gebhart/patrepeval huggingface dataset:
Toward a physical map of the genome of the nematode Caenorhabditis elegans (1986)

A technique for digital characterization and comparison of DNA fragments, using restriction enzymes, is described. The technique is being applied to fragments from the nematode Caenorhabditis elegans (i) to facilitate cross-indexing of clones emanating from different laboratories and (ii) to construct a physical map of the genome. Eight hundred sixty clusters of clones, from 35 to 350 kilobases long and totaling about 60% of the genome, have been characterized.
Metabolic Engineering for the Production of Natural Products (2011)

Natural products and their derivatives play an important role in modern healthcare as frontline treatments for many diseases and as inspiration for chemically synthesized therapeutics. With advances in sequencing and recombinant DNA technology, many of the biosynthetic pathways responsible for the production of these chemically complex yet valuable compounds have been elucidated. With an ever-expanding toolkit of biosynthetic components, metabolic engineering is an increasingly powerful method to improve natural product titers and generate novel compounds. Heterologous production platforms have enabled access to pathways from difficult to culture strains, systems biology and metabolic modeling tools have resulted in increasing predictive and analytic capabilities, advances in expression systems and regulation have enabled the fine-tuning of pathways for increased efficiency, and characterization of individual pathway components has facilitated the construction of hybrid pathways for the production of new compounds. These advances in the many aspects of metabolic engineering not only have yielded fascinating scientific discoveries but also make it an increasingly viable approach for the optimization of natural product biosynthesis.
An International Randomized Trial Comparing Four Thrombolytic Strategies for Acute Myocardial Infarction (1993)

The findings of this large-scale trial indicate that accelerated t-PA given with intravenous heparin provides a survival benefit over previous standard thrombolytic regimens.
Antiaggregants for the mountain pine beetle (1995)

\ / P r o jcct / f x i c n d c ~d t < s a y Recent rese:~rch suggests that use of nonhost compounds or interspecific synomones may imprcwc thc ;~hility of the nntia_ggreg:~tit,n pheromone \~erlwnone to protect v;~lu;~l>le st;~nds of tirrlher against ;~tt;~c.kby the nlount;~in pine bcctlc.(3IPR).Jk~rtdroclorticv 1~0rlric'r.O.vc~c 1 lopki ns.Coupled I S c~hrorn;itogr:~pliic-clcctro:~rlte~lnogr;~l,hic detcc-tion (GC-EAII) studic~s indic.:~tedth;~t hlf'n rcsp~ncit-d to ;ill six-c;irlx)n green Ic;~f alCc>hols testcad [I-hex;~nol, (El-2-hesen-1-01, (1)-2-hescn-1-01, (E)-3-llexcn-1-01, ; ~n d ( 4 -3 -h e x e n -1 -011, ;lnd to four C Y ~I I ~~O ~I I ~~S
Physical and Functional Interactions of the Arf Tumor Suppressor Protein with Nucleophosmin/B23 (2004)

The Arf tumor suppressor inhibits cell cycle progression through both p53-dependent and p53-independent mechanisms, including interference with rRNA processing. Using tandem-affinity-tagged p19(Arf), we purified Arf-associated proteins from mouse NIH 3T3 fibroblasts undergoing cell cycle arrest. Tagged p19(Arf) associated with nucleolar and ribosomal proteins, including nucleophosmin/B23 (NPM), a protein thought to foster the maturation of preribosomal particles. NPM is an abundant protein, only a minor fraction of which binds to p19(Arf); however, a significant proportion of p19(Arf) associates with NPM. The interaction between p19(Arf) and NPM requires amino acid sequences at the Arf amino terminus, which are also required for Mdm2 binding, as well as the central acidic domain of NPM and an adjacent segment that regulates NPM oligomerization. The interaction between p19(Arf) and NPM occurs in primary mouse embryonic fibroblasts, including those lacking both Mdm2 and p53. In an NIH 3T3 derivative cell line (MT-Arf) engineered to conditionally express an Arf transgene, induced p19(Arf) associates with NPM and colocalizes with it in high-molecular-weight complexes (2 to 5 MDa). An NPM mutant lacking its carboxyl-terminal nucleic acid-binding domain oligomerizes with endogenous NPM, inhibits p19(Arf) from entering into 2- to 5-MDa particles, and overrides the ability of p19(Arf) to retard rRNA processing.
Terminal complement complexes and C1/C1 inhibitor complexes in autoimmune thyroid disease. (1989)

