gebhart/patrepeval huggingface dataset:
Gastrin-Enhanced Tumor Growth of a Xenotransplantable Human Gastric Carcinoma in Nude Mice (1980)

A human tumor line serially transplantable in nude mice, originating from a well-differentiated papillo-tubular adenocarcinoma of the stomach, was established. The growth of this tumor was enhanced by daily injection of C-terminal tetrapeptide gastrin into the mice. Although there was little difference in histology, the gastrin-stimulated tumor had larger glandular spaces filled with mucin-like substance than the control tumor. 3H-thymidine uptake of the gastrin stimulated tumor was higher than that of control, as shown by microradiography and counting of radioactivity in tissue homogenates. The plasma membrane fraction of the tumor revealed positive binding for gastrin and the cytosol fraction contained cyclic AMP dependent- and independent protein kinases. Incubation of tumor slices with gastrin caused a conformational change in the enzymes. Therefore we conclude that this G4 tumor line xenotransplantable in nude mice is sensitive to gastrin in its trophic and secretory mechanisms.
The use of glutamine synthetase as a selection marker: recent advances in Chinese hamster ovary cell line generation processes (2013)

Central to the needs of the biopharmaceutical industry to support the development of innovative biologics and biosimilars are more effective and efficient manufacturing processes which require highly productive cell lines with desired quality attributes. New designs of molecules such as antibody humanization have greatly reduced immunogenicity concerns, and advances in cell culture technology including media optimization and process control have driven monoclonal antibody productivities in excess of 10 g/l with peak cell densities in bioreactors climbing to over 35 million per ml. However, over this same timeframe, the fundamental processes utilized for cell line generation have not changed significantly, especially in the selection step for top-producing clonal cell lines. Cell line generation continues to be time consuming and labor intensive and has become the timeline limiting step for the majority of the industry. In order to meet the ‘Fast-to-Proof-of-Principle’ strategy, multiple efforts including ...
A Meta-Theory of Boundary Detection Benchmarks (2013)

Human labeled datasets, along with their corresponding evaluation algorithms, play an important role in boundary detection. We here present a psychophysical experiment that addresses the reliability of such benchmarks. To find better remedies to evaluate the performance of any boundary detection algorithm, we propose a computational framework to remove inappropriate human labels and estimate the intrinsic properties of boundaries.
Analysis of the Fowlpox Virus Genome Region Corresponding to the Vaccinia Virus D6 to A1 Region: Location of, and Variation in, Non-essential Genes in Poxviruses (1990)

The DNA sequence of the fowlpox virus genome corresponding to the vaccinia virus D6 to A1 region has been determined. Translation of this sequence reveals fowlpoxvirus gene homologues corresponding to the D6, D7, D9, D10, D11, D12, D13 and A1 genes of vaccinia virus. In contrast, no gene homologue for the non-essential vaccinia virus D8 gene was present in fowlpox virus. Instead, a gene transcribed from the opposite strand to the vaccinia virus D8 gene showing no homology to any previously sequenced poxvirus gene was present. The amino terminus of the fowlpox virus D9 homologue had undergone substantial changes, including frameshifts which would be predicted to inactivate the gene. Insertion of a gene cartridge composed of the vaccinia virus p7.5 promoter and the lacZ gene into the fowlpox virus D8, D9 and D10 genes in vitro, followed by recombination into fowlpox virus, was carried out. Stable insertion mutants with the correct genotype were obtained for D8 and D9 which, when tested in chickens did not appear to have been attenuated. No stable insertion mutants were obtained for D10, indicating that this gene probably encodes a function which is essential for virus replication. The D8 and D9 genes of fowlpox virus represent useful insertion sites for the construction of recombinant fowlpox virus vaccines.
Analysis of substituted benzene compounds in groundwater using solid-phase microextraction (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnalysis of substituted benzene compounds in groundwater using solid-phase microextractionCatherine L. Arthur, Lisa M. Killam, Safa Motlagh, Megan Lim, David W. Potter, and Janusz PawliszynCite this: Environ. Sci. Technol. 1992, 26, 5, 979–983Publication Date (Print):May 1, 1992Publication History Published online1 May 2002Published inissue 1 May 1992https://doi.org/10.1021/es00029a017Request reuse permissionsArticle Views670Altmetric-Citations235LEARN 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 InReddit PDF (597 KB) Get e-Alertsclose Get e-Alerts
Role of Lymphokines in the Immune Response of the Inner Ear (1989)

