gebhart/patrepeval huggingface dataset:
Dehydrogenases involved in the conversion of succinate to 4-hydroxybutanoate by Clostridium kluyveri (1993)

A pathway of succinate fermentation to acetate and butanoate (butyrate) in Clostridium kluyveri has been supported by the results of 13C nuclear magnetic resonance studies of the metabolic end products of growth and the detection of dehydrogenase activities involved in the conversion of succinate to 4-hydroxybutanoate (succinic semialdehyde dehydrogenase and 4-hydroxybutanoate dehydrogenase). C. kluyveri fermented [1,4-13C]succinate primarily to [1-13C]acetate, [2-13C]acetate, and [1,4-13C]butanoate. Any pathway proposed for this metabolism must account for the reduction of a carboxyl group to a methyl group. Succinic semialdehyde dehydrogenase activity was demonstrated after separation of the crude extracts of cells grown on succinate and ethanol (succinate cells) by anaerobic nondenaturing polyacrylamide gel electrophoresis. 4-Hydroxybutanoate dehydrogenase activity in crude extracts of succinate cells was detected and characterized. Neither activity was found in cells grown on acetate and ethanol (acetate cells). Analysis of cell extracts from acetate cells and succinate cells by sodium dodecyl sulfate-polyacrylamide gel electrophoreses showed that several proteins were present in succinate cell extracts that were not present in acetate cell extracts. In addition to these changes in protein composition, less ethanol dehydrogenase and hydrogenase activity was present in the crude extracts from succinate cells than in the crude extracts from acetate cells. These data support the hypothesis that C. kluyveri uses succinate as an electron acceptor for the reducing equivalents generated from the ATP-producing oxidation of ethanol.
Ridge Regression: Applications to Nonorthogonal Problems (1970)

Abstract This paper is an exposition of the use of ridge regression methods. Two examples from the literature are used as a base. Attention is focused on the RIDGE TRACE which is a two-dimensional graphical procedure for portraying the complex relationships in multifactor data. Recommendations are made for obtaining a better regression equation than that given by ordinary least squares estimation. This article is referred to by:Ridge Regression: A Historical Context
ChemInform Abstract: Aminoalkylindoles: Structure‐Activity Relationships of Novel Cannabinoid Mimetics. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Optical Properties of Pd−Ag and Pt−Ag Nanoboxes Synthesized via Galvanic Replacement Reactions (2005)

Silver nanocubes dispersed in water were transformed into Pd-Ag or Pt-Ag nanoboxes by adding either Na(2)PdCl(4) or Na(2)PtCl(4). By controlling the amount of noble metal salt added, and therefore the molar ratio of Na(2)PdCl(4) or Na(2)PtCl(4) to Ag, we could tune the surface plasmon resonance peak of the nanostructures across the entire visible spectrum, from 440 to 730 nm. Replacement of Ag with Pd resulted in the formation of a nanobox composed of a Pd-Ag alloy single crystal, but the nanobox formed after replacement of Ag with Pt was instead composed of distinct Pt nanoparticles. DDA calculations suggest that both nanoboxes absorb light strongly, with Q(abs)/Q(sca) approximately 5. After galvanic replacement, Pd-Ag and Pt-Ag nanostructures remain SERS active, suggesting their use as a SERS probe for studying the dependence of interfacial chemistry on composition.
Modification of survival pathway gene expression in human breast cancer cells by tetraiodothyroacetic acid (tetrac) (2009)

