsin. Comparison of the immunoblots of chymotryptic digested tau with those of untreated preparations showed that the Alz 50 epitope was more sensitive than other tau epitopes to proteolysis. Cleavage of a 3-4 kDa polypeptide from the periphery of tau was sufficient to remove the Alz 50 epitope, but not the epitopes of Tau 46 (C-end) or Tau 60 (N-end). The distribution of the Alz 50 epitope in endogenously degraded, chymotrypsin or trypsin digested tau fragments was different from that of the Tau 46 epitope known to be located within 38 residues from the C-terminus of the tau molecule. Based on these observations Alz 50 epitope was considered to be located within 3-4 kDa of the N-terminus of tau. A comparison of immunoblots of different tau-reactive antibodies showed similarities between Tau 60 and Tau-2, and between Tau 14, Tau-1, NP14, and Ab 636.7.(ABSTRACT TRUNCATED AT 250 WORDS)
A System Model for Geologic Sequestration of Carbon Dioxide (2008)

In this paperwe describe CO2-PENS, a comprehensive system-level computational model for performance assessment of geologic sequestration of CO2. CO2-PENS is designed to perform probabilistic simulations of CO2 capture, transport, and injection in different geologic reservoirs. Additionally, the long-term fate of CO2 injected in geologic formations, including possible migration out of the target reservoir, is simulated. The simulations sample from probability distributions for each uncertain parameter, leading to estimates of global uncertainty that accumulate through coupling of processes as the simulation time advances. Each underlying process in the system-level model is built as a module that can be modified as the simulation tool evolves toward more complex problems. This approach is essential in coupling processes that are governed by different sets of equations operating at different time-scales. We first explain the basic formulation of the system level model, briefly discuss the suite of process-level modules that are linked to the system level, and finally give an in-depth example that describes the system level coupling between an injection module and an economic module. The example shows how physics-based calculations of the number of wells required to inject a given amount of CO2 and estimates of plume size can impact long-term sequestration costs.
<title>Improved process of reflection holography replication and heat processing</title> (1994)

A method is presented for rapid processing of high volumes of reflection holograms recorded in rolls of DuPont OmniDex<SUP>TM</SUP> photopolymer films. This process includes high-volume continuous holographic replication, color tuning lamination and scroll over heating. Performance data for commercial OmniDex films processed with this method is presented. Performance and yield data from trial production runs demonstrate process capacity of at least 2500 square feet per day.
Results of treatment of 255 patients with metastatic renal cell carcinoma who received high-dose recombinant interleukin-2 therapy. (1995)

High-dose IL-2 appears to benefit some patients with metastatic renal cell carcinoma by producing durable CRs or PRs. Despite severe acute treatment-associated toxicities, IL-2 should be considered for initial therapy of patients with appropriately selected metastatic renal cell carcinoma.
General synthesis of 1,3-dithiol-2-ones (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGeneral synthesis of 1,3-dithiol-2-onesAjit K. Bhattacharya and Alfred G. HortmannCite this: J. Org. Chem. 1974, 39, 1, 95–97Publication Date (Print):January 1, 1974Publication History Published online1 May 2002Published inissue 1 January 1974https://pubs.acs.org/doi/10.1021/jo00915a021https://doi.org/10.1021/jo00915a021research-articleACS PublicationsRequest reuse permissionsArticle Views582Altmetric-Citations51LEARN 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