gebhart/patrepeval huggingface dataset:
MIMIC: A molecular-field matching program. Exploiting applicability of molecular similarity approaches (1997)

This contribution presents the development and applicability of MIMIC, a molecular-field matching program for quantitatively evaluating the similarity between molecules, in a computationally feasible way and assesses the relative orientation that maximizes their similarity. In the present version one can deal with two types of molecular-field similarities, namely steric volume and electrostatic, as well as a combined similarity that takes into account a given contribution from each of them. Besides optimization of the relative spatial orientation by maximizing these similarities, MIMIC can perform exhaustive searches to locate a global similarity maximum candidate and the set of local similarity maxima closest to it. The high accuracy of the approach permits evaluation of the similarity space coverage of each similarity maximum. In addition, the study of the relationships among similarity spaces is proposed as a strategy to better understand the linkage between the different molecular overlay solutions obtained from the use of different molecular-field representations. Finally, calculation of the atomic contributions to the total molecular similarity provides a means for locating maximum similarity loci and for constructing pharmacophore patterns. The methodological bases and a detailed description of how they were implemented in MIMIC to handle molecular matchings between large systems is presented. All current features of the program were applied to a relative ligand-binding problem between two nonnucleoside HIV-1 reverse transcriptase inhibitors. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 934–954, 1997
A Nonvolatile InGaZnO Charge-Trapping-Engineered Flash Memory With Good Retention Characteristics (2010)

We report an amorphous indium gallium zinc oxide (a-IGZO) thin-film transistor nonvolatile memory (NVM). This NVM shows a large 1.2-V extrapolated ten-year memory window, along with low 10-V/-12-V program/erase voltage, fast 1-ms/100-¿s speed, and good endurance. This was achieved using a charge-trap-engineered structure and high- ¿ layers.
Interval gravity-gradient determination concepts (1984)

Abstract Considerable attention has been directed recently to applications of gravity gradients, e.g., Hammer and Anzoleaga (1975), Stanley and Green (1976), Fajklewicz (1976), Butler (1979), Hammer (1979), Ager and Liard (1982), and Butler et al. (1982). Gravity-gradient interpretive procedures are developed from properties of true or differential gradients, while gradients are determined in an interval or finite-difference sense from field gravity data. The relations of the interval gravity gradients to the true or differential gravity gradients are examined in this paper. Figure 1 illustrates the concepts of finite-difference procedures for gravity-gradient determinations. In Figure 1a, a tower structure is illustrated schematically for determining vertical gradients. Gravity measurements are made at two or more elevations on the tower, and various finite-difference or interval values of vertical gradient can be determined. For measurements at three elevations on the tower, for example, three interval gradient determinations are possible: Δg′13/Δz13; Δg′12/Δz12; Δg′23/Δz23; where Δg′13 = gz(h1)−gz(h3) and Δz13 = h1−h3, etc. For a positive downward z-;axis, these definitions for Δg′ij and Δzij will result in positive values for the vertical gradient. Relations of the interval gradients to each other and to the true or differential gradient are examined in this paper.
Farnesol is utilized for isoprenoid biosynthesis in plant cells via farnesyl pyrophosphate formed by successive monophosphorylation reactions (1999)