Tetraiodothyroacetic acid (tetrac) inhibits the cellular actions of thyroid hormone initiated at the hormone receptor on plasma membrane integrin alphavbeta3. Via interaction with the integrin, tetrac is also capable of inhibiting the angiogenic effects of vascular endothelial growth factor and basic fibroblast growth factor. MDA-MB-231 cells are estrogen receptor-negative human breast cancer cells shown to be responsive to tetrac in terms of decreased cell proliferation. Here we describe actions initiated at the cell surface receptor by unmodified tetrac and nanoparticulate tetrac on a panel of survival pathway genes in estrogen receptor-negative human breast cancer (MDA-MB-231) cells. Nanoparticulate tetrac is excluded from the cell interior. Expression of apoptosis inhibitors XIAP (X-linked inhibitor of apoptosis) and MCL1 (myeloid cell leukemia sequence 1) was downregulated by nanoparticulate tetrac in these breast cancer cells whereas apoptosis-promoting CASP2 and BCL2L14 were upregulated by the nanoparticulate formulation. Unmodified tetrac affected only XIAP expression. Expression of the angiogenesis inhibitor thrombospondin 1 (THBS1) gene was increased by both formulations of tetrac, as was the expression of CBY1, a nuclear inhibitor of catenin activity. The majority of differentially regulated Ras-oncogene family members were downregulated by nanoparticulate tetrac. The latter downregulated expression of epidermal growth factor receptor gene and unmodified tetrac did not. Nanoparticulate tetrac has coherent anti-cancer actions on expression of differentially-regulated genes important to survival of MDA-MB-231 cells.
Sequence-Specific DNA Binding by the c-Myc Protein (1990)

While it has been known for some time that the c-Myc protein binds to random DNA sequences, no sequence-specific binding activity has been detected. At its carboxyl terminus, c-Myc contains a basic--helix-loop-helix (bHLH) motif, which is important for dimerization and specific DNA binding, as demonstrated for other bHLH protein family members. Of those studied, most bHLH proteins bind to sites that contain a CA- -TG consensus. In this study, the technique of selected and amplified binding-sequence (SAAB) imprinting was used to identify a DNA sequence that was recognized by c-Myc. A purified carboxyl-terminal fragment of human c-Myc that contained the bHLH domain bound in vitro in a sequence-specific manner to the sequence, CACGTG. These results suggest that some of the biological functions of Myc family proteins are accomplished by sequence-specific DNA binding that is mediated by the carboxyl-terminal region of the protein.
&lsquo;Lupus-Prone&rsquo; Mice Are Susceptible to Organ-Specific Autoimmune Disease, Experimental Allergic Encephalomyelitis (1994)

Immunization with the multideterminant autoantigen myelin basic protein (MBP) causes experimental allergic encephalomyelitis (EAE), a T-cell-mediated autoimmune disease that serves as a model for multiple sclerosis (MS). MBP peptides Ac1-11 and p35-47 induce potent EAE in mice of the H-2u haplotype. T cells specific for Ac1-11 predominantly utilize one T-cell receptor (TCR) V beta gene segment, V beta 8.2. All T-cell clones and hybridomas analyzed, regardless of TCR V beta usage, utilize D beta 2 and J beta 2 elements. The NZW mouse strain (H-2z), which contributes to the spontaneous 'lupus-like' illness in (NZB x NZW)F1 mice, has a genomic deletion encompassing D beta 2 and J beta 2 gene segments. The NZW strain expresses class II (I-A and I-E) genes which share identical sequences with H-2u class II. We investigated whether these strains are susceptible to EAE induced with intact MBP and known encephalitogenic MBP peptides. In vitro analysis demonstrated that NZW antigen-presenting cells (APC) can present MBP and MBP peptide Ac1-11 to an encephalitogenic T-cell clone derived from an H-2u mouse, confirming the functional identity of NZW class-II (I-A) molecules with their respective H-2u class-II gene products. In vivo results demonstrated that NZW and (NZB x NZW)F1 mice are susceptible to EAE induced with intact MBP and Ac1-11. MBP p35-47 caused EAE in (NZB x NZW)F1 mice, which express alleles for both the normal (NZB) TCR beta-gene locus, and the abnormal (NZW) TCR beta-gene locus containing the J beta 2 deletion.(ABSTRACT TRUNCATED AT 250 WORDS)
Neuronal activity recorded extracellularly from in situ canine mediastinal ganglia (1988)