In secondary inner ear responses against keyhole limpet hemocyanin (KLH), the characterization of interleukin-2 levels in perilymph and serum developing over 5 days in Hartley guinea pigs was investigated using an immunoassay. No interleukin-2 levels were detectable at Day 0 in serum and perilymph. The earliest perilymph IL-2 levels were observed after 6 h, peaking at 18 h and decreasing to zero by Day 5. In contrast, during this observation period, no IL-2 was detectable in serum or perilymph from control ears. Since previous work has identified T-helper cells in the endolymphatic sac, this site appears to be the probable source of interleukins. This study provides further support for the existence of an inner ear immune response which is regulated by lymphokines. Furthermore, interleukins may be a chemoattractant for cells entering the cochlea during the immune response.
Discovering the Interactions between Circular RNAs and RNA-binding Proteins from CLIP-seq Data using circScan (2017)

Abstract Although tens of thousands of circular RNAs (circRNAs) have been identified in mammalian genomes, only few of them have been characterized with biological functions. Here, we report a new approach, circScan, to identify regulatory interactions between circRNAs and RNA-binding proteins (RBPs) by discovering back-splicing reads from Cross-Linking and Immunoprecipitation followed by high-throughput sequencing (CLIP-seq) data. By using our method, we have systematically scanned ~1500 CLIP-seq datasets, and identified ~12540 and ~1090 novel circRNA-RBP interactions in human and mouse genomes, respectively, which include all known interactions between circRNAs and Argonaute (AGO) proteins. More than twenty novel interactions were further experimentally confirmed by RNA Immunoprecipitation quantitative PCR (RIP-qPCR). Importantly, we uncovered that some natural circRNAs interacted with cap-independent translation factors eukaryotic initiation factor 3 (eIF3) and N6-Methyladenosine (m 6 A), indicating they can be translated into proteins. These findings demonstrate that circRNAs are regulated by various RBPs, suggesting they may play important roles in diverse biological processes.
The Molecular Chaperone Ydj1 Is Required for the p34 CDC28 -Dependent Phosphorylation of the Cyclin Cln3 That Signals Its Degradation (1996)

The G1 cyclin Cln3 of the yeast Saccharomyces cerevisiae is rapidly degraded by the ubiquitin-proteasome pathway. This process is triggered by p34CDC28-dependent phosphorylation of Cln3. Here we demonstrate that the molecular chaperone Ydj1, a DnaJ homolog, is required for this phosphorylation. In a ydj1 mutant at the nonpermissive temperature, both phosphorylation and degradation of Cln3 were deficient. No change was seen upon inactivation of Sis1, another DnaJ homolog. The phosphorylation defect in the ydj1 mutant was specific to Cln3, because no reduction in the phosphorylation of Cln2 or histone H1, which also requires p34CDC28, was observed. Ydj1 was required for Cln3 phosphorylation and degradation rather than for the proper folding of this cyclin, since Cln3 produced in the ydj1 mutant was fully active in the stimulation of p34CDC28 histone kinase activity. Moreover, Ydj1 directly associates with Cln3 in close proximity to the segment that is phosphorylated and signals degradation. Thus, binding of Ydj1 to this domain of Cln3 seems to be essential for the phosphorylation and breakdown of this cyclin. In a cell-free system, purified Ydj1 stimulated the p34CDC28-dependent phosphorylation of the C-terminal segment of Cln3 and did not affect phosphorylation of Cln2 (as was found in vivo). The reconstitution of this process with pure components provides evidence of a direct role for the chaperone in the phosphorylation of Cln3.
Heterogeneity of Degradation of B‐Cell Endocytosed Monoclonal Antibodies Reacting with Different sIgM Epitopes (1989)

