gebhart/patrepeval huggingface dataset:
Inhibition by cyclosporin A of rodent malaria in vivo and human malaria in vitro (1982)

The development and course of normally lethal parasitemias in mice inoculated intraperitoneally with erythrocytic stages of Plasmodium yoelii or Plasmodium berghei were markedly affected by treatment with the antilymphoid drug cyclosporin A (CS-A). When the first of four daily subcutaneous 25-mg/kg doses of CS-A was given at the time of parasite inoculation, patent infections failed to develop. If begun up to 5 days earlier, this same treatment regimen prolonged the prepatent period, attenuated parasitemia, and reduced mortality. In mice with patient infections, two consecutive daily 25-mg/kg doses of CS-A were sufficient to terminate parasitemias which, after several days, reappeared but were self-limiting. This pattern of apparent cure followed by transient recrudescence remained unaltered even when daily treatment with the same drug dose was continued for 3 weeks. Recrudescence was associated with the emergence of parasite populations that were relatively resistant to CS-A and, in the case of P. yoelii, of reduced virulence. In more limited experiments, CS-A was found to be active in vitro against erythrocytic stages of the human malarial parasite palsmodium falciparum. Depending on the concentration of drug in the culture medium, parasite growth was either prevented or inhibited.
PCR and Restriction Endonuclease Analysis for Rapid Identification of Human Adenovirus Subgenera (2000)

Subgenus identification of adenoviruses is of clinical importance and is as informative as identification by serotype in most clinical situations. A PCR-based identification of adenovirus subgenera A, B, C, D, E, and F and sometimes serotypes is described. The PCR uses nonnested primer pair ADRJC1-ADRJC2, which targets a highly conserved region of the adenovirus hexon gene, has a sensitivity of 10 to 40 copies of adenovirus type 2 (Ad2) DNA, and generates 140-bp PCR products from adenovirus serotypes representative of all the subgroups. The PCR products of all subgroups can be differentiated on the basis of the restriction fragment patterns produced by a total of five restriction endonucleases. In addition, serotypes Ad40 and Ad41 (subgroup F) and important serotypes of subgroup D (Ad8, Ad10, Ad19, and Ad37) can easily be differentiated, but serotypes within subgroups B and C cannot. The method was assessed by blind subgenus identification of 56 miscellaneous clinical isolates of adenoviruses. The identities of these isolates at the subgenus level by the PCR correlated 91% (51 of 56) with the results of serotyping by the neutralization test, and 9% (5 of 56) of clinical isolates produced discordant results.
Rapid screening for polymorphisms in dextromethorphan and mephenytoin metabolism. (1990)

1. The phenotyping parameters for dextromethorphan and mephenytoin were assessed in 48 normal male volunteers following administration of each metabolic probe drug on separate occasions and together according to a randomized 3-way crossover design. 2. Neither the urinary S-/R-mephenytoin ratio nor the dextromethorphan metabolic ratio were altered significantly by coadministration of the probe drugs. 3. Five-hundred and nineteen subjects were screened for expression of mephenytoin 4-hydroxylase and dextromethorphan O-demethylase activity following the coadministration of mephenytoin and dextromethorphan. The activity was determined in each case by methods not requiring any quantitative measurements. 4. Nineteen (3.7%) of the subjects were identified as poor metabolizers (PMs) of mephenytoin and 35 subjects (6.7%) as PMs of dextromethorphan. 5. All PMs of dextromethorphan were confirmed by more rigorous evaluation of the metabolic ratio.
Towards consistent generation of pancreatic lineage progenitors from human pluripotent stem cells (2015)

Human pluripotent stem cells can in principle be used as a source of any differentiated cell type for disease modelling, drug screening, toxicology testing or cell replacement therapy. Type I diabetes is considered a major target for stem cell applications due to the shortage of primary human beta cells. Several protocols have been reported for generating pancreatic progenitors by in vitro differentiation of human pluripotent stem cells. Here we first assessed one of these protocols on a panel of pluripotent stem cell lines for capacity to engender glucose sensitive insulin-producing cells after engraftment in immunocompromised mice. We observed variable outcomes with only one cell line showing a low level of glucose response. We, therefore, undertook a systematic comparison of different methods for inducing definitive endoderm and subsequently pancreatic differentiation. Of several protocols tested, we identified a combined approach that robustly generated pancreatic progenitors in vitro from both embryo-derived and induced pluripotent stem cells. These findings suggest that, although there are intrinsic differences in lineage specification propensity between pluripotent stem cell lines, optimal differentiation procedures may consistently direct a substantial fraction of cells into pancreatic specification.
Using Cohort Scheduling to Enhance Server Performance (Extended Abstract) (2001)