The potential role of complement activation and the membrane attack complex in the pathogenesis of Graves' disease and Hashimoto's thyroiditis has been investigated by measuring serum concentrations of the C1r-C1s-C1 inhibitor complex (C1/C1-inh) and the terminal complement complex (TCC), and by studying the binding to thyroid tissue of monoclonal and polyclonal antibodies against TCC neoantigens. Serum C1/C1-inh and TCC concentrations were significantly increased in 29 patients with untreated Graves' disease compared with 47 healthy subjects (P less than 0.001 for both), and decreased significantly after carbimazole treatment in 18 of these patients for whom post-treatment samples were available (P less than 0.01 and P less than 0.02, respectively). The serum TCC concentration, but not that of C1/C1-inh, was also significantly increased in 15 patients with Hashimoto's thyroiditis compared with the 47 healthy subjects (P less than 0.001). TCCs were identified by immunohistochemical staining around the thyroid follicles in thyroidectomy specimens from patients with Graves' disease (six out of six) and Hashimoto's thyroiditis (two out of two); normal thyroid tissue from two subjects showed no staining. These results suggest a role for complement, in particular the membrane attack complex in the pathogenesis of autoimmune thyroid disease.
Expression of embryonic tau protein isoforms persist during adult neurogenesis in the hippocampus (2006)

Tau is a microtubule-associated protein with a developmentally regulated expression of multiple isoforms. The neonatal isoform is devoid of two amino terminal inserts and contains only three instead of four microtubule-binding repeats (0N/3R-tau). We investigated the temporal expression pattern of 0N-tau and 3R-tau in the rat hippocampus. After the decline of 0N- and 3R-tau immunoreactivity during the postnatal development both isoforms remain highly expressed in a few cells residing beneath the granule cell layer. Coexpression of the polysialylated neuronal cell adhesion molecule, doublecortin, and incorporated bromodeoxyuridine showed that these cells are proliferating progenitor cells. In contrast mature granule cells express the adult tau protein isoform containing one aminoterminal insert domain (1N-tau). Therefore a shift in tau isoform expression takes place during adult neurogenesis, which might be related to migration, differentiation, and integration in the granule cell layer. A model for studying shifts in tau isoform expression in a defined subset of neurons might help to understand the etiology of tauopathies, when isoform composition is crucial for neurodegeneration, as in Pick's disease or FTDP-17.
THE ROLE OF MONOCYTE CHEMOATTRACTANT PROTEIN‐1 (MCP‐1) IN THE PATHOGENESIS OF COLLAGEN‐INDUCED ARTHRITIS IN RATS (1997)

Collagen-induced arthritis was produced in rats by intradermal immunization with type II collagen and the expression and production of monocyte chemoattractant protein-1 (MCP-1) were examined by immunohistochemistry, enzyme-linked immunosorbent assay (ELISA), and Northern blot analysis. Two to three weeks after the immunization, the hindfeet showed swelling and redness, followed by the development of severe arthritis, particularly in the ankle joints. During this period, prominent infiltration of neutrophils and macrophages was observed. Sandwich ELISA and Northern blot analysis revealed that MCP-1 concentrations in the joint lavages and MCP-1 mRNA levels in the joint tissues both peaked at 2 weeks after the immunization. By immunohistochemistry, various types of cells, particularly neutrophils, macrophages, synovial cells, and vascular endothelial cells, stained positively for MCP-1. Finally, injection of a neutralizing monoclonal antibody against rat MCP-1 significantly decreased the number of exudate macrophages in the lesions and reduced the ankle swelling by about 30 per cent compared with controls. These results suggest that MCP-1 plays a critical role in this model in the recruitment of monocytes and in the development of arthritis. © 1997 John Wiley & Sons, Ltd.
Effect of chymotrypsin C and related proteins on pancreatic cancer cell migration (2011)