The degradation of a panel of monoclonal antibodies (MoAb) bound to surface IgM (sIgM) was studied in three human Burkitt's lymphoma cell lines. The panel included MoAb that recognize several distinct epitopes associated with the F(c mu)5 domain, the c mu 2 domain and kappa or lambda light chains. The amount of degraded MoAb and the rate of their degradation varied considerably between the various antibodies. Properties of MoAb such as avidity or ability to cross-link sIgM did not significantly influence their degradation. The most consistent correlation between rate of degradation and MoAb used was the location of the epitope recognized by the individual MoAb. Thus, 7 out of 8 anti-light chain MoAb were degraded at a higher rate than 5 out of 5 anti-F(c mu)5 MoAb. One anti-c mu 2 MoAb was degraded at a rate similar to the majority of anti-light chain MoAb. The intracellular transport of an anti-kappa light chain MoAb and an anti-F(c mu)5 MoAb was studied in detail by subcellular fractionation in sucrose gradients. We found that the anti-kappa light chain MoAb was transported more rapidly to lysosomes than the anti-F(c mu)5 MoAb, showing that they were sorted differently intracellularly.
The growth and properties of Al and AlN films on GaN(0001)–(1×1) (1996)

The growth, structure, and annealing behavior of Al films, formed by in situ vapor deposition on GaN(0001)–(1×1) near 25 °C, have been studied using Auger, electron energy loss, x ray and ultraviolet photoemission spectroscopies and low-energy electron diffraction. Film growth occurs by a Stranski–Krastanov process with reaction at the immediate interface leading to metallic Ga. Annealing at ≳800 °C leads to release of N, which reacts with Al to form a (1×1)-ordered layer of AlN, possibly alloyed with a small amount of Ga. The AlN layer has been characterized using the various spectroscopies, and the work function, band bending, and electron affinity of GaN and of the AlN overlayer have been obtained. The Al/GaN Schottky barrier height has been measured and compared with previous results for Ni/GaN.
Fast delta Hadamard transform (1981)

In many fields (e.g., spectroscopy, imaging spectroscopy, photoacoustic imaging, coded aperture imaging) binary bit patterns known as m sequences are used to encode (by multiplexing) a series of measurements in order to obtain a larger throughput. The observed measurements must be decoded to obtain the desired spectrum (or image in the case of coded aperture imaging). Decoding in the past has used a technique called the fast Hadamard transform (FHT) whose chief advantage is that it can reduce the computational effort from N(2) multiplies to N log(2) N additions or subtractions. However, the FHT has the disadvantage that it does not readily allow one to sample more finely than the number of bits used in the m sequence. This can limit the obtainable resolution and cause confusion near the sample boundaries (phasing errors). We have developed both 1-D and 2-D methods (called fast delta Hadamard transforms, FDHT) which overcome both of the above limitations. Applications of the FDHT are discussed in the context of Hadamard spectroscopy and coded aperture imaging with uniformly redundant arrays. Special emphasis has been placed on how the FDHT can unite techniques used by both of these fields into the same mathematical basis.
Estimation of the reproductive number of novel coronavirus (COVID-19) and the probable outbreak size on the Diamond Princess cruise ship: A data-driven analysis (2020)

The median with 95% CI of R0 of COVID-19 was about 2.28 (2.06-2.52) during the early stage experienced on the Diamond Princess cruise ship. The future daily incidence and probable outbreak size is largely dependent on the change of R0. Unless strict infection management and control are taken, our findings indicate the potential of COVID-19 to cause greater outbreak on the ship.
Soluble intercellular adhesion molecule-1 inhibits MHC-restricted specific T cell/tumor interaction. (1993)

Intercellular adhesion molecule-1 (ICAM-1)/LFA-1-mediated cell-cell adhesion is essential for various immunologic functions. It was previously shown that some of these, including non-MHC-restricted cytotoxicity, could be inhibited by soluble forms of ICAM-1. Here, we characterize the effects of soluble ICAM-1 on MHC-restricted specific T cell/melanoma interactions. Tumor-infiltrating lymphocyte (TIL) clones, as well as melanoma lines from the same tumor specimens, were established. The TIL clones used were able to form conjugates with the autologous tumor and to kill it in an MHC-restricted way. TIL/melanoma interaction also induced increased cytokine production in TIL. Using this system, we could demonstrate that purified soluble ICAM-1 (950 ng/ml) or 12-fold concentrated cell-free melanoma supernatants, containing shed ICAM-1 (1000 ng/ml), were able to inhibit conjugate formation between T cell clones and the autologous melanoma cells as efficiently as mAb against CD11a. In addition, free ICAM-1 abrogated the MHC-restricted killing of the melanoma exerted by T cell clones and blocked the induction of cytokines in T cells due to the contact with autologous tumor cells.
Characterization of the Lithium/Oxygen Organic Electrolyte Battery (2002)

The effects that electrolyte and air cathode formulation have on discharge capacity, rate capability, and the rechargeability of the lithium/oxygen organic electrolyte cell were characterized. To characterize the effects of cell formulation on the discharge reaction, we used techniques including static and dynamic gas consumption measurements and scanning electron microscopy. It was found that electrolyte formulation has the largest effect on discharge capacity and rate capability. Electrode processing is also important in determining discharge capacity at low rate. The Brunauer-Emmett-Teller surface area of the carbon black used to prepare the air electrode is not a significant factor in determining discharge capacity. The discharge product was found to depend on both discharge rate and electrolyte formulation. This is understood in terms of the concentration of oxygen in the electrolyte during discharge. © 2002 The Electrochemical Society. All rights reserved.
Innate immune responses induced by CpG oligodeoxyribonucleotide stimulation of ovine blood mononuclear cells (2003)

Examples exist in the literature that demonstrate that treatment with immunostimulatory cytosine-phosphate-guanosine (CpG)-DNA can protect mice against infection by intracellular pathogens. There are, however, few studies reporting that CpG-DNA offers similar disease protection in other species. In this study, we assessed the potential of a class A and class B CpG oligodeoxynucleotide (ODN) to induce innate immune responses in sheep, an outbred species. Using peripheral blood mononuclear cells, we have for the first time demonstrated CpG-ODN-induced innate immune responses, including natural-killer-like activity [non-major histocompatibility complex (MHC)-restricted cytotoxicity], interferon-alpha secretion and 2'-5'A oligoadenylate synthetase activity, that could contribute to immune protection in sheep. The type and magnitude of these responses were dependent on ODN class and non-MHC-restricted killing was not associated with interferon-gamma production. The latter observation is in contrast with observations reported for mice and humans. These observations support the conclusion that differences in CpG-ODN-induced responses exist among species and that specific ODN sequences can significantly influence innate immune responses.
Use of denaturing gradient gel electrophoresis for detection of mutation and prospective diagnosis in late onset ornithine transcarbamylase deficiency (1990)

Ornithine transcarbamylase (ornithine carbamoyl-transferase, EC 2.1.3.3) deficiency is an X-linked inborn error of metabolism with considerable phenotypic variability in affected males. Using a combination of the polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE), we defined a mutation in a family in whom affected males have significant residual enzyme activity. A C → T change in the first nucleotide of codon 277 resulted in the substitution of a tryptophan for an arginine at amino acid 245 of the mature protein. This change appears to represent a deleterious mutation rather than a polymorphism on the basis of several factors: the change occurs at a highly conserved arginine residue, significant size and change differences exist between arginine and tryptophan, and this change was not seen on DGGE screening of 26 unrelated individuals representing 43 chromosomes. Diagnosis of an at-risk male newborn in this family was performed using direct mutational analysis. In families with partial enzyme deficiencies in whom biochemical data may be difficult to evaluate, direct detection of mutations at the OTC locus permits definitive diagnosis. This represents the first description of a mutation in late onset OTC deficiency and demonstrates direct mutational analysis by DGGE for prospective diagnosis in a genetic disorder.
Histone acetylation may suppress human glioma cell proliferation when p21WAF/Cip1 and gelsolin are induced (2002)

