gebhart/patrepeval huggingface dataset:
RNAi knockdown of Par‐4 inhibits neurosynaptic degeneration in ALS‐linked mice (2004)

Evidence from human amyotrophic lateral sclerosis (ALS) patients and ALS-linked Cu/Zn superoxide dismutase (Cu/Zn-SOD) transgenic mice bearing the mutation of glycine to alanine at position 93 (G93A) suggests that the pro-apoptotic protein prostate apoptosis response-4 (Par-4) might be a critical link in the chain of events leading to motor neuron degeneration. We now report that Par-4 is enriched in synaptosomes and post-synaptic density from the ventral horn of the spinal cord. Levels of Par-4 in synaptic compartments increased significantly during rapid and slow declining stages of muscle strength in hSOD1 G93A mutant mice. In the pre-muscle weakness stage, hSOD1 G93A mutation sensitized synaptosomes from the ventral horn of the spinal cord to increased levels of Par-4 expression following excitotoxic and apoptotic insults. In ventral spinal synaptosomes, Par-4-mediated production of pro-apoptotic cytosolic factor(s) was significantly enhanced by the hSOD1 G93A mutation. RNA interference (RNAi) knockdown of Par-4 inhibited mitochondrial dysfunction and caspase-3 activation induced by G93A mutation in synaptosomes from the ventral horn of the spinal cord, and protected spinal motor neurons from apoptosis. These results identify the synapse as a crucial cellular site for the cell death promoting actions of Par-4 in motor neurons, and suggest that targeted inhibition of Par-4 by RNAi may prove to be a neuroprotective strategy for motor neuron degeneration.
Oxidative Stress-mediated, Post-translational Loss of MafA Protein as a Contributing Mechanism to Loss of Insulin Gene Expression in Glucotoxic Beta Cells (2005)

Glucose toxicity in pancreatic islet beta cells causes loss of insulin gene expression, content, and secretion due to loss of binding of transcription factors, most notably PDX-1 and RIPE-3b1 activator, to the promoter region of the insulin gene. Recently, RIPE-3b1 activator was cloned and identified as the mammalian homologue of avian MafA/Maf-L (MafA). This enabled us to carry out more extensive studies of the role of MafA in glucotoxicity than were hitherto possible. Northern analysis of glucotoxic HIT-T15 cells revealed normal amounts of MafA mRNA, but Western analysis demonstrated a 97 +/- 1% reduction in MafA protein (p < 0.0001). The proteasome is a likely site for MafA degradation as lactacystin, an irreversible proteasome inhibitor, caused an accumulation of MafA protein. Antioxidants have previously been shown to prevent the adverse effects of glucose toxicity on beta cell function both in vivo and in vitro. In the current study, chronic culturing of HIT-T15 cells with the antioxidant N-acetylcysteine (NAC) prevented loss of MafA protein (late passage = 18.9 +/- 10.4% of early passage, p < 0.001; late passage with NAC = 68.7 +/- 19.7% of early passage, p = not significant) and loss of DNA binding (late passage = 63.7 +/- 9% of early passage, p < 0.02; late passage with NAC = 116 +/- 10% of early passage, p = not significant). Additionally, transient transfection of PDX-1 or MafA cDNA into glucotoxic cells increased PDX-1 and MafA protein levels and individually increased insulin promoter activity (untreated = 34%, PDX-1 = 70%, MafA = 78%; percentage of activity of early passage cells), whereas the combined transfection of MafA and PDX-1 completely restored insulin promoter activity. This recovery of promoter activity following transient transfection had no effect on endogenous insulin mRNA. However, adenoviral infection of MafA and PDX-1 significantly increased endogenous insulin mRNA levels by 93% (121 +/- 9 versus 233 +/- 18 density light units; n = 5, p < 0.001). We conclude that the absence of MafA protein from beta cells via chronic oxidative stress contributes importantly to the loss of endogenous insulin gene expression as glucose toxicity develops.
Review of ring perception algorithms for chemical graphs (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReview of ring perception algorithms for chemical graphsGeoffrey M. Downs, Valerie J. Gillet, John D. Holliday, and Michael F. LynchCite this: J. Chem. Inf. Comput. Sci. 1989, 29, 3, 172–187Publication Date (Print):August 1, 1989Publication History Published online1 May 2002Published inissue 1 August 1989https://pubs.acs.org/doi/10.1021/ci00063a007https://doi.org/10.1021/ci00063a007research-articleACS PublicationsRequest reuse permissionsArticle Views692Altmetric-Citations67LEARN 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 options Get e-Alerts
Photodynamic antimicrobial chemotherapy (PACT) (1998)

