gebhart/patrepeval huggingface dataset:
Evaluation of Advanced Structure-Based Virtual Screening Methods for Computer-Aided Drug Discovery (2007)

Computational virtual screening has become an essential platform of drug discovery for the efficient identification of active candidates. Moleculardocking, a key technology of receptor-centric virtual screening, is commonly used to predict the binding affinities of chemical compounds on target receptors. Despite the advancement and extensive application of these methods, substantial improvement is still required to increase their accuracy and time-efficiency. Here, we evaluate several advanced structure-based virtual screening approaches for elucidating the rank-order activity of chemical libraries, and the quantitative structureactivity relationship (QSAR). Our results show that the ensemble-average free energy estimation, including implicit solvation energy terms, significantly improves the hit enrichment of the virtual screening. We also demonstrate that the assignment of quantum mechanical-polarized (QM-polarized) partial charges to docked ligands contributes to the reproduction of the crystal pose of ligands in the docking and scoring procedure.
The PREMIER study: A multicenter, randomized, double‐blind clinical trial of combination therapy with adalimumab plus methotrexate versus methotrexate alone or adalimumab alone in patients with early, aggressive rheumatoid arthritis who had not had previous methotrexate treatment (2005)

In this population of patients with early, aggressive RA, combination therapy with adalimumab plus MTX was significantly superior to either MTX alone or adalimumab alone in improving signs and symptoms of disease, inhibiting radiographic progression, and effecting clinical remission.
Mutational analysis of the active site of RNase of Bacillus intermedius (BINASE) (1994)

To elucidate the functional role of some residues in the active site of binase, the extracellular ribonuclease of Bacillus intermedius, we used site-directed mutagenesis. On cleavage of various substrates the catalytic activity of binase mutant His101 Glu is 2.0-2.7% of that for the native enzyme. The decrease in activity is determined mainly by the decrease in molecular rate constant kcat, with almost unchanged affinity of the enzyme for the substrate, characterized by KM. This is the expected result if His101 acts as an general acid, donating a proton to the leaving group on cleavage of a phosphodiester bond. The replacement of Lys26 by Ala causes a reduction in the enzyme activity to 13-33%, depending on the substrate. The activity decreases are due to changes in both kcat and KM for poly(A) and poly(A) but in kcat alone for GpA. In the latter case the effect is far less than that seen in the homologous mutation in the closely related enzyme, barnase.
Cloning and expression in Saccharomyces cerevisiae of a Trichoderma reesei beta-mannanase gene containing a cellulose binding domain (1995)

beta-Mannanase (endo-1,4-beta-mannanase; mannan endo-1,4-beta-mannosidase; EC 3.2.1.78) catalyzes endo-wise hydrolysis of the backbone of mannan and heteromannans, including hemicellulose polysaccharides, which are among the major components of plant cell walls. The gene man1, which encodes beta-mannanase, of the filamentous fungus Trichoderma reesei was isolated from an expression library by using antiserum raised towards the earlier-purified beta-mannanase protein. The deduced beta-mannanase consists of 410 amino acids. On the basis of hydrophobic cluster analysis, the beta-mannanase was assigned to family 5 of glycosyl hydrolases (cellulase family A). The C terminus of the beta-mannanase has strong amino acid sequence similarity to the cellulose binding domains of fungal cellulases and is preceded by a serine-, threonine-, and proline-rich region. Consequently, the beta-mannanase is probably organized similarly to the T. reesei cellulases, having a catalytic core domain separated from the substrate-binding domain by an O-glycosylated linker. Active beta-mannanase was expressed and secreted by using the yeast Saccharomyces cerevisiae as the host. The results indicate that the man1 gene encodes the two beta-mannanases with different isoelectric points (pIs 4.6 and 5.4) purified earlier from T. reesei.
A Solvent Extraction Process for Tar Sand by (2015)

