gebhart/patrepeval huggingface dataset:
Prostaglandin D2 generation after activation of rat and human mast cells with anti-IgE. (1982)

Anti-IgE-dependent activation of rat and human mast cells resulted in the preferential generation of the cyclooxygenase products prostaglandin D2 (PGD2) and prostaglandin I2 (PGI2) in the rat and PGD2 in the human. The average net generation of PGD2, determined by gas chromatography-mass spectrometry, was 13.1 ng/10(6) purified rat mast cells and 39.5 ng/10(6) dispersed, enriched human mast cells. After IgE-dependent activation, there was a linear relationship between the net quantities of PGD2 generated and of histamine secreted from dispersed human pulmonary cells when the number of mast cells was varied but the total number of cells was held constant, indicating that it is the number of mast cells participating in IgE-dependent activation, rather than total mast cell number, that determines PGD2 generation. A linear relationship was also shown between PGD2 generation, determined by radioimmunoassay, and the release of the granule marker beta-hexosaminidase from purified rat mast cells on the dose-response portion of the plot of their response to anti-IgE challenge. With higher concentrations of anti-IgE, PGD2 generation from rat mast cells plateaued, whereas net percent beta-hexosaminidase release increased further. In kinetic studies of rat mast cells activated with anti-IgE, the onset (1 to 2 min) and time of maximum generation (5 to 10 min) for PGD2 were delayed relative to the onset (15 to 30 sec) and completion (1 to 2 min) of beta-hexosaminidase release. Thus, the extracellular appearance of PGD2 during IgE-dependent mast cell activation represents a response additional to the secretion of granule-associated mediators.
Guest‐Dependent Flexible Coordination Networks with Fluorinated Ligands (2007)

Guest-dependent flexible coordination networks are formed from 1,4-bis(4-pyridylmethyl)tetrafluorobenzene (bpf), 4,4'-bis(4-pyridylmethyl)octafluorobiphenyl (bpfb), 2,6-bis(4-pyridylmethyl)hexafluoronaphthalene (2,6-bpfn), and 2,7-bis(4-pyridylmethyl)hexafluoronaphthalene (2,7-bpfn) with Cd(NO3)2 in the presence of various organic compounds. The reaction of bpf affords one-dimensional cyclic chains, two-dimensional rhombus grid sheets, and three-dimensional diamond frameworks with threefold interpenetration. The reaction of bpfb mainly affords two-dimensional rhombus grid sheets with twofold parallel interpenetration. The reaction of 2,6-bpfn affords a one-dimensional ladder and two-dimensional rhombus grid, twisted grid, and herringbone sheets. The reaction of 2,7-bpfn affords two-dimensional rhombus grid sheets and grid sheets with dumbbell-shaped cavities. This diversity of network topologies is induced by interactions between the guest molecules and the flexible ligand frameworks.
Mechanisms for the Shape‐Control and Shape‐Evolution of Colloidal Semiconductor Nanocrystals (2003)

Abstract The shape of CdSe and other semiconductor nanocrystals is controlled, producing dots, rods, rice‐shaped particles, tetrapods, or other elongated shapes. Monomer concentration in the growth solution is the determining factor in shape‐control and shape‐evolution. The elongated shapes could be transformed into more spherical shapes if the monomer concentration in the solution was lowered to a certain level, and spherically shaped nanocrystals could grow to elongated shapes by simply increasing the monomer concentration. The precursors are stable, inexpensive, and relatively non‐toxic, and therefore good choices for the growth of nearly monodisperse and shape‐controlled nanocrystals.
Lipoxin A4 and 8-isoprostane in the exhaled breath condensate of children hospitalized for status asthmaticus* (2011)

8-Isoprostane was elevated and Lipoxin A4 is decreased in the exhaled breath condensate of children recovering from status asthmaticus in a pediatric intensive care unit. These data may provide new insight into the pathophysiology of asthma in children in this clinical setting.
The predominance of CD8+ T cells after infection with measles virus suggests a role for CD8+ class I MHC-restricted cytotoxic T lymphocytes (CTL) in recovery from measles. Clonal analyses of human CD8+ class I MHC-restricted CTL. (1990)