The ability of Nicotiana tabacum cell cultures to utilize farnesol (F-OH) for sterol and sesquiterpene biosynthesis was investigated. [(3)H]F-OH was readily incorporated into sterols by rapidly growing cell cultures. However, the incorporation rate into sterols was reduced by greater than 70% in elicitor-treated cell cultures whereas a substantial proportion of the radioactivity was redirected into capsidiol, an extracellular sesquiterpene phytoalexin. The incorporation of [(3)H]F-OH into sterols was inhibited by squalestatin 1, suggesting that [(3)H]F-OH was incorporated via farnesyl pyrophosphate (F-P-P). Consistent with this possibility, N. tabacum proteins were metabolically labeled with [(3)H]F-OH or [(3)H]geranylgeraniol ([(3)H]GG-OH). Kinase activities converting F-OH to farnesyl monophosphate (F-P) and, subsequently, F-P-P were demonstrated directly by in vitro enzymatic studies. [(3)H]F-P and [(3)H]F-P-P were synthesized when exogenous [(3)H]F-OH was incubated with microsomal fractions and CTP. The kinetics of formation suggested a precursor-product relationship between [(3)H]F-P and [(3)H]F-P-P. In agreement with this kinetic pattern of labeling, [(32)P]F-P and [(32)P]F-P-P were synthesized when microsomal fractions were incubated with F-OH and F-P, respectively, with [gamma-(32)P]CTP serving as the phosphoryl donor. Under similar conditions, the microsomal fractions catalyzed the enzymatic conversion of [(3)H]GG-OH to [(3)H]geranylgeranyl monophosphate and [(3)H]geranylgeranyl pyrophosphate ([(3)H]GG-P-P) in CTP-dependent reactions. A novel biosynthetic mechanism involving two successive monophosphorylation reactions was supported by the observation that [(3)H]CTP was formed when microsomes were incubated with [(3)H]CDP and either F-P-P or GG-P-P, but not F-P. These results document the presence of at least two CTP-mediated kinases that provide a mechanism for the utilization of F-OH and GG-OH for the biosynthesis of isoprenoid lipids and protein isoprenylation.
Reaction of nitriles under acidic conditions. Part I. A general method of synthesis of condensed pyrimidines (1980)

Abstract Nitriles are known to give rise to salts of different compositions with halogen acids. Many of the reactions undergone by nitriles under the influence of halogen acids are, in many cases, assumed to proceed via the intermediate formation of highly reactive imidoyl derivatives. The intermediates produced, in situ , by the reaction of nitriles with hydrogen chloride should, in principle, be capable of reacting with compounds containing appropriately placed nucleophilic and electrophilic centers leading to the formation of a heterocycle incorporating the C=N of the nitrile. Thus, the reaction of aliphatic, aromatic and heterocyclic nitriles with a variety of ortho aminocarbonyl derivatives such as nitriles, amides, esters and ketones of benzene, thiophen, furan, pyrrole, benzothiophene and pyridothiophene have been found to yield the corresponding condensed pyrimidines in fair to good yields. This constitutes a facile and versatile one‐pot synthesis of condensed pyrimidines.
HAGE, the helicase antigen as a biomarker for breast cancer prognosis (WO2013144616) (2014)

Тo identify patients who could be treated, a more detailed analysis taking into account, the full distribution spectrum of HAGE expression is desirable.
TRAF6 promotes TGFβ-induced invasion and cell-cycle regulation via Lys63-linked polyubiquitination of Lys178 in TGFβ type I receptor (2015)

Transforming growth factor β (TGFβ) can act either as a tumor promoter or a tumor suppressor in a context-dependent manner. High levels of TGFβ are found in prostate cancer tissues and correlate with poor patient prognosis. We recently identified a novel TGFβ-regulated signaling cascade in which TGFβ type I receptor (TβRI) is activated by the E3 ligase TNF-receptor-associated factor 6 (TRAF6) via the Lys63-linked polyubiquitination of TβRI. TRAF6 also contributes to activation of TNF-α-converting enzyme and presenilin-1, resulting in the proteolytic cleavage of TβRI and releasing the intracellular domain of TβRI, which is translocated to the nucleus to promote tumor invasiveness. In this report, we provide evidence that Lys178 of TβRI is polyubiquitinated by TRAF6. Moreover, our data suggest that TRAF6-mediated Lys63-linked ubiquitination of the TβRI intracellular domain is a prerequisite for TGFβ regulation of mRNA for cyclin D1 (CCND1), expression, as well as for the regulation of other genes controlling the cell cycle, differentiation, and invasiveness of prostate cancer cells.
Noncovalent Formation of Polyglycine II-Type Structure by Hexagonal Self-Assembly of Linear Polymolecular Chains (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTNoncovalent Formation of Polyglycine II-Type Structure by Hexagonal Self-Assembly of Linear Polymolecular ChainsToshimi Shimizu, Masaki Kogiso, and Mitsutoshi MasudaView Author Information Department of Organic Materials National Institute of Materials and Chemical Research 1-1 Higashi, Tsukuba, Ibaraki 305, Japan Cite this: J. Am. Chem. Soc. 1997, 119, 26, 6209–6210Publication Date (Web):July 2, 1997Publication History Received17 March 1997Published online2 July 1997Published inissue 1 July 1997https://pubs.acs.org/doi/10.1021/ja970844rhttps://doi.org/10.1021/ja970844rrapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views573Altmetric-Citations55LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Amides,Crystal structure,Molecules,Noncovalent interactions,Supramolecular structures and assemblies Get e-Alerts
Vector Choice Determines Immunogenicity and Potency of Genetic Vaccines against Angola Marburg Virus in Nonhuman Primates (2010)