A process has been investigated for solvent extraction of bitumen from Sunnyside, Utah, tar sands. The Sunnyside deposit, in east central Utah, has 1 to 2 billion barrels of geological reserves with a richness of 6 to 10 wtX bitumen. In this process, the ore is crushed and the bitumen is dissolved from the mineral in mix tanks. The bitumen and oil is separated from the coarse mineral by hydrocyclones and from the fines by pentane-deasphaltening. The solvent is recovered from the mineral by centrifuges, filters, and rotary kiln steam strippers, and from the bitumen by multi-effect evaporators. Hydrocyclone tests with one- and four-inch hydrocyclones demonstrated that 97 % of the mineral matter could be removed from the bitumen. The experimental data were used to develop mathematical models for predicting feed rate and cut size. Since the accuracy of the model was quite good, it was used to design the hydrocyclones for the process.
Use of a novel agarose gel-digesting enzyme for easy and rapid purification of PCR-amplified DNA for sequencing. (1992)

The use of a novel gel-digesting enzyme preparation provides an easy, rapid and convenient method to quantitatively recover PCR-amplified DNA from low melting point agarose gels. The PCR products purified using this method were readily sequenced and yielded good and unambiguous sequence data.
Corrections to the ‘Enhancement of microwave tomography through the use electrically conducting enclosures’ (2009)

The authors considered the problem of performing microwave tomography inside conducting enclosures and presented several examples comparing enclosedregion inversions directly with open-region inversions. The results presented were produced with a code containing two errors. Please see the PDF for further details.
Statistical mechanical model of diffusion of complex penetrants in polymers. II. Applications (1979)

Abstract The theory of Part I is applied to the diffusion of several aromatic diffusants in two “smooth chained” polymers: poly(ethylene terephthalate) (PET) and natural rubber. Modifications of the theory necessary to accommodate vinyl polymers are discussed and applied to benzene in PMA and PEA. In all cases the theory agrees satisfactorily with the experimental D(0,T) and D(c,T)/D(0,T) data, and the values of the disposable r g and Δ parameters are of the expected order. The limiting Arrhenius behavior of benzene in natural rubber appears to be correctly predicted. The cell model is definitely more appropriate than the free volume model for the calculation of enfolding chain effects in highly crystalline PET. For the three amorphous polymers the two models give comparable results, the cell model being somewhat superior for natural rubber and PMA.
Alterations in 5-HT 1B Receptor Function by p11 in Depression-Like States (2006)

The pathophysiology of depression remains enigmatic, although abnormalities in serotonin signaling have been implicated. We have found that the serotonin 1B receptor [5-hydroxytryptamine (5-HT1B) receptor] interacts with p11. p11 increases localization of 5-HT1B receptors at the cell surface. p11 is increased in rodent brains by antidepressants or electroconvulsive therapy, but decreased in an animal model of depression and in brain tissue from depressed patients. Overexpression of p11 increases 5-HT1B receptor function in cells and recapitulates certain behaviors seen after antidepressant treatment in mice. p11 knockout mice exhibit a depression-like phenotype and have reduced responsiveness to 5-HT1B receptor agonists and reduced behavioral reactions to an antidepressant.
Identification of Mycoplasma pneumoniae proteins associated with hemadsorption and virulence (1982)

Twenty-two mutants of Mycoplasma pneumoniae spontaneously deficient in hemadsorption were isolated. Examination of mutant protein profiles by one- and two-dimensional polyacrylamide gel electrophoresis permitted the grouping of these mutants into four classes. The largest class of mutants was deficient in four high-molecular-weight proteins (215,000, 210,000, 190,000, and 140,000). A second class of mutants lacked three proteins previously designated A, B, and C (72,000, 85,000, and 37,000, respectively). A single mutant, in addition to lacking proteins A, B, and C, was missing a fourth protein of 165,000 molecular weight. The remaining mutants exhibited protein profiles apparently identical to that of the wild-type strain. All mutant strains attached to the respiratory epithelium of hamster tracheal rings in vitro at reduced levels; however, mutants lacking proteins A, B, and C recognized only neuraminidase-insensitive receptors. None of the mutants tested produced detectable pneumonia in intranasally inoculated hamsters, although one mutant class demonstrated low-level survival in vivo.
Progression of Aortic Valve Calcification (2001)