Whereas the photodynamic therapy (PDT) of cancer has recently shown rapid clinical acceptance, photodynamic antimicrobial chemotherapy (PACT)--which predates the related cancer regimen--is not widely appreciated. Like PDT, PACT utilizes photosensitizers and visible or ultraviolet light in order to give a phototoxic response, normally via oxidative damage. Currently, the major use of PACT is in the disinfection of blood products, particularly for viral inactivation, although more clinically-based protocols are being developed, e.g. in the treatment of oral infection. The technique has been shown to be effective in vitro against bacteria (including drug-resistant strains), yeasts, viruses and parasites. A wide range of photosensitizers, both natural and synthetic, is available with differing physicochemical make-up and light-absorption properties. PACT is proposed as a potential, low-cost approach to the treatment of locally occurring infection.
The Pharmacist “Toolbox” for Smoking Cessation (2012)

Annually there are 500 000 preventable deaths in the United States caused by smoking; as health care professionals, pharmacists have a unique opportunity to advise, assess, and assist patients to quit smoking. This review article provides pharmacists with a "toolbox" containing an overview of pharmacologic and nonpharmacologic methods for smoking cessation. Currently approved over-the-counter (OTC) and prescription medications (nicotine replacement therapy, varenicline, and bupropion) are summarized, and nonpharmacologic therapies discussed include cognitive therapy and hypnosis. In addition to traditional therapies some potential approaches to smoking cessation are addressed, including nicotine immunizations and electronic cigarettes.
Notch signaling as a target in multimodality cancer therapy. (2000)

Notch signaling is an extremely conserved and widely used mechanism controlling cell fate determination. Recent evidence shows that Notch receptors regulate cell differentiation, proliferation and apoptosis in many cells, including neoplastic cells. In the context of cancer experimental immunotherapy and multimodality therapy, the Notch signaling network is acquiring increasing importance for its possible roles in both neoplastic cells and the immune system. In this review, we discuss: (i) the roles of Notch signaling in cancer cells and the immune system; and (ii) strategies through which Notch-targeting biologicals may be used to increase the effectiveness of multimodality cancer treatment, including cancer vaccines.
Field guide to next‐generation DNA sequencers (2011)

The diversity of available 2(nd) and 3(rd) generation DNA sequencing platforms is increasing rapidly. Costs for these systems range from < $100,000 to more than $1,000,000, with instrument run times ranging from minutes to weeks. Extensive trade-offs exist among these platforms. I summarize the major characteristics of each commercially available platform to enable direct comparisons. In terms of cost per megabase (Mb) of sequence, the Illumina and SOLiD platforms are clearly superior (≤ $0.10/Mb vs. > $10/Mb for 454 and some Ion Torrent chips). In terms of cost per nonmultiplexed sample and instrument run time, the Pacific Biosciences and Ion Torrent platforms excel, with the 454 GS Junior and Illumina MiSeq also notable in this regard. All platforms allow multiplexing of samples, but details of library preparation, experimental design and data analysis can constrain the options. The wide range of characteristics among available platforms provides opportunities both to conduct groundbreaking studies and to waste money on scales that were previously infeasible. Thus, careful thought about the desired characteristics of these systems is warranted before purchasing or using any of them. Updated information from this guide will be maintained at: http://dna.uga.edu/ and http://tomato.biol.trinity.edu/blog/.
Autolysis of Escherichia coli (1980)

Autolysis of unwashed exponential-phase Escherichia coli cells was efficiently promoted by first submitting them to a quick downshock with distilled water before an upshock with 0.5 M sodium acetate, pH 6.5. The association of these two osmotic shocks had a remarkable synergistic effect and led to significant decreases in turbidity and viability. Different factors influencing the rate of cell lysis were examined. A close correlation was established between autolysis and the degradation of peptidoglycan. Both phenomena were induced by the same shock treatment, followed similar kinetics, and were efficiently blocked by addition of divalent cations. Cell lysis was also inducible by a shock treatment with 10(-3) M ethylenediaminetetraacetic acid or ethylene glycol-bis(beta-aminoethyl ether)-N,N-tetraacetic acid and blocked by the addition of divalent cations.
Mucin‐induced apoptosis of monocyte‐derived dendritic cells during maturation (2008)