article Share on Using Cohort Scheduling to Enhance Server Performance (Extended Abstract) Authors: James R. Larus Microsoft Research, Redmond, WA Microsoft Research, Redmond, WAView Profile , Michael Parkes Microsoft Research, Redmond, WA Microsoft Research, Redmond, WAView Profile Authors Info & Claims ACM SIGPLAN NoticesVolume 36Issue 8Aug. 2001 pp 182–187https://doi.org/10.1145/384196.384222Online:01 August 2001Publication History 20citation501DownloadsMetricsTotal Citations20Total Downloads501Last 12 Months14Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Accurate measurement of high-speed package and interconnect parasitics (2003)

The feasibility of using high-speed wafer probes to measure accurately the parasitics associated with packages and interconnects used in conjunction with high-speed integrated circuits is demonstrated. A way of calibrating out the fixture-related errors while providing a reconfigurable mechanical interface to specific points of interest is demonstrated. These points can be at the perimeter and also internal. Calibration at the point of interface to the structure under test and a well-controlled mechanical interface enable large numbers of highly repeatable measurements to be made easily and accurately. The effect is to extend the full capability of test instrumentation to the physical points of interest, with accuracy and repeatability from site to site. The ability to calibrate at the probe tips is necessary to eliminate distortions from cables and probes. Some sources of errors, such as crosstalk, should be minimized in the probe, since they are difficult to correct in most cases.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Intragenic mutation analysis of the human epidermal growth factor receptor (EGFR) gene in malignant human oral keratinocytes. (1999)

Alteration in epidermal growth factor receptor (EGFR) expression is frequently associated with malignant transformation of epithelial tissues, including oral mucosa. This study examines the mutations in the coding region of the human EGFR gene in normal and malignant human oral keratinocytes. To examine the intragenic mutations in the human EGFR gene, a panel of normal and malignant human oral keratinocytes were examined by a nonisotopic RNase cleavage assay. Two consistent alterations were detected. First, a polymorphism, which generates a unique BsrI restriction site, was detected at position 2073. This BsrI polymorphism was present only in malignant keratinocytes. Second, Southern blot hybridization of PCR products revealed that there is a truncated EGFR mRNA (approximately 1.5-kb) in oral squamous cell carcinoma cell lines. Similar analysis in normal cell lines revealed that this truncated EGFR transcript is also present. Immunoblotting revealed the presence of this truncated form of EGFR in all keratinocyte cell lines. These data permit us to conclude that there exists a novel truncated form of EGFR in human oral keratinocytes. Furthermore, there exists a tumor-associated BsrI polymorphic site at position 2073. The potential biological relevance of the truncated receptor and the utility of the BsrI polymorphic site for diagnostic applications are currently being explored.
Catechol Polymers for pH-Responsive, Targeted Drug Delivery to Cancer Cells (2011)

A novel cell-targeting, pH-sensitive polymeric carrier was employed in this study for delivery of the anticancer drug bortezomib (BTZ) to cancer cells. Our strategy is based on facile conjugation of BTZ to catechol-containing polymeric carriers that are designed to be taken up selectively by cancer cells through cell surface receptor-mediated mechanisms. The polymer used as a building block in this study was poly(ethylene glycol), which was chosen for its ability to reduce nonspecific interactions with proteins and cells. The catechol moiety was exploited for its ability to bind and release borate-containing therapeutics such as BTZ in a pH-dependent manner. In acidic environments, such as in cancer tissue or the subcellular endosome, BTZ dissociates from the polymer-bound catechol groups to liberate the free drug, which inhibits proteasome function. A cancer-cell-targeting ligand, biotin, was presented on the polymer carriers to facilitate targeted entry of drug-loaded polymer carriers into cancer cells. Our study demonstrated that the cancer-targeting drug-polymer conjugates dramatically enhanced cellular uptake, proteasome inhibition, and cytotoxicity toward breast carcinoma cells in comparison with nontargeting drug-polymer conjugates. The pH-sensitive catechol-boronate binding mechanism provides a chemoselective approach for controlling the release of BTZ in targeted cancer cells, establishing a concept that may be applied in the future toward other boronic acid-containing therapeutics to treat a broad range of diseases.
How Vergil expanded the Underworld inAeneid6 (2001)