Quantification of AVC by EBT permits new insights into the progression of aortic valve sclerosis. We observed a strong influence of LDL cholesterol level on the progression of AVC and CC, suggesting that lipid-lowering therapy may decrease the progression of aortic valve calcification.
OPTIMIZATION OF CATIONIC LIPOSOME-MEDIATED GENE TRANSFER TO HUMAN BRONCHIAL EPITHELIAL CELLS EXPRESSING WILD-TYPE OR ABNORMAL CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR (CFTR) (1999)

We determined optimum conditions for delivering DNA to transformed human bronchial epithelial cells expressing wild-type (BEAS) or abnormal (2CF) cystic fibrosis transmembrane conductance regulator (CFTR) using cationic liposomes (Lipofectin, [N-(N,N-dimethylaminoethane)carbamyl] cholesterol[DC-Chol]/dioleoylphosphatidylethanolamine[DOPE], or LipofectAMINE) and reporter genes which measured overall transgene expression (luciferase) or the fraction of cells transfected (heat-stable alkaline phosphatase). All liposomes showed dose-related toxicity. Optimal liposome and lipid: DNA ratios were different for BEAS than for 2CF cells. For all 3 liposome preparations, small particle size and net cationic charge related to transfection efficiency. Both LipofectAMINE and DC-Chol/DOPE transfected a maximum of 3% of BEAS cells, but luciferase expression could be increased without increasing the fraction of cells transfected. LipofectAMINE transfected a maximum of 6% of 2CF cells, and luciferase expression could be increased with no further increase in fraction of transfected cells. DC-Chol/DOPE transfected over 12% of 2CF cells with relatively small increases in luciferase expression. We conclude that an optimal cationic liposome and lipid: DNA ratio for transfecting bronchial epithelial cells depends on: (1) small particle size and net cationic charge, (2) whether the cells have the cystic fibrosis defect, and (3) whether the desired outcome is transfection of the maximum fraction of the cells or maximum total expression of the transgene.
Glucosamine and Chondroitin for Treating Symptoms of Osteoarthritis (2000)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Targeting the extracellular scavenger DNASE1L3 on SLE (2017)

Systemic lupus erythematosus (SLE) is characterized by breakdown of immune tolerance to self-antigens, production of large amount of anti-nuclear antibodies (ANA) and immune-mediated injury in multiple organs. Anti-dsDNA antibody is one of the major components of ANA and has been proven to play major pathogenic role in the tissue damage of SLE. The production of anti-DNA antibodies in SLE has long been associated with defective clearance of apoptotic nuclear debris, which when entering the circulation, may form microparticles (MP) containing DNA and other nuclear components (1). The investigation of the underlying mechanism for impaired clearance of apoptotic cells has been focused on an endonuclease, DNASE1, which can degrade chromatin into low molecular weight fragments, and is associated with disposal of apoptotic nuclear debris. The role of DNASE1 has been implicated in the pathogenesis of SLE for several decades (2). For example, an earlier study in a murine model for DNASE1-deficiency demonstrated that the presence of ANA, and deposition of immune complex in glomeruli developed full-blown glomerulonephritis. Reduced serum DNASE1 activity was found to be linked to the development of autoantibodies and active SLE disease in patients and lupus-prone mice (3). However, the reasons for such an association, as well as the basis for increased concentration of DNA in the serum were not well understood.
Genetic and Functional Dissection of HTRA1 and LOC387715 in Age-Related Macular Degeneration (2010)