Pancreatic cancer is a malignant cancer with a high mortality rate. The amount of chymotrypsin C in pancreatic cancer cells is only 20% of that found in normal cells. Chymotrypsin C has been reported to be involved in cancer cell apoptosis, but its effect on pancreatic cancer cell migration is unclear. We performed cell migration scratch assays and Transwell experiments, and found that cell migration ability was downregulated in pancreatic cancer Aspc-1 cells that overexpressed chymotrypsin C, whereas the cell migration ability was upregulated in Aspc-1 cells in which chymotrypsin C was suppressed. Two-dimensional fluorescence differential in gel electrophoresis/mass spectrometry method was used to identify the proteins that were differentially expressed in Aspc-1 cells that were transfected with plasmids to induce either overexpression or suppressed expression of chymotrypsin C. Among 26 identified differential proteins, cytokeratin 18 was most obviously correlated with chymotrypsin C expression. Cytokeratin 18 is expressed in developmental tissues in early stages of cancer, and is highly expressed in most carcinomas. We speculated that chymotrypsin C might regulate pancreatic cancer cell migration in relation to cytokeratin 18 expression.
mRNA-programmed translation pauses in the targeting of E. coli membrane proteins (2014)

In all living organisms, ribosomes translating membrane proteins are targeted to membrane translocons early in translation, by the ubiquitous signal recognition particle (SRP) system. In eukaryotes, the SRP Alu domain arrests translation elongation of membrane proteins until targeting is complete. Curiously, however, the Alu domain is lacking in most eubacteria. In this study, by analyzing genome-wide data on translation rates, we identified a potential compensatory mechanism in E. coli that serves to slow down the translation during membrane protein targeting. The underlying mechanism is likely programmed into the coding sequence, where Shine-Dalgarno-like elements trigger elongation pauses at strategic positions during the early stages of translation. We provide experimental evidence that slow translation during targeting and improves membrane protein production fidelity, as it correlates with better folding of overexpressed membrane proteins. Thus, slow elongation is important for membrane protein targeting in E. coli, which utilizes mechanisms different from the eukaryotic one to control the translation speed.
Inhibition of [3H]‐(+)‐MK 801 binding to rat brain sections by CPP and 7‐chlorokynurenic acid: an autoradiographic analysis (1993)

1. The regional binding of [3H]-(+)-5-methyl-10,11-dihydro-5H-dibenzo (a,d)cyclohepten-5,10-imine maleate ([3H]-(+)-MK 801) to sections of rat brain was measured by an in vitro quantitative autoradiographic technique. A heterogeneous distribution of binding sites was observed. 2. High values of binding were detected in the hippocampal formation and cerebral cortex, while very low binding was found in cerebellum. [3H]-(+)-MK 801 binding was not detectable in white matter tracts or in the brain stem. 3. [3H]-(+)-MK 801 binding was inhibited by increasing concentrations of both 7-chlorokynurenate (1-1000 microM) and ((+)-2-carboxypiperazine-4-yl)propyl-1-phosphonic acid (CPP) (0.1-100 microM). High concentrations of both drugs were able to inhibit completely specific [3H]-(+)-MK 801 binding. 4. IC50 values calculated for both 7-chlorokynurenate and CPP-induced [3H]-(+)-MK 801 binding inhibition were similar in all brain regions analyzed. 5. The inhibitory action of 7-chlorokynurenate and that of CPP on [3H]-(+)-MK 801 binding were reversed by addition of glycine and glutamate respectively. 6. It is concluded that activation of glycine and N-methyl-D-aspartate (NMDA) receptors is obligatory for the binding of [3H]-(+)-MK 801 to occur in all of the brain regions examined in the present study. Furthermore, on the basis of the similar regional sensitivities of [3H]-(+)-MK 801 binding to the inhibitory action of 7-chlorokynurenate and CPP, a single pharmacological classification of the NMDA receptor complex in brain is suggested. The cerebellum was not included in the study due to the very low level of [3H]-(+)-MK 801 binding detected under the experimental conditions used.
Cell Signaling and Neuronal Death (2006)