Stimulation of PBMC, in children recovering from acute measles, with autologous EBV-transformed and measles virus (MV)-infected lymphoblastoid cell lines (B-LCL) expanded primarily MV-specific CD8+ T cells. A large number of CD8+ T cell clones were obtained either by passaging of bulk cultures at limiting dilutions or by direct cloning of PBMC without previous stimulation in bulk culture. The MV-specific CD8+ T cell clones responding in a proliferative and a CTL assay were found to be class I MHC restricted. In contrast, CD4+ MV-specific T cell clones, which were generated by the same protocol, recognized MV in association with class II MHC molecules. Analysis of processing requirements for Ag presentation to CD8+ and CD4+ T cell clones, measured by the effect of chloroquine in a proliferative T cell response, revealed that both types of T cells recognized MV Ag processed via the endogenous/cytoplasmic pathway. Thus, these studies indicate that, as in most other viral infections and in contrast to previous suggestions, the class I MHC-restricted CTL response by CD8+ T cells may be an important factor in the control and elimination of MV infection. Therefore, the role proposed for CD4+ class II-restricted T cells in recovery from measles needs to be reevaluated.
Quantification of Sleepiness: A New Approach (1973)

ABSTRACT The Stanford Sleepiness Scale (SSS) is a self‐rating scale which is used to quantify progressive steps in sleepiness. The present study investigated whether the SSS cross‐validates with performance on mental tasks and whether the SSS demonstrates changes in sleepiness with sleep loss. Five college student S s were given a brief test of memory and the Wilkinson Addition Test in 2 test sessions and The Wilkinson Vigilance Test in 2 other sessions spaced throughout a 16‐hr day for 6 days. S s made SSS ratings every 15 min during their waking activities. On night 4, S s underwent all night sleep deprivation. On all other nights, S s were allowed only 8 hrs in bed. Mean SSS ratings correlated r = .68 with performance on the Wilkinson Tests. Discrete SSS ratings correlated r = .47 with performance on the memory test. Moreover, mean baseline SSS ratings were found to be significantly lower than corresponding ratings of the deprivation period.
Defining the mode, energetics and specificity with which a macrocyclic hexaoxazole binds to human telomeric G-quadruplex DNA (2007)

Oxazole-containing macrocycles represent a promising class of anticancer agents that target G-quadruplex DNA. We report the results of spectroscopic studies aimed at defining the mode, energetics and specificity with which a hexaoxazole-containing macrocycle (HXDV) binds to the intramolecular quadruplex formed by the human telomeric DNA model oligonucleotide d(T2AG3)4 in the presence of potassium ions. HXDV binds solely to the quadruplex nucleic acid form, but not to the duplex or triplex form. HXDV binds d(T2AG3)4 with a stoichiometry of two drug molecules per quadruplex, with these binding reactions being coupled to the destacking of adenine residues from the terminal G-tetrads. HXDV binding to d(T2AG3)4 does not alter the length of the quadruplex. These collective observations are indicative of a nonintercalative 'terminal capping' mode of interaction in which one HXDV molecule binds to each end of the quadruplex. The binding of HXDV to d(T2AG3)4 is entropy driven, with this entropic driving force reflecting contributions from favorable drug-induced alterations in the configurational entropy of the host quadruplex as well as in net hydration. The 'terminal capping' mode of binding revealed by our studies may prove to be a general feature of the interactions between oxazole-containing macrocyclic ligands (including telomestatin) and intramolecular DNA quadruplexes.
Influence of OCT Signal Strength on Macular, Optic Nerve Head, and Retinal Nerve Fiber Layer Parameters (2010)

Significantly larger macular and optic nerve head OCT measurements were obtained with increasing signal strength measurements, although absolute differences in macular measurements were small and are of questionable clinical importance. The results support the robustness of OCT in providing precise macular imaging.
Cathepsin B-cleavable doxorubicin prodrugs for targeted cancer therapy (2012)

Doxorubicin (DOX) is one of the most effective cytotoxic anticancer drugs used for the treatment of hematological malignancies, as well as a broad range of solid tumors. However, the clinical applications of this drug have long been limited due to its severe dose‑dependent toxicities. Therefore, DOX derivatives and analogs have been developed to address this issue. A type of DOX prodrug, cleaved by cathepsin B (Cat B), which is highly upregulated in malignant tumors and premalignant lesions, has been developed to achieve a higher DOX concentration in tumor tissue and a lower concentration in normal tissue, so as to enhance the efficacy and reduce toxicity to normal cells. In this review, we focused on Cat B-cleavable DOX prodrugs and discussed the efficacy of these prodrugs, demonstrated by preclinical and clinical developments.
Purification and characterization of the human brain insulin receptor. (1986)