The immunogenicity and durability of genetic vaccines are influenced by the composition of gene inserts and choice of delivery vector. DNA vectors are a promising vaccine approach showing efficacy when combined in prime-boost regimens with recombinant protein or viral vectors, but they have shown limited comparative efficacy as a stand-alone platform in primates, due possibly to suboptimal gene expression or cell targeting. Here, regimens using DNA plasmids modified for optimal antigen expression and recombinant adenovirus (rAd) vectors, all encoding the glycoprotein (GP) gene from Angola Marburg virus (MARV), were compared for their ability to provide immune protection against lethal MARV Angola infection. Heterologous DNA-GP/rAd5-GP prime-boost and single-modality rAd5-GP, as well as the DNA-GP-only vaccine, prevented death in all vaccinated subjects after challenge with a lethal dose of MARV Angola. The DNA/DNA vaccine induced humoral responses comparable to those induced by a single inoculation with rAd5-GP, as well as CD4(+) and CD8(+) cellular immune responses, with skewing toward CD4(+) T-cell activity against MARV GP. Vaccine regimens containing rAd-GP, alone or as a boost, exhibited cellular responses with CD8(+) T-cell dominance. Across vaccine groups, CD8(+) T-cell subset dominance comprising cells exhibiting a tumor necrosis factor alpha (TNF-alpha) and gamma interferon (IFN-gamma) double-positive functional phenotype was associated with an absence or low frequency of clinical symptoms, suggesting that both the magnitude and functional phenotype of CD8(+) T cells may determine vaccine efficacy against infection by MARV Angola.
Soy‐Based Infant Formula Supplemented with DHA and ARA Supports Growth and Increases Circulating Levels of these Fatty Acids in Infants (2007)

Healthy term infants (n = 244) were randomized to receive: (1) control, soy-based formula without supplementation or (2) docosahexaenoic acid-arachidonic acid (DHA + ARA), soy-based formula supplemented with at least 17 mg DHA/100 kcal (from algal oil) and 34 mg ARA/100 kcal (from fungal oil) in a double-blind, parallel group trial to evaluate safety, benefits, and growth from 14 to 120 days of age. Anthropometric measurements were taken at 14, 30, 60, 90, and 120 days of age and 24-h dietary and tolerance recall were recorded at 30, 60, 90, and 120 days of age. Adverse events were recorded throughout the study. Blood samples were drawn from subsets of 25 infants in each group. Capillary column gas chromatography was used to analyze the percentages of fatty acids in red blood cell (RBC) lipids and plasma phospholipids. Compared with the control group, percentages of fatty acids such as DHA and ARA in total RBC and plasma phospholipids were significantly higher in infants in the DHA + ARA group at 120 days of age (P < 0.001). Growth rates did not differ significantly between feeding groups at any assessed time point. Supplementation did not affect the tolerance of formula or the incidence of adverse events. Feeding healthy term infants soy-based formula supplemented with DHA and ARA from single cell oil sources at concentrations similar to human milk significantly increased circulating levels of DHA and ARA when compared with the control group. Both formulas supported normal growth and were well tolerated.
ChemInform Abstract: Synthesis of 1‐(3‐(1,2,4‐Triazol‐1‐yl)‐2,3,6‐trideoxy‐L‐arabino‐ hexofuranosyl)uracils via an α,β‐Unsaturated Aldehydohexose (1992)

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.
Systemic Host Responses in Severe Sepsis Analyzed by Causative Microorganism and Treatment Effects of Drotrecogin Alfa (Activated) (2003)