In a recent article published in the CQ I argued the likelihood that in comparable underworld scenes Vergil modelled Charon's challenge to Aeneas in Aeneid 6.388–97 on Aeacus' challenge to Heracles in a surviving fragment of the tragedy Pirithous composed by either Euripides or Critias, and I took the episode to be a reinforcement or a possible modification of E. Norden's suggestion that Aeneas' descent into the Underworld is modelled on a catabasis of Heracles. In the play Aeacus sees a figure approaching him and demands to know of the stranger both his identity and his business in coming. Heracles responds by giving his name and explaining that he has come hither at Eurystheus' command to fetch Cerberus alive from Hades and bring him to Mycenae's gates. Heracles must then have overcome Aeacus. for we next find Theseus and Heracles conversing in the Underworld about Pirithous. Earlier in the play Pirithous had lamented that he still languishes in Hades for having attempted, with Theseus as his accomplice, to carry off from the world below the goddess Persephone to be his bride. In the usual version both heroes are caught and punished in the world below and only Theseus is rescued by Heracles. In this play, however, Heracles now heaps praise upon Theseus for his loyalty in electing to stay with his friend Pirithous in Hades. Heracles then rescues both heroes.
Analysis of Biological Effects and Signaling Properties of Flt-1 (VEGFR-1) and KDR (VEGFR-2) (2001)

Endothelial cells express two related vascular endothelial growth factor (VEGF) receptor tyrosine kinases, KDR (kinase-insert domain containing receptor, or VEGFR-2) and Flt-1 (fms-like tyrosine kinase, or VEGFR-1). Although considerable experimental evidence links KDR activation to endothelial cell mitogenesis, there is still significant uncertainty concerning the role of individual VEGF receptors for other biological effects such as vascular permeability. VEGF mutants that bind to either KDR or Flt-1 with high selectivity were used to determine which of the two receptors serves to mediate different VEGF functions. In addition to mediating mitogenic signaling, selective KDR activation was sufficient for the activation of intracellular signaling pathways implicated in cell migration. KDR stimulation caused tyrosine phosphorylation of both phosphatidylinositol 3-kinase and phospholipase Cgamma in primary endothelial cells and stimulated cell migration. KDR-selective VEGF was also able to induce angiogenesis in the rat cornea to an extent indistinguishable from wild type VEGF. We also demonstrate that KDR, but not Flt-1, stimulation is responsible for the induction of vascular permeability by VEGF.
Some properties of polyethylene glycol:phenylalanine ammonia-lyase adducts. (1979)

Methoxypolyethylene glycol of 5000 daltons (PEG) was attached covalently to phenylalanine ammonia-lyase from Rhodotorula glutinis. Attachment of sufficient quantities of PEG to phenylalanine ammonia-lyase substantially reduces immunological recognition and clearance of the conjugated enzyme in mice. The modified enzyme demonstrates altered catalytic properties such as shifts in the pH and temperature optima, an increase in the Michaelis-Menten constant, and a lowered Vmax in comparison with the native enzyme. PEG-phenylalanine ammonia-lyase has increased resistance to proteolytic digestion, particularly when in the presence of cinnamate, a competitive inhibitor, while the native enzyme is rapidly inactivated. In the ultracentrifuge PEG-phenylalanine ammonia-lyase exhibits a lower sedimentation rate than the unmodified enzyme, despite the fact that it is much larger. The electrophoretic mobility of PEG-phenylalanine ammonia-lyase is greatly decreased in comparison to the unmodified enzyme. PEG-phenylalanine ammonia-lyase had a much longer blood-circulating life in mice, both initially and after a number of injections, than did the native enzyme. PEG-phenylalanine ammonia-lyase was a good immunogen but a poor antigen in mice and rabbits, that is, it readily induced antibody formation, but reacted poorly in vitro with the antibodies that were formed against it.
Structural classification and properties of ketoacyl synthases (2011)