The insulin receptor from human brain cortex was purified by a combination monoclonal antibody affinity column and a wheat germ agglutinin column. This purified receptor preparation exhibited major protein bands of apparent Mr = 135,000 and 95,000, molecular weights comparable to those for the alpha and beta subunits of the purified human placental and rat liver receptors. A minor protein band of apparent Mr = 120,000 was also observed in the brain receptor preparation. Crosslinking of 125I-insulin to all three receptor preparations was found to preferentially label a protein of apparent Mr = 135,000. In contrast, cross-linking of 125I-labeled insulin-like growth factor I to the brain preparation preferentially labeled the protein of apparent Mr = 120,000. The purified brain insulin receptor was found to be identical with the placental insulin receptor in the amount of neuraminidase-sensitive sialic acid and reaction with three monoclonal antibodies to the beta subunit of the placental receptor. In contrast, a monoclonal antibody to the insulin binding site recognized the placental receptor approximately 300 times better than the brain receptor. These results indicate that the brain insulin receptor differs from the receptor in other tissues and suggests that this difference is not simply due to the amount of sialic acid on the receptor.
Manipulation of the Rapamycin Effector Domain. Selective Nucleophilic Substitution of the C7 Methoxy Group (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTManipulation of the Rapamycin Effector Domain. Selective Nucleophilic Substitution of the C7 Methoxy GroupJuan I. Luengo, Arda Konialian-Beck, Leonard W. Rozamus, and Dennis A. HoltCite this: J. Org. Chem. 1994, 59, 22, 6512–6513Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://pubs.acs.org/doi/10.1021/jo00101a006https://doi.org/10.1021/jo00101a006research-articleACS PublicationsRequest reuse permissionsArticle Views495Altmetric-Citations19LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Botulinum neurotoxin subtype A2 enters neuronal cells faster than subtype A1 (2010)

Botulinum neurotoxins (BoNTs), the causative agent of human botulism, are the most potent naturally occurring toxins known. BoNT/A1, the most studied BoNT, is also used as an important biopharmaceutical. In this study, the biological activity of BoNT/A1 is compared to that of BoNT/A2 using neuronal cell models. The data obtained indicate faster and increased intoxication of neuronal cells by BoNT/A2 than BoNT/A1, and that the mechanism underlying this increased toxicity is faster and more efficient cell entry that is independent of ganglioside binding. These results have important implications for the development of new BoNT based therapeutics and BoNT countermeasures.
BEDOPS: high-performance genomic feature operations (2012)

http://code.google.com/p/bedops/ includes binaries, source and documentation.
Chromatin Structure Regulates Gene Conversion (2007)

Homology-directed repair is a powerful mechanism for maintaining and altering genomic structure. We asked how chromatin structure contributes to the use of homologous sequences as donors for repair using the chicken B cell line DT40 as a model. In DT40, immunoglobulin genes undergo regulated sequence diversification by gene conversion templated by pseudogene donors. We found that the immunoglobulin Vlambda pseudogene array is characterized by histone modifications associated with active chromatin. We directly demonstrated the importance of chromatin structure for gene conversion, using a regulatable experimental system in which the heterochromatin protein HP1 (Drosophila melanogaster Su[var]205), expressed as a fusion to Escherichia coli lactose repressor, is tethered to polymerized lactose operators integrated within the pseudo-Vlambda donor array. Tethered HP1 diminished histone acetylation within the pseudo-Vlambda array, and altered the outcome of Vlambda diversification, so that nontemplated mutations rather than templated mutations predominated. Thus, chromatin structure regulates homology-directed repair. These results suggest that histone modifications may contribute to maintaining genomic stability by preventing recombination between repetitive sequences.
Analog FIR Filter Integrated Circuit (2017)