A common haplotype on 10q26 influences the risk of age-related macular degeneration (AMD) and encompasses two genes, LOC387715 and HTRA1. Recent data have suggested that loss of LOC387715, mediated by an insertion/deletion (in/del) that destabilizes its message, is causally related with the disorder. Here we show that loss of LOC387715 is insufficient to explain AMD susceptibility, since a nonsense mutation (R38X) in this gene that leads to loss of its message resides in a protective haplotype. At the same time, the common disease haplotype tagged by the in/del and rs11200638 has an effect on the transcriptional upregulation of the adjacent gene, HTRA1. These data implicate increased HTRA1 expression in the pathogenesis of AMD and highlight the importance of exploring multiple functional consequences of alleles in haplotypes that confer susceptibility to complex traits.
Recombinant osteoprotegerin decreases tumor burden and increases survival in a murine model of multiple myeloma. (2003)

The aim of the present study was to determine whether modifying the local bone environment with osteoprotegerin (OPG), the soluble decoy receptor for receptor activator of nuclear factor-kappaB (RANK) ligand, could affect tumor burden and survival in the 5T33MM murine model of multiple myeloma. Treatment of mice, injected with 5T33MM cells, with recombinant OPG (Fc-OPG) caused a significant decrease in serum paraprotein and tumor burden and a significant increase in time to morbidity. This was associated with a decrease in osteoclast number in vivo but had no effect on apoptosis and proliferation of 5T33MM cells in vitro. These data indicate that targeting the bone microenvironment by inhibiting the interaction between RANK ligand and RANK with Fc-OPG not only inhibits the development of myeloma bone disease but also decreases tumor growth and increases survival.
A New ECG enhancement algorithm for stress ECG tests (2006)

In real situations, ECG recordings are often corrupted by artifacts. Two dominant artifacts present in ECG are: 1) High frequency noise caused by electromyogram indu-ced noise, power line interferences, or mechanical forces acting on the electrodes; 2) Baseline wander that may be due to respiration or the motion of the patients or the ins-truments. These artifacts severely limit the utility of the recorded ECG and thus need to be removed for better cli-nical evaluation. Several methods have been developed for ECG enhancement. In this paper, we proposed a new ECG enhancement method based on the recently developed Em-pirical Mode Decomposition (EMD). The proposed EMD-based method is able to remove both high frequency noise and baseline wander with minimum signal distortion. The method is validated through experiments on the MIT-BIH databases. 1.
Oct‐4 Expression in Adult Human Differentiated Cells Challenges Its Role as a Pure Stem Cell Marker (2007)

The Oct-4 transcription factor, a member of the POU family that is also known as Oct-3 and Oct3/4, is expressed in totipotent embryonic stem cells (ES) and germ cells, and it has a unique role in development and in the determination of pluripotency. ES may have their postnatal counterpart in the adult stem cells, recently described in various mammalian tissues, and Oct-4 expression in putative stem cells purified from adult tissues has been considered a real marker of stemness. In this context, normal mature adult cells would not be expected to show Oct-4 expression. On the contrary, we demonstrated, using reverse transcription-polymerase chain reaction (PCR) (total RNA, Poly A+), real-time PCR, immunoprecipitation, Western blotting, band shift, and immunofluorescence, that human peripheral blood mononuclear cells, genetically stable and mainly terminally differentiated cells with well defined functions and a limited lifespan, express Oct-4. These observations raise the question as to whether the role of Oct-4 as a marker of pluripotency should be challenged. Our findings suggest that the presence of Oct-4 is not sufficient to define a cell as pluripotent, and that additional measures should be used to avoid misleading results in the case of an embryonic-specific gene with a large number of pseudogenes that may contribute to false identification of Oct-4 in adult stem cells. These unexpected findings may provide new insights into the role of Oct-4 in fully differentiated cells. Disclosure of potential conflicts of interest is found at the end of this article.
Sorting human beta-cells consequent to targeted expression of green fluorescent protein. (1998)