Ketoacyl synthases (KSs) catalyze condensing reactions combining acyl-CoA or acyl-acyl carrier protein (acyl-ACP) with malonyl-CoA to form 3-ketoacyl-CoA or with malonyl-ACP to form 3-ketoacyl-ACP. In each case, the resulting acyl chain is two carbon atoms longer than before, and CO2 and either CoA or ACP are formed. KSs also join other activated molecules in the polyketide synthesis cycle. Our classification of KSs by their primary and tertiary structures instead of by their substrates and the reactions that they catalyze enhances insights into this enzyme group. KSs fall into five families separated by their characteristic primary structures, each having members with the same catalytic residues, mechanisms, and tertiary structures. KS1 members, overwhelmingly named 3-ketoacyl-ACP synthase III or its variants, are produced predominantly by bacteria. Members of KS2 are mainly produced by plants, and they are usually long-chain fatty acid elongases/condensing enzymes and 3-ketoacyl-CoA synthases. KS3, a very large family, is composed of bacterial and eukaryotic 3-ketoacyl-ACP synthases I and II, often found in multidomain fatty acid and polyketide synthases. Most of the chalcone synthases, stilbene synthases, and naringenin-chalcone synthases in KS4 are from eukaryota. KS5 members are all from eukaryota, most are produced by animals, and they are mainly fatty acid elongases. All families except KS3 are split into subfamilies whose members have statistically significant differences in their primary structures. KS1 through KS4 appear to be part of the same clan. KS sequences, tertiary structures, and family classifications are available on the continuously updated ThYme (Thioester-active enzYme) database.
Synthesis of epidermal growth factor receptor in human A431 cells. Glycosylation-dependent acquisition of ligand binding activity occurs post-translationally in the endoplasmic reticulum. (1986)

It was previously demonstrated that the epidermal growth factor (EGF) receptor in human A431 cells undergoes a slow post-translational modification by which it acquires EGF binding capacity (Slieker, L.J., and Lane, M.D. (1985) J. Biol. Chem. 260, 687-690). In this report, the role of glycosylation in the acquisition of ligand binding activity and in the intracellular translocation of the receptor precursor is characterized. Human A431 cells were incubated with [35S]methionine, and 35S-labeled EGF receptors were purified either by immunoprecipitation (total receptor) or by adsorption to an EGF affinity matrix (high affinity, or active receptor). The half-time for receptor activation is approximately 30 min and precedes its acquisition of resistance to endo-beta-N-acetylglucosaminidase H (t 1/2 = 75 min), a medial Golgi event. Activation is blocked by tunicamycin and is markedly slowed (t 1/2 = 120 min) by 1-deoxynojirimycin, an inhibitor of glucosidase I. In the latter case, the oligosaccharide chains are not further processed to complex forms. Treatment of the active high mannose receptor with endo-beta-N-acetylglucosaminidase H generates a fully active aglycoreceptor polypeptide, indicating that core oligosaccharide addition is a prerequisite for activation but that oligosaccharide chains are not intrinsically required for EGF binding. Subcellular fractionation studies showed that the EGF receptor is activated in the endoplasmic reticulum and that translocation from that organelle is extremely slow (t 1/2 = 75 min). Since the latter translocation rate approximates that for the acquisition of the resistance to endoglycosidase H, transit from the endoplasmic reticulum appears to be rate-limiting for the maturation of the receptor. Both tunicamycin and 1-deoxynojirimycin inhibit exit from the endoplasmic reticulum in parallel with their effects on the acquisition of binding activity. Immunoprecipitation of 35S-labeled EGF receptor with antiphosphotyrosine antibody in the presence of ATP suggested that the autophosphorylation activity of the receptor is also acquired post-translationally. The possible correlation of this to EGF binding activity is discussed.
Self-Assembly of Monodispersed Spherical Colloids into Complex Aggregates with Well-Defined Sizes, Shapes, and Structures (2001)

The self-assembly of polystyrene beads into a variety of polygonal and polyhedral clusters is reported. The Figure shows a schematic illustration of the procedure used to form these well-defined clusters under physical confinement. These aggregates will be useful as new types of building blocks in hierarchical self-assembly to generate mesostructured, 3D systems of high complexity.
Modulation of Cytokine Production by Dehydroepiandrosterone (DHEA) Plus Melatonin (MLT) Supplementation of Old Mice (1998)