Spontaneous activity of 226 neurons was recorded from in situ mediastinal ganglia in 10 dogs. Forty-two percent of these were active during specific phases of the cardiac cycle, primarily during systole. Cardiovascular-related activity occurred when systolic pressure was between approximately 70 and 185 mmHg (1 mmHg = 133.3 Pa) whether the pressure was altered by positive inotropic pharmacological agents or cross clamping of the aorta. Twenty percent of the identified neurons displayed respiratory-related activity which occurred during positive pressure inflation or deflation. Thirty-eight percent of the identified neurons displayed bursts of activity or sporadic activity. The activity of 17% of the identified neurons was altered by gentle mechanical distortion of localized regions of the neck, left elbow, ventral thoracic wall, ventral abdominal wall, superior vena cava, right ventricle, or aorta. In the majority of instances cardiovascular- or respiratory-related activity persisted following acute decentralization, indicating that neurons in mediastinal ganglia can function in the absence of influences of central nervous system neurons. Five percent of the identified neurons were activated by single 1-4 ms, 10-20 V stimuli delivered at 0.5 Hz to the nerves connected with either the cranial or the caudal poles of the mediastinal ganglion or the ansae. These neurons were activated after a fixed latency when 0.5 Hz was used and in most instances when 10 Hz was used. These data indicate that 5% or less of the neurons identified projected axons out of the mediastinal ganglia investigated.(ABSTRACT TRUNCATED AT 250 WORDS)
Locomotion of medical micro robot with spiral ribs using mucus (2002)

An intracorporeal microrobot will not become practical unless an efficient and low invasive driving device is developed. This paper presents a new technology to drive medical microrobots and experimental results which confirm the new principle. Thrust force up to 1 N was measured when gap width was small and sliding speed was high. While it is pointed out that rupture of fluid film may limit the magnitude of thrust force. The experimental study also confirms that as thrust force arises only due to hydrodynamic action and direct contact does not arise, low invasive operation is possible if good lubrication conditions are kept.
VLSI technologies for artificial neural networks (1989)

VLSI systems, basic integrated circuits, and silicon technologies are discussed. Novel circuit and design principles that provide a foundation for the implementation of a wide variety of neural network models in silicon are described. The key issues for a successful integration of neural systems are identified. The realization of algorithms in silicon is examined. Special-purpose hardware for carrying out the activation and transfer function and for the connection elements is discussed. A brief overview of the current silicon technologies is provided.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Bacterial flagellin is a dominant antigen in Crohn disease (2004)

Chronic intestinal inflammation, as seen in inflammatory bowel disease (IBD), results from an aberrant and poorly understood mucosal immune response to the microbiota of the gastrointestinal tract in genetically susceptible individuals. Here we used serological expression cloning to identify commensal bacterial proteins that could contribute to the pathogenesis of IBD. The dominant antigens identified were flagellins, molecules known to activate innate immunity via Toll-like receptor 5 (TLR5), and critical targets of the acquired immune system in host defense. Multiple strains of colitic mice had elevated serum anti-flagellin IgG2a responses and Th1 T cell responses to flagellin. In addition, flagellin-specific CD4(+) T cells induced severe colitis when adoptively transferred into naive SCID mice. Serum IgG to these flagellins, but not to the dissimilar Salmonella muenchen flagellin, was elevated in patients with Crohn disease, but not in patients with ulcerative colitis or in controls. These results identify flagellins as a class of immunodominant antigens that stimulate pathogenic intestinal immune reactions in genetically diverse hosts and suggest new avenues for the diagnosis and antigen-directed therapy of patients with IBD.
Heat shock proteins and antigens of Mycobacterium tuberculosis (1991)

The heat shock response of Mycobacterium tuberculosis has been characterized in detail by one- and two-dimensional polyacrylamide gel electrophoresis after metabolic labeling with [35S]methionine and 14C-amino acids. A temperature increase from 37 to 42 degrees C induced elevated synthesis of three major proteins corresponding to the DnaK, GroEL, and GroES proteins of M. tuberculosis previously identified as prominent antigens. At higher temperatures (45 to 48 degrees C), synthesis of GroEL decreased and novel heat shock proteins with molecular masses of 90, 28, 20, and 15 kDa were observed. These new proteins did not comigrate with known antigens during two-dimensional gel electrophoresis. The heat shock response is discussed with regard to the possible importance of transcriptional regulation of mycobacterial genes in vivo.
Nanoparticle precursor route to low-temperature spray deposition of CdTe thin films (1995)