Neuro-OncologyHistone deacetylase inhibitors that increase histone acetylation on transformed cells are being investigated as unique anticancer drugs.The aim of this investigation was to evaluate an antiproliferative activity of the histone deacetylase inhibitors sodium butyrate (NaBT) and trichostatin A on 5 glioma cell lines, T98G, A172, U-87 MG, U-118 MG, and U-373 MG, with the examination of the altered expressions in p21 and gelsolin genes.Treatment with 5-mM NaBT and 40 ng/ml trichostatin A for 48 h caused more than a 50% growth inhibition in 5 cell lines as measured by cell proliferation assays.An increase in histone acetylation was con rmed in each cell line.After treatment with 5 mM NaBT, T98G, A172, and U118 cells undergo apoptosis as indicated by DNA ladder formation.Treatment with NaBT and trichostatin A also decreased DNA synthesis as examined by the uorescence-activated cell sorting analysis in T98G and U87 cells.In addition to the suppression of cell growth, the up regulation of p21 and gelsolin expression was observed after treatment with NaBT, especially in T98G cells.Maximum expression of p21 and gelsolin was observed within 24 h after treatment.Results from our in vitro studies indicate that the treatment of human glioma cells with one of the histone deacetylase inhibitors suppresses cell growth with decreasing DNA synthesis and
Successful treatment of severe psoriasis and psoriatic arthritis with adalimumab (2004)

Adalimumab, a fully human-derived recombinant monoclonal antibody against tumour necrosis factor-alpha, has been shown to be effective for the treatment of patients with moderately to severely active rheumatoid arthritis. We report two patients with long-standing recalcitrant psoriasis and psoriatic arthritis who, after multiple treatment failures with conventional and experimental antipsoriatic medications, both responded to treatment with adalimumab. Significant clinical improvement was noted in both skin and joint disease in the two patients after several weeks of treatment with adalimumab. We are unaware of previous published reports of adalimumab therapy in patients with psoriasis and psoriatic arthritis.
The human papillomavirus type 16 E6 and E7 oncoproteins independently induce numerical and structural chromosome instability. (2002)

The development of genomic instability is a hallmark of high-risk human papillomavirus (HPV) associated cervical carcinogenesis. We have previously shown that the HPV-16 E7 oncoprotein rapidly subverts mitotic fidelity by inducing abnormal centrosome numbers and multipolar mitotic spindles. Here we report that expression of HPV-16 E6 and E7 independently results in various mitotic abnormalities. HPV-16 E6 and E7 were each associated with unaligned or lagging chromosomal material, indicating relaxation of spindle checkpoint control. Moreover, by overwhelming checkpoint control mechanisms that may prevent cells with multiple spindle poles to enter anaphase, expression of HPV-16 E6 and E7 leads to a small but significant number of cells with altered polarity at later stages of the cell division process. In addition to changes that have the potential to give rise to numerical chromosome imbalances, we discovered that expression of HPV-16 E7 could trigger anaphase bridge formation to an extent similar to that of high-risk HPV E6. Anaphase bridges typically develop after chromosomal breaks and alterations of chromosomal structure. Further investigation of mechanisms by which HPV-16 E6 and E7 contribute to the destabilization of the host cell genome revealed that both high-risk HPV oncoproteins induce DNA damage. Moreover, expression of HPV-16 E7 was associated with an increased number of cells exhibiting nuclear foci of phosphorylated histone H2AX as well as activation of cell cycle checkpoints triggered by DNA repair. Our results therefore suggest that HPV oncoproteins are a source for both numerical and structural chromosome instability during HPV-associated carcinogenesis.