Analog FIR filters are critical components of advanced data processing and communication systems. Unlike digital filters, they do not utilize clock signals, but require broad-band analog delay units and variable-gain linear amplifiers. This paper describes a 9-tap linear FIR filter IC with a novel tree-shaped architecture based on an internal transmission line with a special configuration and variable-gain linear amplifiers with multi-cell binary gain control. The IC has been implemented in an advanced SiGe BiCMOS technology that features hetero-junction bipolar transistors with fT=210GHz. The fabricated IC operates at data rates above 25Gbps.
Pancreatic Glucagon-Like Peptide-1 Receptor Couples to Multiple G Proteins and Activates Mitogen-Activated Protein Kinase Pathways in Chinese Hamster Ovary Cells* (1999)

Chinese hamster ovary (CHO) cells stably expressing the human insulin receptor and the rat glucagon-like peptide-1 (GLP-1) receptor (CHO/GLPR) were used to study the functional coupling of the GLP-1 receptor with G proteins and to examine the regulation of the mitogen-activated protein (MAP) kinase signaling pathway by GLP-1. We showed that ligand activation of GLP-1 receptor led to increased incorporation of GTP-azidoanilide into Gs alpha, Gq/11 alpha, and Gi1,2 alpha, but not Gi3 alpha. GLP-1 increased p38 MAP kinase activity 2.5- and 2.0-fold over the basal level in both CHO/GLPR cells and rat insulinoma cells (RIN 1046-38), respectively. Moreover, GLP-1 induced phosphorylation of the immediate upstream kinases of p38, MKK3/MKK6, in CHO/GLPR and RIN 1046-38 cells. Ligand-stimulated GLP-1 receptor produced 1.45- and 2.7-fold increases in tyrosine phosphorylation of 42-kDa extracellular signal-regulated kinase (ERK) in CHO/GLPR and RIN 1046-38 cells, respectively. In CHO/GLPR cells, these effects of GLP-1 on the ERK and p38 MAP kinase pathways were inhibited by pretreatment with cholera toxin (CTX), but not with pertussis toxin. The combination of insulin and GLP-1 resulted in an additive response (1.6-fold over insulin alone) that was attenuated by CTX. In contrast, the ability of insulin alone to activate these pathways was insensitive to either toxin. Our study indicates a direct coupling between the GLP-1 receptor and several G proteins, and that CTX-sensitive proteins are required for GLP-1-mediated activation of MAP kinases.
Mechanisms of Immunopathology in Murine Models of Central Nervous System Demyelinating Disease (2006)

Many disorders of the CNS, such as multiple sclerosis (MS), are characterized by the loss of the myelin sheath surrounding nerve axons. MS is associated with infiltration of inflammatory cells into the brain and spinal cord, which may be the primary cause of demyelination or which may be induced secondary to axonal damage. Both the innate and adaptive arms of the immune system have been reported to play important roles in myelin destruction. Numerous murine demyelinating models, both virus-induced and/or autoimmune, are available, which reflect the clinical and pathological variability seen in human disease. This review will discuss the immunopathologic mechanisms involved in these demyelinating disease models.
Solid-phase epitaxial growth of Ge-Si alloys made by ion implantation (1992)

Solid-phase epitaxial growth was studied in germanium-implanted 〈100〉 silicon wafers as a function of germanium fluence, annealing temperature, and time. MeV He Rutherford backscattering in channeling conditions, cross-sectional transmission electron microscopy, double-crystal x-ray diffraction, and secondary-ion mass spectroscopy techniques were used to characterize the samples. At low fluences, up to 1×1015 cm−2 at 130 keV, the crystallization kinetics is similar to that measured on self-amorphized silicon. In the high-dose samples, prepared by multiple implants with a total dose of 3.12×1016 cm−2, the growth rate at fixed temperatures decreases. A comparison with literature data, obtained by similar experiments performed on amorphized uniform GexSi100−x films prepared by molecular-beam epitaxy or chemical-vapor deposition, reveals that the concentration gradient, unavoidable in implanted samples mainly at the end of the ion range region, is strictly connected with the observed decrease.
Silicon-mediated synthesis of new amphiphilic oligomers (1997)

A series of amphiphilic oligomers have been synthesized in which the hydrophobic component was polyisobutylene, polystyrene, poly(methyl methacrylate) or dodecane, and the hydrophilic component was poly(vinyl alcohol) or poly(methacrylic acid). These syntheses exploited the chain extension chemistry of aldehyde-functionalized materials using silyl aldol polymerization or the group transfer polymerization of methacrylates. The interfacial character of these new amphiphilic oligomers was examined using water/toluene emulsification tests. © 1997 John Wiley & Sons, Inc.
Production and Characterization of Recombinant Human Plasminogen(S741C-Fluorescein) (1997)