In this letter we report a nanoparticle-derived route to CdTe thin films. CdTe nanoparticles 39±8 Å in diameter, prepared by an organometallic route, were characterized by x-ray diffraction, UV-Vis spectroscopy, transmission electron microscopy, and energy dispersive x-ray spectroscopy. CdTe thin-film deposition was realized by spraying a nanoparticle/butanol colloid onto SnO2-coated glass substrates at variable susceptor temperatures. The resultant CdTe films were characterized by atomic force microscopy, x-ray diffraction, and UV-Vis spectroscopy. Smooth and dense CdTe thin films were obtained using growth temperatures ∼200 °C less than conventional spray pyrolysis. A growth temperature dependence upon CdTe grain size formation and crystallinity was observed by atomic force microscopy and x-ray diffraction. UV-Vis characterization revealed a transformation in the optical properties of the CdTe thin films as a function of growth temperature.
Overexpression of the Tobacco Tsi1 Gene Encoding an EREBP/AP2-Type Transcription Factor Enhances Resistance against Pathogen Attack and Osmotic Stress in Tobacco (2001)

Jeong Mee Park, Chang-Jin Park, Suk-Bae Lee, Byung-Kook Ham, Ryoung Shin, Kyung-Hee Paek, Overexpression of the Tobacco Tsi1 Gene Encoding an EREBP/AP2-Type Transcription Factor Enhances Resistance against Pathogen Attack and Osmotic Stress in Tobacco, The Plant Cell, Vol. 13, No. 5 (May, 2001), pp. 1035-1046
Compilation, alignment, and phylogenetic relationships of DNA polymerases (1993)

This is an update of an earlier compilation and alignment of DNA polymerase sequences (Ito and Braithwaite, 1991). As in the previous compilation, we attempted to compile complete sequences, to facilitate the identification of conserved and viable regions of the DNA polymerases (1). This update includes, for the first time, three DNA polymerase sequences from Archaea (2); two new members of the Family A DNA polymerases; and 19 new members of the Family B DNA polymerases. In addition, we included nucleases that have related amino acid sequences to E.coli DNA polymerase I, and the sequence of E.coli DNA polymerase HI (e-subunit) was aligned to Family C due to its homology to Bacillus subtilis DNA polymerase HI. As in the previous compilation (1), Family A DNA polymerases are named for their homology to the product of the polA gene specifying E.coli DNA polymerase I; Family B DNA polymerases are named for their homology to the product of the polB gene encoding E.coli DNA polymerase II; and Family C DNA polymerases are named for their homology to the product of the polC encoding E. coli DNA polymerase HI alpha subunit. Table 1 summarizes the molecular weights and isoelectric points of each DNA polymerase and nuclease. Table 1 also serves as a reference guide to the sequences shown in Figures 1A, IB, and 1C. Since no new sequences were published for the Family X DNA polymerases (/Mike), we have excluded them from this compilation.
Medicinal Chemistry of hERG Optimizations:  Highlights and Hang-Ups (2006)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTMedicinal Chemistry of hERG Optimizations: Highlights and Hang-UpsCraig Jamieson, Elizabeth M. Moir, Zoran Rankovic, and Grant WishartView Author Information Medicinal Chemistry, Organon Laboratories Ltd., Newhouse, Lanarkshire ML1 5SH, Scotland, U.K. Cite this: J. Med. Chem. 2006, 49, 17, 5029–5046Publication Date (Web):July 27, 2006Publication History Received31 March 2006Published online27 July 2006Published inissue 1 August 2006https://pubs.acs.org/doi/10.1021/jm060379lhttps://doi.org/10.1021/jm060379lreview-articleACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views10346Altmetric-Citations366LEARN 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-Alertsclose SUBJECTS:Modification,Optimization,Partition coefficient,Redox reactions,Selectivity Get e-Alerts
Mesoderm-inducing factors: a small class of molecules (1988)