The past few decades have revealed that cell death can be precisely programmed with two principal forms, apoptosis and necrosis. Besides pathophysiological alterations, physiologic processes, such as the pruning of neurons during normal development and the involution of the thymus, involve apoptosis. This review focuses on the role of inter- and intracellular signaling systems in cell death, especially in the nervous system. Among neurotransmitters, glutamate and nitric oxide have been most extensively characterized and contribute to cell death in excitotoxic damage, especially in stroke and possibly in neurodegenerative diseases. Within cells, calcium, the most prominent of all intracellular messengers, mediates diverse forms of cell death with actions modulated by many proteins, including IP3 receptors, calcineurin, calpain, and cytochrome c.
Electron Probe Microanalysis of Noncarious Enamel and Dentin and Calcified Tissues in Mottled Teeth (1969)

A quantitative chemical distribution of five elements in several undecalcified sections of teeth was determined by the electron microprobe method. The calcium (Ca)/ phosphorus (P) weight percent ratios were determined in scans through the enamel and dentin, and characteristic curves for the concentration of the trace elements magnesium (Mg), sodium (Na), and chlorine (Cl) were obtained.
[Enhancement of photoassimilate utilization by manipulation of ADP-glucose pyrophosphorylase gene]. Final progress report (1999)

Part 1 of this research focuses on patterns of gene expression of ADPG-pyrophosphorylase in native and transgenic potato plants. To elucidate the mechanism controlling AGP expression during plant development, the expression of the potato tuber AGP small subunit (sAGP) gene was analyzed in transgenic potato plants using a promoter-{beta}-glucuronidase expression system. Part II evaluated the structure-function relationships of AGP.
Packaged polarization-insensitive WDM monitor with low loss (7.3 dB) and wide tuning range (4.5 nm) (1998)

Low-cost high-performance wavelength-division-multiplexing (WDM) monitors and receivers are key components in WDM transmission and local area optical networks. A semiconductor arrayed waveguide grating integrated with a photodiode is attractive because of its small size and simple fabrication process. A low-loss (7.3 dB) polarization-insensitive packaged WDM monitor has been fabricated in an industry-standard butterfly-type module. The eight-channel monitors, which have 200-GHz channel spacing, can be tuned simultaneously in the 4.5-nm range.
More Light on Who Wrote the Title Page (2001)

Research Article| October 01 2001 More Light on Who Wrote the Title Page Clyde J. Williams Clyde J. Williams Clyde J. Williams is associate professor of ancient scripture at BYU, where he received his Ed.D. His special interests include studying and teaching the Book of Mormon, and he is the editor and compiler of books on the teachings of Harold B. Lee, Howard W. Hunter, and Lorenzo Snow. Search for other works by this author on: This Site Google Journal of Book of Mormon Studies (1992-2007) (2001) 10 (2): 28–29. https://doi.org/10.5406/jbookmormstud.10.2.0028 Cite Icon Cite Share Icon Share Facebook Twitter LinkedIn MailTo Permissions Search Site Citation Clyde J. Williams; More Light on Who Wrote the Title Page. Journal of Book of Mormon Studies (1992-2007) 1 October 2001; 10 (2): 28–29. doi: https://doi.org/10.5406/jbookmormstud.10.2.0028 Download citation file: Zotero Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All Scholarly Publishing CollectiveUniversity of Illinois PressJournal of Book of Mormon Studies Search Advanced Search The text of this article is only available as a PDF. Copyright 2001 by the Board of Trustees of the University of Illinois2001 Article PDF first page preview Close Modal Issue Section: Feature Articles You do not currently have access to this content.
Transduction of Primitive Human Marrow and Cord Blood-Derived Hematopoietic Progenitor Cells With Adeno-Associated Virus Vectors (1999)