Clinical trials with novel therapeutic agents for severe sepsis have suggested that patients might respond differently depending on causative microorganism. Data from a large, placebo-controlled trial of recombinant human drotrecogin alfa (activated) (DrotAA) were analyzed by type of causative microorganism for treatment-associated differences in mortality, coagulopathy, and inflammatory response. Compared with placebo, mortality rates associated with DrotAA were consistently reduced for each microorganism group (gram-positive bacteria, gram-negative bacteria, mixed bacteria, fungi, other, and unknown microbial etiology), with a stratified relative risk (RR) of 0.80 (95% confidence interval [CI], 0.69-0.94). The greatest reduction in the mortality rate was for Streptococcus pneumoniae infection (RR, 0.56; 95% CI, 0.35-0.88). Levels of coagulation and inflammation biomarkers varied with different pathogens at study entry. Results demonstrate that DrotAA, administered as an adjunct to standard anti-infective therapy, can improve the rate of survival for patients who develop severe sepsis regardless of causative microorganism.
The Activation State of p38 Mitogen-Activated Protein Kinase Determines the Efficiency of ATP Competition for Pyridinylimidazole Inhibitor Binding (1998)

The serine/threonine kinase p38 is a ubiquitous, highly conserved, stress responsive, signal-transducing enzyme. It regulates the production of proinflammatory mediators and is the target of the cytokine synthesis inhibitory pyridinylimidazoles. We have expressed human p38 in Drosophila S2 cells and characterized preparations of mixed unphosphorylated/monophosphorylated (inactive) and homogeneously diphosphorylated (active) forms of the enzyme. We observed that only the active preparation of the enzyme has significant kinase activity when assayed using an ATF2-GST fusion protein as the substrate. We determined that the value of KM[ATP] in this reaction is 25 microM and that the pyridinylimidazole inhibitor of p38 kinase activity, SB203580, competes with ATP. We have found that a tritiated pyridinylimidazole, SB202190, has an equal affinity for both the active and inactive forms of the enzyme and that SB203580 competes with it equally well for binding to either form of the enzyme. However, ATP can compete with the tritiated inhibitor for binding to only the active form of the enzyme. Further, we demonstrate in vivo that at concentrations consistent with its IC50 as a cytokine inhibitor, SB203580 can inhibit stimulus-induced phosphorylation of p38 at the Thr-Gly-Tyr activation motif. Our observations suggest that pyridinylimidazoles may block the biological activity of p38 kinase by binding to the inactive form of p38 and reducing its rate of activation. Under these conditions, ATP would not effectively compete with the inhibitors in vivo.
Age-Related DNA Methylation Changes in Normal Human Prostate Tissues (2007)

Our findings show aberrant hypermethylation as a function of age in the normal prostate tissues. Such age-related methylation may precede and predispose to full-blown malignancy.
Common components in the assembly of type 4 fimbriae, DNA transfer systems, filamentous phage and protein‐secretion apparatus: a general system for the formation of surface‐associated protein complexes (1993)

The Pseudomonas aeruginosa genes pilB-D and pilQ are necessary for the assembly of type 4 fimbriae. Homologues of these genes and of the subunit (pilin) gene have been described in various different bacterial species, but not always in association with type 4 fimbrial biosynthesis and function. Pil-like proteins are also involved in protein secretion, DNA transfer by conjugation and transformation, and morphogensis of filamentous bacteriophages. It seems likely that the Pil homologues function in the processing and export of proteins resembling type 4 fimbrial subunits, and in their organization into fimbrial-like structures. These may either be true type 4 fimbriae, or components of protein complexes which act in the transport of macromolecules (DNA or protein) into or out of the cell. Some PilB-like and PilQ-like proteins are apparently also involved in the assembly of non-type 4 polymeric structures (filamentous phage virions and conjugative pili). The diverse studies summarized in this review are providing insight into an extensive infrastructural system which appears to be utilized in the formation of a variety of cell surface-associated complexes.
Crystal structure of the carbon monoxide-substrate-cytochrome P-450CAM ternary complex (1989)