Mesoderm-inducing factors (MIF's) from chick embryos, XTC cells and WEHI-3 cells were studied using various procedures. The object was to find whether they are similar to heparin-binding growth factors (HBGFs-the only known pure mesoderm-inducing substances) and, if not, whether they are similar to each other. The major active components from all three MIF sources behave as somewhat hydrophobic, acid-stable molecules and do not bind to heparin. They all have relative molecular masses of about 13,000 measured by HPLC size exclusion chromatography. The isoelectric points measured by chromatofocusing were 6.7 (WEHI) and 7.7 (XTC). The chick MIF seemed somewhat heterogeneous by chromatofocusing and a portion of its activity bound to heparin sepharose. All three MIFs have similar effects on explants of Xenopus blastula ectoderm to the heparin-binding growth factors, causing an elongation at the time of gastrulation followed by the development of mesenchyme, mesothelium and muscle cells, the proportion of muscle increasing with dose. Unlike the HBGFs they all also induce notochord if sufficiently high concentrations are used. Our study shows that the MIFs examined here form a small group of potent agents distinct from the HBGFs and from other known growth and differentiations factors. Their occurrence in various tissues and cell lines suggests that they have functions in the adult organism as well as during early development.
Myositis Induced by Naked DNA Immunization with the Gene for Histidyl-tRNA Synthetase (1997)

Polymyositis is regarded as an autoimmune inflammatory muscle disease. A major subgroup of patients have autoantibodies to cellular histidyl-transfer RNA synthetase (HRS). We have analyzed the role of the autoantigen HRS in the induction of murine myositis in a comparative study of inoculation of BALB/c mice with recombinant HRS protein versus naked DNA coding for HRS. Adult BALB/c mice produced antibodies to human HRS following inoculation with HRS protein and adjuvant, but myositis was not observed. Alternatively, expression plasmid DNA constructs encoding full-length and truncated human HRS were inoculated intramuscularly in gene transfer studies. DNA-inoculated mice produced relatively low anti-HRS antibody titers. However, in contrast to recombinant HRS protein-inoculated mice, HRS gene transfer induced pathology with evidence of cellular infiltration of perivascular and endomysial regions of the inoculated muscle. Multiple inoculations of a plasmid construct encoding a hybrid molecule consisting of HRS and the transferrin receptor cytoplasmic tail induced the highest levels of antibodies and persisting cellular infiltration. Unlike HRS, expression of influenza virus hemagglutinin (HA) following inoculation of an HA plasmid did not induce myositis. Transfer of naked DNA constructs expressing HRS is likely to provide valuable information on the autoimmune response to this protein and its role in the development of myositis.
A Quantitative Study to Assess the Value of Pressure Data Acquired with In-Situ Permanent Sensors in Complex 3D Reservoir Models Subject to Two-Phase Fluid Flow (2003)

Abstract Recent advances in smart well completion technologies have enabled the dynamic acquisition of in-situ pressure measurements with sensors in direct hydraulic contact with rock formations. In addition to the immediate impact of in-situ sensors as tools for real-time, reactive reservoir management and control, usage of in-situ pressure sensors has long-term benefits. Devising an optimal macro-management strategy for hydrocarbon reservoirs requires more than a tool for instantaneous monitoring and control. Precise knowledge of the spatial distribution of petrophysical properties is essential for accurate reservoir delineation, management, and production forecasting. From the formation evaluation viewpoint, large volumes of flow-related data constitute an attractive prospect for robust and accurate characterization of reservoirs. In addition to static information in the form of geostatistical, seismic, and geologic data, usage of dynamic measurements remains imperative to construct accurate reservoir models amenable to production forecast. In this paper, we address the quantitative estimation of three-dimensional (3D) spatial distributions of permeability and porosity from pressure measurements acquired with in-situ permanent sensors. A pilot waterflood operation conducted with a conventional five-spot pattern is chosen as example for our numerical experiments. We assume in-situ permanent pressure sensors to be an integral part of the production-well completion and to remain completely isolated from the hydraulics of the wellbore. Therefore, these sensors perform uncorrupted measurements of in-situ formation fluid pressures. Quantitative estimation of spatial distributions of permeability and porosity is approached with a novel subspace approach and a modified Gauss-Newton inversion algorithm. This inversion strategy incorporates an adjoint formulation for the efficient computation of model sensitivities. In our inversions, the physics of two-phase fluid-flow in the 3D spatial domain is rigorously incorporated into the assessment of distributions of petrophysical properties from in-situ permanent-sensor pressure data. Comparisons are shown of the enhancement in spatial resolution and reduction of uncertainty when using in-situ permanent sensors with respect to estimations performed via standard history matching techniques.