We evaluated the capacity of adeno-associated virus (AAV) vectors to transduce primitive human myeloid progenitor cells derived from marrow and cord blood in long-term cultures and long-term culture-initiating cell (LTC-IC) assays. Single-colony analyses showed that AAV vectors transduced CD34(+) and CD34(+)38(-) clonogenic cells in long-term culture. Gene transfer was readily observed in LTC-ICs derived from 5-, 8-, and 10-week cultures. Recombinant AAV (rAAV) transduction was observed in every donor analyzed, although a wide range of gene transfer frequencies (5% to 100%) was noted. AAV transduction of LTC-ICs was stable, with week-8 and -10 LTC-ICs showing comparable or better transduction relative to week-5 LTC-ICs. Fluorescence in situ hybridization (FISH) analyses performed to determine the fate of AAV vectors in transduced cells showed that 9% to 28% of CD34(+) and CD34(+)38(-) cells showed stable vector integration as evidenced by chromosome-associated signals in metaphase spreads. Comparisons of interphase and metaphase FISH suggested that a fraction of cells also contained episomal vector at early time points after transduction. Despite the apparent loss of the episomal forms with continued culture, the number of metaphases containing integrated vector genomes remained stable long term. Transgene transcription and placental alkaline phosphatase (PLAP) expression was observed in CD34(+), CD34(+)38(-) LTC-ICs in the absence of selective pressure. These results suggest that primitive myeloid progenitors are amenable to genetic modification with AAV vectors.
Detection of Pro- and Anti-Inflammatory Cytokines in Stools of Patients with Inflammatory Bowel Disease (1998)

Measurement of cytokines in stools may be a useful and noninvasive means of understanding pathophysiology and clinical monitoring in inflammatory bowel disease.
Why Output Only Modal Analysis is a Desirable Tool for a Wide Range of Practical Applications (2003)

In this paper the basic principles in output modal testing and analysis are presented and discussed. A brief review of the techniques for output-only modal testing and identification is presented, and it is argued, that there is now a wide range of techniques for effective identification of modal parameters of practical interest – including the mode shape scaling factor – with a high degree of accuracy. It is also argued that the output-only technology offers the user a number of advantages over traditional modal testing. The output-only modal technology allows the user to perform a modal analysis in an easier way and in many cases more effectively than traditional modal analysis methods. It can be applied for modal testing and analysis on a wide range of structures and not only for problems generally investigated using traditional modal analysis, but also for those requiring load estimation, vibration level estimation and fatigue analysis.
Enhanced Interleukin Production after Long-Term Administration of Erythromycin Stearate (1990)

The effects of erythromycin stearate (10 mg/kg/day) were studied on productions of interleukin (IL)-1 and -2 in mice after a long-term treatment. A 28-day treatment resulted in higher levels of IL-1 production by macrophages and of IL-2 production by splenocytes, while a 7-day treatment did not increase them. T-cell growth factor activity of IL-2 preparation prepared on day 28 of treatment as determined by HT-2 cell proliferation was reduced by about 40% in the presence of anti-murine IL-4 monoclonal antibodies, while control IL-2 activity was not reduced. Furthermore, a 28-day treatment with erythromycin stearate increased concanavalin A-induced blastogenesis of splenocytes significantly. These results suggest that long-term treatment with erythromycin stearate can stimulate host defense by increasing interleukin production.
Differential Constitutive Activation of the Epidermal Growth Factor Receptor in Non–Small Cell Lung Cancer Cells BearingEGFRGene Mutation and Amplification (2007)

The identification of somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) in patients with non-small cell lung cancer (NSCLC) and the association of such mutations with the clinical response to EGFR tyrosine kinase inhibitors (TKI), such as gefitinib and erlotinib, have had a substantial effect on the treatment of this disease. EGFR gene amplification has also been associated with an increased therapeutic response to EGFR-TKIs. The effects of these two types of EGFR alteration on EGFR function have remained unclear, however. We have now examined 16 NSCLC cell lines, including eight newly established lines from Japanese NSCLC patients, for the presence of EGFR mutations and amplification. Four of the six cell lines that harbor EGFR mutations were found to be positive for EGFR amplification, whereas none of the 10 cell lines negative for EGFR mutation manifested EGFR amplification, suggesting that these two types of EGFR alteration are closely associated. Endogenous EGFRs expressed in NSCLC cell lines positive for both EGFR mutation and amplification were found to be constitutively activated as a result of ligand-independent dimerization. Furthermore, the patterns of both EGFR amplification and EGFR autophosphorylation were shown to differ between cell lines harboring the two most common types of EGFR mutation (exon 19 deletion and L858R point mutation in exon 21). These results reveal distinct biochemical properties of endogenous mutant forms of EGFR expressed in NSCLC cell lines and may have implications for treatment of this condition.