Tissue levels of the antioxidants melatonin (MLT) and dehydroepiandrosterone (DHEA) decline with age, and this decline is correlated with immune dysfunction. The aim of the current study is to determine whether hormone supplementation with MLT and DHEA together would synergize to reverse immune senescence. Old (16.5 months) female C57BL/6 mice were treated with DHEA, MLT, or DHEA + MLT. As expected, splenocytes were significantly (P < 0.05) higher in old mice as compared to young mice. DHEA, MLT, and DHEA + MLT significantly (P < 0.005) increased B cell proliferation in young mice. However, only MLT and DHEA + MLT significantly (P < 0.05) increased B cell proliferation in old mice. DHEA, MLT, and DHEA + MLT help to regulate immune function in aged female C57BL/6 mice by significantly (P < 0.05) increasing Th1 cytokines, IL-2, and IFN-gamma or significantly (P < 0.05) decreasing Th2 cytokines, IL-6, and IL-10, thus regulating cytokine production. DHEA and MLT effectively modulate suppressed Th1 cytokine and elevated Th2 cytokine production; however, their combined use produced only a limited additive effect.
Estimation of maximum power supply noise for deep sub-micron designs (1998)

We propose a new technique for generating a small set of patterns to estimate the maximum power supply noise of deep sub-micron designs. We first build the charge/discharge current and output voltage waveform libraries for each cell, taking power and ground pin characteristics, the power net RC and other input characteristics as parameters. Based on the cells' current and voltage libraries, the power supply noise of a 2-vector sequence can be estimated efficiently by a cell-level waveform simulator. We then apply the Genetic Algorithm based on the efficient waveform simulator to generate a small set of patterns producing high power supply noise. Finally, the results are validated by simulating the obtained patterns using a transistor level simulator. Our experimental results show that the patterns generated by our approach produce a tight lower bound on the maximum power supply noise.
The growth factor-like effects of tumor necrosis factor-alpha. Stimulation of glucose transport activity and induction of glucose transporter and immediate early gene expression in 3T3-L1 preadipocytes (1990)

In the present study, the ability of tumor necrosis factor-alpha (TNF) to stimulate hexose transport in quiescent 3T3-L1 fibroblasts has been examined. Activation of transport occurred in a dose- and time-dependent manner, with maximal stimulation (6-8-fold) observed 16 h after exposure to 2.5 nM TNF. Early activation of hexose transport by TNF (2-fold within 30 min) was associated with increased plasma membrane immunoreactive glucose transporters. Prolonged exposure to TNF (16 h) resulted in a 2-fold increase in glucose transporter content of both plasma and inner membrane compartments. The magnitude of increased glucose transport (6-8-fold) was greater than the increased content of plasma membrane glucose transporters (2-fold), suggesting that the TNF-treatment altered the intrinsic activity of the glucose transporters. Increased transcription of the glucose transporter (GLUT-1) gene, as well as several immediate-early genes (c-fos, c-jun, jun-B, and beta-actin) was observed within 15 min of exposure to TNF. Transcriptional activation of immediate-early genes was tightly coupled to subsequent accumulation of their respective mRNAs. However, increased GLUT-1 mRNA (8 h after TNF treatment) was due to an apparent 3-fold increase in the stability of this message and not to increased transcription. The time course of TNF-induced hexose transport occurred concomitant with a 6-fold increase in total RNA synthesis which preceded a 3-fold increase in protein synthesis. Moreover, TNF induced cell-cycle progression through S-phase, as measured by aphidicolin-sensitive thymidine uptake. Phorbol myristate acetate also stimulated hexose transport as well as expression of the GLUT-1 gene and several immediate-early genes in quiescent 3T3-L1 cells. TNF-induced immediate-early gene expression was intact in PMA-pretreated cells (with the exception of GLUT-1 and beta-actin genes where the response was muted), suggesting the involvement of multiple pathways in TNF signal transduction. Our results indicate that TNF initiates mitogenic events in quiescent 3T3-L1 fibroblasts reminiscent of serum-derived growth factors.