A variant of recombinant plasminogen with the plasmin active site serine (S741) replaced by cysteine was produced and labeled with fluorescein at this residue to provide the derivative Plg(S741C-fluorescein). Studies of cleavage, conformation, and fibrin-binding properties of the derivative showed it to be a good model substrate to study plasminogen activation. Both in solution and in a fully polymerized fibrin clot, cleavage of the single chain zymogen to the two-chain "plasmin" molecule was accompanied by a 50% quench of fluorescence intensity. This change allows facile, continuous monitoring of the kinetics of cleavage. Measurements of cleavage by single chain t-PA within intact, fully polymerized 3 microM fibrin yielded apparent kcat and Km values of (0.08 s-1, 0.52 microM) and (0.092 s-1, 0.098 microM) for [Glu1]- and [Lys78]Plg(S741C-fluorescein), respectively. These values are similar to those obtained by others with plasma plasminogen. The approach used here might generally be useful in simplifying the analysis of zymogen activation kinetics in cases where the product (protease) has a great influence on its own formation via positive or negative feedback loops.
Coherent detection of freely propagating terahertz radiation by electro-optic sampling (1996)

We report the demonstration of an electro-optic sampling technique that allows for the detection of freely propagating terahertz radiation. Coherent sampling is performed in a poled polymer device that is physically separated from the emitter. The poling electrodes in the sampling element are found to have an integrating effect on the incident terahertz field. The shot noise limited minimum detectable field in the polymer is 100 (mV/cm)/√Hz. We discuss methods by which the sensitivity may be significantly enhanced.
CD11c as a Transcriptional Biomarker to Predict Response to Anti-TNF Monotherapy With Adalimumab in Patients With Rheumatoid Arthritis (2009)

We performed transcription profiling using monocytes to identify predictive markers of response to anti-tumor necrosis factor (anti-TNF) therapy in patients with rheumatoid arthritis (RA). Several potential predictors of response were identified, including CD11c. Validation in samples from independent cohorts (total of n = 27 patients) using reverse transcription-PCR confirmed increased expression of CD11c in responders to adalimumab (100% sensitivity; 91.7% specificity, power 99.6%; alpha = 0.01). Pretherapy CD11c levels significantly correlated with the response criteria as defined by the American College of Rheumatology (ACR) (r = 0.656, P < 0.0001). However, CD11c was neither predictive of response to methotrexate (MTX) alone (n = 34) nor to MTX in combination with adalimumab (n = 16). Clinical responders revealed a reset to a normal expression pattern of resident/inflammatory monocyte markers, which was absent in nonresponders. Therefore, an analysis of key cell types identifies potentially predictive biomarkers that may help to restrict the use of adalimumab to therapy responders. Larger studies, including studies of monotherapy with other drugs, are now needed to confirm and validate the specificity of CD11c for anti-TNF biologics.
Activated d16HER2 Homodimers and SRC Kinase Mediate Optimal Efficacy for Trastuzumab (2014)

A splice isoform of the HER2 receptor that lacks exon 16 (d16HER2) is expressed in many HER2-positive breast tumors, where it has been linked with resistance to the HER2-targeting antibody trastuzumab, but the impact of d16HER2 on tumor pathobiology and therapeutic response remains uncertain. Here, we provide genetic evidence in transgenic mice that expression of d16HER2 is sufficient to accelerate mammary tumorigenesis and improve the response to trastuzumab. A comparative analysis of effector signaling pathways activated by d16HER2 and wild-type HER2 revealed that d16HER2 was optimally functional through a link to SRC activation (pSRC). Clinically, HER2-positive breast cancers from patients who received trastuzumab exhibited a positive correlation in d16HER2 and pSRC abundance, consistent with the mouse genetic results. Moreover, patients expressing high pSRC or an activated "d16HER2 metagene" were found to derive the greatest benefit from trastuzumab treatment. Overall, our results establish the d16HER2 signaling axis as a signature for decreased risk of relapse after trastuzumab treatment.