Pancreatic islets of Langerhans are composed of four major endocrine cell types with a smaller number of nonendocrine cells. To study the molecular constituents and function of just one subpopulation of islet cells, it is necessary to sort them from the other cell types. While rat beta-cells can be sorted by autofluorescence-activated flow cytometry, this has not proved possible on a routine and reproducible basis for human beta-cells. In the present study, we have selectively labeled human beta-cells with green fluorescent protein (GFP), allowing for their sorting by flow cytometry. Human islet cells were infected with replication-defective (attenuated) recombinant adenovirus expressing GFP driven by the rat insulin I promoter (Ad-RIP-GFP) for targeted expression in beta-cells, or beta-galactosidase driven by the promiscuous cytomegalovirus (CMV) promoter (Ad-CMV-beta-gal) as control. Whereas the majority of islet cells can be infected by adenovirus, as shown by control infection with Ad-CMV-beta-gal, increased fluorescence after infection with Ad-RIP-GFP was limited to insulin-containing beta-cells. Infection of islet cells with Ad-RIP-GFP resulted reproducibly in the appearance of a population of intensely fluorescent cells, when analyzed by flow cytometry. These cells were sorted using a fluorescence-activated cell sorter (FACS) and shown by immunofluorescence to consist of >95% beta-cells. The targeted expression of GFP thus allows for preparation of human beta-cells purified close to homogeneity. This method should be readily applicable in any laboratory with FACS capability.
Antibacterials. Synthesis and structure-activity studies of 3-aryl-2-oxooxazolidines. 1. The B group (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAntibacterials. Synthesis and structure-activity studies of 3-aryl-2-oxooxazolidines. 1. The B groupWalter A. Gregory, David R. Brittelli, C. L. J. Wang, Mark A. Wuonola, Ronald J. McRipley, David C. Eustice, Virginia S. Eberly, Andrew M. Slee, Martin Forbes, and P. T. BartholomewCite this: J. Med. Chem. 1989, 32, 8, 1673–1681Publication Date (Print):August 1, 1989Publication History Published online1 May 2002Published inissue 1 August 1989https://pubs.acs.org/doi/10.1021/jm00128a003https://doi.org/10.1021/jm00128a003research-articleACS PublicationsRequest reuse permissionsArticle Views1754Altmetric-Citations160LEARN 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 Get e-Alerts
Glycosyl-phosphatidylinositol-anchored or integral membrane forms of CD14 mediate identical cellular responses to endotoxin. (1993)

Endotoxin stimulates leukocytes to release cytokines that initiate septic shock in humans and animals. CD14, a glycosyl-phosphatidylinositol-anchored membrane glycoprotein, is an endotoxin receptor on leukocytes, and endotoxin binding to CD14 induces cytokine production. Here we show that glycosyl-phosphatidylinositol-anchored or integral membrane CD14 mediates identical cellular responses to endotoxin, including NF-kappa B activation and protein tyrosine phosphorylation. We also show that an anti-CD14 monoclonal antibody that does not block endotoxin binding to CD14 nonetheless inhibits cell activation by endotoxin. These findings suggest that binding of endotoxin to cell-surface CD14 is followed by subsequent interactions of the endotoxin-CD14 complex with additional membrane component(s) that enable transmembrane signaling. This function of CD14 may be prototypic for other members of the glycosyl-phosphatidylinositol-anchored family of proteins that do not play a primary role in signal transduction but rather are the principal ligand-binding units of membrane-bound receptor complexes.
RPE65Gene Delivery Restores Isomerohydrolase Activity and Prevents Early Cone Loss inRpe65−/−Mice (2006)

RPE65 gene delivery generates isomerohydrolase activity and restores retinoid profile in Rpe65-/- mice. Regeneration of 11-cis retinal is essential for survival of cone photoreceptors.