Many tumors arising from epithelial tissues produce mucins, which readily come into contact with infiltrating cells in cancer tissues. MUC2 mucins were purified from the conditioned medium of a colorectal cancer cell line, LS180 cells. It is known that in cancer patients, the number of dendritic cells (DCs) is reduced and their function is impaired. Mature DCs were generated from human peripheral blood monocytes through successive treatments with GM-CSF and IL-4, and then with proinflammatory mediators. When monocytes were cultured in the presence of MUC2 mucins in addition to GM-CSF and IL-4 at an early stage of development, mature DCs expressing CD83 decreased and apoptotic cells increased in a dose-dependent manner. During the development of DCs, sialic acid-binding Ig-like lectin (Siglec)-3 was constantly expressed. We prepared recombinant soluble Siglec-3 corresponding to the ectodomain of Siglec-3 and confirmed the binding of soluble Siglec-3 to the MUC2 mucins, probably through alpha2,6-sialic acid-containing O-glycans including a sialyl Tn antigen, which is known to bind to Siglec-3. Apoptosis was partially inhibited by anti-Siglec-3 mAb or recombinant soluble Siglec-3. These results suggest that apoptosis was partially induced through the ligation of the MUC2 mucins with Siglec-3.
Genetic dissection of susceptibility to murine ovarian teratomas that originate from parthenogenetic oocytes. (1997)

The LT/Sv mouse strain is characterized by its abnormally high incidence of spontaneous ovarian teratomas. These tumors have been shown to originate from parthenogenetic oocytes, which are spontaneously induced to divide. Both spontaneous parthenogenesis and ovarian teratomas are extremely rare for other mouse strains, including C57BL/6J. To identify the genes responsible for this unique phenotype of female LT/Sv mice, we performed linkage analysis of female (C57BL/6J x LT/Sv)F2 mice. A locus on chromosome 6 designated Ots1 (ovarian teratoma susceptibility) was identified as the single major locus that increases the frequency of teratomas in a semidominant manner.
Freight Transport Mode Choice Behavior:Lesson From A Small Sample Size Analysis (2000)

Freight transport plays an important role in the logistic process. An effective and efficient freight transport system is required by all parties involved: producers, consumers, the society, and the government. The freight transport chosen by related agents within industries considers several aspects. This paper touches upon the freight transport choice process implemented by selected industries in Java, Indonesia. This research utilizes a disaggregate approach using stated preference technique for data collecting. Nested multinominal logit models produce preliminary findings which can further be analyzed so as to improve the research.
Myeloma as a model for the process of metastasis: implications for therapy (2012)

Multiple myeloma (MM) is a plasma cell dyscrasia characterized by the presence of multiple myelomatous "omas" throughout the skeleton, indicating that there is continuous trafficking of tumor cells to multiple areas in the bone marrow niches. MM may therefore represent one of the best models to study cell trafficking or cell metastasis. The process of cell metastasis is described as a multistep process, the invasion-metastasis cascade. This involves cell invasion, intravasation into nearby blood vessels, passage into the circulation, followed by homing into predetermined distant tissues, the formation of new foci of micrometastases, and finally the growth of micrometastasis into macroscopic tumors. This review discusses the significant advances that have been discovered in the complex process of invasion-metastasis in epithelial carcinomas and cell trafficking in hematopoietic stem cells and how this process relates to progression in MM. This progression is mediated by clonal intrinsic factors that mediate tumor invasiveness as well as factors present in the tumor microenvironment that are permissive to oncogenic proliferation. Therapeutic agents that target the different steps of cell dissemination and progression are discussed. Despite the significant advances in the treatment of MM, better therapeutic agents that target this metastatic cascade are urgently needed.
Photodesorption and Trapping of Molecular Oxygen at the TiO2(110)−Water Ice Interface (2001)

By means of temperature programmed desorption (TPD), static secondary ion mass spectroscopy (SSIMS), and electron energy loss spectroscopy (EELS), we have investigated further the states of oxygen adsorbed on rutile TiO2. Previous work has shown that annealing the (110) surface in a vacuum produces isolated bridging oxygen vacancies, and that these vacancies are intimately connected with molecular and dissociative oxygen adsorption channels. We find that at 115 K illumination of the oxygen-exposed surface with 4.1 eV photons results in photodesorption of the oxygen associated with a TPD state centered on 410 K, in contrast to the remaining oxygen destined for a dissociative channel. An unusual effect of water overlayers on the photochemical properties of the O/TiO2(110) system is explored. For thick overlayers, it is possible to generate via UV irradiation a previously unobserved oxygen TPD state. Evidence is presented for this new O2 TPD state originating from the photolysis of an O2−water adduct.
Expression of Foreign Genes in Insects Using Baculovirus Vectors (1989)

Although the insect circulatory system is involved in a multitude of vital physiological processes, it has gone grossly understudied. This review highlights this critical physiological system by detailing the structure and function of the circulatory ...Read More
Butyrate induces selective transcriptional activation of a hypomethylated embryonic globin gene in adult erythroid cells (1988)

An animal model of hemoglobin switching has been developed in which anemic adult chickens are treated with 5-azacytidine and sodium butyrate or alpha-aminobutyric acid, thereby resulting in activation of the embryonic rho-globin gene in adult erythroid cells. In vitro nuclear runoff transcription assays using erythroid nuclei from treated birds show that the mechanism of activation of the rho-globin gene is transcriptional whereas no transcriptional activation of the embryonic epsilon-globin gene occurs. The action of 5-azacytidine appears to be as an inhibitor of DNA methylation because other S-phase active cytotoxic drugs, when substituted for 5-azacytidine, do not cause demethylation of the embryonic globin genes, nor do they allow transcriptional activation to occur. Embryonic rho-globin gene activation in this model is not due to selection of primitive erythroid cells since a subpopulation of primitive erythroid cells is not evident either morphologically or when cells are probed for embryonic and adult globin RNA by in situ hybridization. These studies show that demethylation by 5-azacytidine is a prerequisite but not sufficient cis- regulatory event for a high level of transcriptional activation of the embryonic rho-globin gene in adult erythroid cells in vivo. The possible basis for the selective transcriptional activation by sodium butyrate in this system is discussed.
Identification of root rot fungi in nursery seedlings by nested multiplex PCR (1996)

The internal transcribed spacer (ITS) of the ribosomal DNA (rDNA) subunit repeat was sequenced in 12 isolates of Cylindrocladium floridanum and 11 isolates of Cylindrocarpon destructans. Sequences were aligned and compared with ITS sequences of other fungi in GenBank. Some intraspecific variability was present within our collections of C. destructans but not in C. floridanum. Three ITS variants were identified within C. destructans, but there was no apparent association between ITS variants and host or geographic origin. Two internal primers were synthesized for the specific amplification of portions of the ITS for C. floridanum, and two primers were designed to amplify all three variants of C. destructans. The species-specific primers amplified PCR products of the expected length when tested with cultures of C, destructans and C. floridanum from white spruce, black spruce, Norway spruce, red spruce, jack pine, red pine, and black walnut from eight nurseries and three plantations in Quebec. No amplification resulted from PCR reactions on fungal DNA from 26 common contaminants of conifer roots. For amplifications directly from infected tissues, a nested primer PCR using two rounds of amplification was combined with multiplex PCR approach resulting in the amplification of two different species-specific PCR fragments in the same reaction. First, the entire ITS was amplified with one universal primer and a second primer specific to fungi; a second round of amplification was carried out with species-specific primers that amplified a 400-bp PCR product from C. destructans and a 328-bp product from C. floridanum. The species-specific fragments were amplified directly from infected roots from which one or the two fungi had been isolated.
Structure and membrane topology of TAPA-1 (1991)

TAPA-1 (the target of an antiproliferative antibody) is a 26-kDa cell surface protein expressed on most human cell lines. TAPA-1 is a member of an evolutionarily related family of cell surface proteins all of which contain four transmembrane domains. A model is proposed for topology of TAPA-1 based on proteolysis studies in the in vitro translated protein embedded into microsomal membranes. This analysis predicts that the amino and the carboxyl termini of the molecule are cytoplasmic and that the two hydrophilic regions of the molecule are extracellular. The antigenic epitope of the human TAPA-1 is contained within a subregion of the second extracellular domain of the protein. This is the only region in the protein that has not been tightly conserved in mammalian evolution.
Nonequilibrium boron doping effects in low-temperature epitaxial silicon films (1987)

We report the first preparation of in situ boron-doped epilayers by a low-temperature chemical vapor deposition process (T=550 °C). Boron incorporation is approximately linear in source gas concentration, and active levels of boron incorporation exceeding 1×1020 B/cm3 have been achieved in as-deposited 550 °C epilayers. This value exceeds solid solubility limits for boron in silicon at these temperatures by two orders of magnitude, and highlights the nonequilibrium nature of this process. High resolution transmission electron microscopy lattice imaging of this material shows it to be free of boron precipitates, while both plane view transmission electron microscopy and x-ray topography fail to reveal extended defects. Utilizing low-temperature processing throughout, p/n junctions have been fabricated in several of the in situ doped layers, with essentially ideal junction quality factors (n=1.0 –1.05) found for junctions of 1×106 μm2.
Synthesis and Evaluation of 2-(Arylamino)imidazoles as α2-Adrenergic Agonists (1997)

A series of 2-(arylamino)imidazoles was synthesized and evaluated for activity at alpha 1- and alpha 2-adrenoceptors. This class of agents has been shown to have potent and selective agonist activity at the alpha 2-adrenoceptors. The most potent member of this class, 2-[(5-methyl-1,4-benzodioxan-6yl)amino]imidazole, proved efficacious for the reduction of intraocular pressure upon topical administration and for the reduction of blood pressure upon intravenous administration. During the course of our studies, we developed a new reagent that allowed rapid assembly of the target compounds. This reagent, N-(2,2-diethoxyethyl)carbodiimide, was convenient to prepare and was stable under low-temperature storage conditions.