The crystal structure of the ternary complex formed between carbon monoxide (CO), camphor, and ferrous cytochrome P-450CAM has been refined to an R value of 17.9% at 1.9-A resolution. To accommodate the CO molecule, the substrate, camphor, moves about 0.8 A while at the same time remaining in nonbonded contact with CO. The average temperature factor of the camphor atoms is about 50% higher in the CO complex, suggesting that the camphor is more loosely bound in this ternary complex. The Fe-C-O angle is about 166 degrees, and thus, CO appears to be bent from the heme normal, as it is in various CO-globin complexes, due to steric interactions with active site groups. The oxygen atom of the CO molecule is nestled into a groove formed by an unusual helical hydrogen bond in the distal helix between the highly conserved Thr 252 and Gly 248 residues. In the transition from the ferric camphor-bound binary complex to the ferrous CO-camphor-bound ternary complex, the heme iron atom moves into the plane defined by the pyrrole nitrogens by about 0.41 A. Although the axial Cys ligand also moves toward the heme, the S-Fe bond stretches from about 2.20 A in the absence of CO to about 2.41 A once CO has bound.
Sensitive and Quantitative Detection of Anti-Poly(ethylene glycol) (PEG) Antibodies by Methoxy-PEG-Coated Surface Plasmon Resonance Sensors (2017)

Pre-existing and induced anti-poly(ethylene glycol) (PEG) antibodies (abs) have been shown to be related with limitation of therapeutic efficacy and reduction in tolerance of several therapeutic agents. However, the current methods to detect anti-PEG abs are tedious and usually lack quantification. A facile, rapid, sensitive, and reliable technique to detect anti-PEG abs is highly desired in both research and clinic settings. In this work, we have presented a surface plasmon resonance (SPR) biosensor technique for the detection of anti-PEG abs and compared three PEG surface chemistries. Methoxy-PEG (mPEG) 5k was found to have the best performance. The detection of anti-PEG abs directly from diluted blood serum was achieved within 40 min. Detection sensitivity is as good as or better than enzyme-linked immunosorbent assay (ELISA). Furthermore, different antibody isotypes can be quantitatively differentiated by adopting secondary antibodies. A pilot study has been performed to analyze clinical blood samples using this technology, demonstrating its potential as a convenient and powerful method to prescreen and monitor anti-PEG abs in the patients before or after they receive treatment with PEG-containing drugs.
Recent Developments in Ring Opening Polymerization of Lactones for Biomedical Applications (2003)

Aliphatic polyesters prepared by ring-opening polymerization of lactones are now used worldwide as bioresorbable devices in surgery (orthopaedic devices, sutures, stents, tissue engineering, and adhesion barriers) and in pharmacology (control drug delivery). This review presents the various methods of the synthesis of polyesters and tailoring the properties by proper control of molecular weight, composition, and architecture so as to meet the stringent requirements of devices in the medical field. The effect of structure on properties and degradation has been discussed. The applications of these polymers in the biomedical field are described in detail.
Word level model checking---avoiding the Pentium FDIV error (1996)

Article Free Access Share on Word level model checking—avoiding the Pentium FDIV error Authors: E. M. Clarke School of Computer Science, Carnegie Mellon University, Pittsburgh, PA School of Computer Science, Carnegie Mellon University, Pittsburgh, PAView Profile , M. Khaira Intel Development Labs., Intel Corporation, 5200 NE Elam Young Pkwy, Hillsboro, OR Intel Development Labs., Intel Corporation, 5200 NE Elam Young Pkwy, Hillsboro, ORView Profile , X. Zhao School of Computer Science, Carnegie Mellon University, Pittsburgh, PA and Intel Development Labs., Intel Corporation, 5200 NE Elam Young Pkwy, Hillsboro, OR School of Computer Science, Carnegie Mellon University, Pittsburgh, PA and Intel Development Labs., Intel Corporation, 5200 NE Elam Young Pkwy, Hillsboro, ORView Profile Authors Info & Claims DAC '96: Proceedings of the 33rd annual Design Automation ConferenceJune 1996 Pages 645–648https://doi.org/10.1145/240518.240640Published:01 June 1996Publication History 20citation393DownloadsMetricsTotal Citations20Total Downloads393Last 12 Months52Last 6 weeks7 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF