gebhart/patrepeval huggingface dataset:
An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast [published erratum appears in Nucleic Acids Res 1998 Apr 1;26(7):following 1855] (1998)

We have developed an activator/repressor expression system for budding yeast in which tetracyclines control in opposite ways the ability of tetR-based activator and repressor molecules to bind tetO promoters. This combination allows tight expression of tetO- driven genes, both in a direct (tetracycline-repressible) and reverse (tetracycline-inducible) dual system. Ssn6 and Tup1, that are components of a general repressor complex in yeast, have been tested for their repressing properties in the dual system, using lacZ and CLN2 as reporter genes. Ssn6 gives better results and allows complete switching-off of the regulated genes, although increasing the levels of the Tup1-based repressor by expressing it from a stronger promoter improves repressing efficiency of the latter. Effector-mediated shifts between expression and non-expression conditions are rapid. The dual system here described may be useful for the functional analysis of essential genes whose conditional expression can be tightly controlled by tetracyclines.
Combinatorial and computational approaches in structure-based drug design. (1998)

The increasing number of protein 3D structures and the success of structure-based approaches has led to the development of several experimental and theoretical techniques for the rational design of protein ligands. Combinatorial chemistry significantly speeds up the synthesis of potential new drug candidates. Diversity considerations, as well as the use of 3D structural information of the biological targets, reduce the size of huge libraries to a reasonable number of rationally-designed ligands. New NMR techniques (SAR by NMR) allow the construction of high-affinity ligands from small molecules with much lower affinities. Computer-aided drug design uses building, linking, and/or rigid docking procedures to search for ligands for a certain binding site. Scoring functions provide a rank order of the designed ligands according to their estimated binding affinities. Further developments in computer-aided drug design are automated approaches for the flexible alignment of molecules, the flexible docking of ligands to their binding sites, and the stepwise assembly of synthetically easily accessible ligands from combinatorial libraries of fragments.
Selective silencing of DNA‐specific B lymphocytes delays lupus activity in MRL/lpr mice (2007)

The pathological DNA-specific B lymphocytes in lupus are logical targets for a selected therapeutic intervention. We have hypothesized that it should be possible to suppress selectively the activity of these B cells in lupus mice by administering to them an artificial molecule that cross-links their surface immunoglobulins with the inhibitory FcgammaIIb surface receptors. A hybrid molecule was constructed by coupling the DNA-mimicking DWEYSVWLSN peptide to a monoclonal anti-mouse FcgammaRIIb antibody. This chimeric antibody was added to cultured spleen cells from sick MRL/lpr mice, immunized with diphtheria toxoid, resulting in reduction of the numbers of anti-DNA but not of anti-diphtheria IgG antibody-producing cells. Intravenous infusions with the DNA-peptide antibody chimera to 7-wk-old animals prevented the appearance of IgG anti-DNA antibodies and of albuminuria in the next 2 months. The administration of the DNA-peptide chimeric antibody to 18 wk-old mice with full-blown disease resulted in the maintenance of a flat level of IgG anti-DNA antibodies and in delay of the aggravation of the lupus glomerulonephritis. The use of chimeric antibodies targeting inhibitory B lymphocyte receptors represents a novel approach for the selective suppression of autoreactive disease-associated B cells in autoimmune diseases.
Ultrahigh resistivity aluminum nitride grown on mercury cadmium telluride (2001)

Aluminum nitride insulating layers have been grown at room temperature with a film resistivity of 3.3×1016 Ω cm on mercury cadmium telluride substrates. Insulator breakdown fields of 640 MV/m were reached. Capacitance–voltage measurements with Al/AlN/Hg0.76Cd0.24Te metalinsulator-semiconductor devices demonstrate band bending at the semiconductor surface indicating that damage to the substrate was minimized during film growth. A fixed interface charge density (given here as total charge per unit area divided by the electron charge=Qss/q) of +2×1011 cm−2 and a slow interface state density of 4×1010 cm−2 were measured. The procedures for achieving these high quality insulating layers are reported. Frequency dependent dielectric constant and dielectric loss tangent measurements, carried out at room temperature and 100 K, are also presented.
Adeno-Associated Virus Type 2-Mediated Gene Transfer: Role of Cellular T-Cell Protein Tyrosine Phosphatase in Transgene Expression in Established Cell Lines In Vitro and Transgenic Mice In Vivo (2003)

The use of adeno-associated virus type 2 (AAV) vectors has gained attention as a potentially useful alternative to the more commonly used retrovirus and adenovirus vectors for human gene therapy. However, the transduction efficiency of AAV vectors varies greatly in different cells and tissues in vitro and in vivo. We have documented that a cellular protein that binds the immunosuppressant drug FK506, termed the FK506-binding protein (FKBP52), interacts with the single-stranded D sequence within the AAV inverted terminal repeats, inhibits viral second-strand DNA synthesis, and consequently limits high-efficiency transgene expression (K. Qing, J. Hansen, K. A. Weigel-Kelley, M. Tan, S. Zhou, and A. Srivastava, J. Virol., 75: 8968-8976, 2001). FKBP52 can be phosphorylated at both tyrosine and serine/threonine residues, but only the phosphorylated forms of FKBP52 interact with the D sequence. Furthermore, the tyrosine-phosphorylated FKBP52 inhibits AAV second-strand DNA synthesis by greater than 90%, and the serine/threonine-phosphorylated FKBP52 causes approximately 40% inhibition, whereas the dephosphorylated FKBP52 has no effect on AAV second-strand DNA synthesis. In the present study, we have identified that the tyrosine-phosphorylated form of FKBP52 is a substrate for the cellular T-cell protein tyrosine phosphatase (TC-PTP). Deliberate overexpression of the murine wild-type (wt) TC-PTP gene, but not that of a cysteine-to-serine (C-S) mutant, caused tyrosine dephosphorylation of FKBP52, leading to efficient viral second-strand DNA synthesis and resulting in a significant increase in AAV-mediated transduction efficiency in HeLa cells in vitro. Both wt and C-S mutant TC-PTP expression cassettes were also used to generate transgenic mice. Primitive hematopoietic stem/progenitor cells from wt TC-PTP-transgenic mice, but not from C-S mutant TC-PTP-transgenic mice, could be successfully transduced by recombinant AAV vectors. These studies corroborate the fact that tyrosine phosphorylation of the cellular FKBP52 protein strongly influences AAV transduction efficiency, which may have important implications in the optimal use of AAV vectors in human gene therapy.
Functional Implications of Intracellular Phase Transitions (2018)

Intracellular environments are heterogeneous milieus comprised of macromolecules, osmolytes, and a range of assemblies that include membrane-bound organelles and membraneless biomolecular condensates. The latter are nonstoichiometric assemblies of protein and RNA molecules. They represent distinct phases and form via intracellular phase transitions. Here, we present insights from recent studies and provide a perspective on how phase transitions that lead to biomolecular condensates might contribute to cellular functions.
Effects of Topical Nitroglycerin and Flurbiprofen in the Rat Comb Burn Model (1999)

Burn injury is known to cause thrombosis and occlusion of dermal vessels that come in direct contact with thermal energy. Progressive ischemia secondary to diminished blood flow may compromise dermal tissues immediately surrounding the primary burn site. A standardized brass bar was used to create uniform full-thickness "comb" burns on 10 rat backs. Topical petrolatum (N = 2), 2% nitroglycerin (N = 4), and 5% flurbiprofen (N = 4) was applied to the burns at 2 and 4 hours postinjury. The vascular patency of dermal vessels was visualized directly by latex vascular casts made 24 hours after the burn injury. The vascular casts showed an absence of patent vessels within the direct burn sites in all treatment groups, and within the burn interspaces of the petrolatum-treated rats. Interspacial dermal vessel patency was seen in the 2% nitroglycerin and 5% flurbiprofen-treated rats. Topical 2% nitroglycerin and 5% flurbiprofen applied 2 and 4 hours postinjury effectively prevented interspacial dermal vessel thrombosis at 24 hours postinjury.
Cytoplasmic pH and free Mg2+ in lymphocytes. (1982)

Measurements have been made of cytoplasmic pH, (pHi) and free Mg2+ concentration, ( [Mg2+]i), in pig and mouse lymphocytes. pHi was measured in four ways: by a digitonin null-point technique; by direct measurement of the pH of freeze-thawed cell pellets; from the 31P nuclear magnetic resonance (NMR) spectrum of intracellular inorganic phosphate; and by the use of a newly synthesized, intracellularly-trappable fluorescent pH indicator. In HEPES buffered physiological saline with pH 7.4 at 37 degrees C, pHi was close to 7.0. Addition of physiological levels of HCO3- and CO2 transiently acidified the cells by approximately 0.1 U. Mitogenic concentrations of concanavalin A (Con A) had no measurable effect on pH in the first hour. [Mg2+]i was assessed in three ways: (a) from the external Mg2+ null-point at which the ionophore A23187 produced no net movement of Mg2+ or H+; (b) by Mg-sensitive electrode measurements in freeze-thawed pellets; and (c) from the 31P nuclear magnetic resonance spectrum of the gamma-phosphate of intracellular ATP. Total cell Mg2+ was approximately 12 mmol per liter cell water. The NMR data indicated [Mg2+]i greater than 0.5 mM. The null-point method gave [Mg2+]i approximately 0.9 nM. The electrode measurements gave 1.35 mM, which was thought to be an overestimate. Exposure to mitogenic doses of Con A for 1 h gave no detectable change in total or free Mg2+.
ChemInform Abstract: Direct Addition of TMS‐Acetylene to Aldimines Catalyzed by a Simple, Commercially Available Ir(I) Complex. (2002)

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.
Supported Membranes: Scientific and Practical Applications (1996)

Scientific and practical applications of supported lipid-protein bilayers are described. Membranes can be covalently coupled to or separated from solids by ultrathin layers of water or soft polymer cushions. The latter systems maintain the structural and dynamic properties of free bilayers, forming a class of models of biomembranes that allow the application of a manifold of surface-sensitive techniques. They form versatile models of low-dimensionality complex fluids, which can be used to study interfacial forces and wetting phenomena, and enable the design of phantom cells to explore the interplay of lock-and-key forces (such as receptor-ligand binding) and universal forces for cell adhesion. Practical applications are the design of (highly selective) receptor surfaces of biosensors on electrooptical devices or the biofunctionalization of inorganic solids.
Calcification by Escherichia coli (1974)

Escherichia coli K-12, grown in a synthetic medium containing metastable calcium phosphate, formed intracellular biological apatite crystals.
Comparison of autoantibody specificities between traditional and bead‐based assays in a large, diverse collection of patients with systemic lupus erythematosus and family members (2012)

The frequencies of ANAs detected by a bead-based assay are lower than those detected by IIF in European American patients with SLE. These assays have strong positive predictive values across ethnic groups, provide useful information for clinical care, and provide unique insights into familial aggregation and autoantibody clustering.
Peptide Deformylase:  A New Type of Mononuclear Iron Protein (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTPeptide Deformylase: A New Type of Mononuclear Iron ProteinP. T. Ravi Rajagopalan, X. Christopher Yu, and Dehua PeiView Author Information Department of Chemistry and Biological Mass Spectrometry Facility The Ohio State University 100 West 18th Avenue, Columbus, Ohio 43210 Cite this: J. Am. Chem. Soc. 1997, 119, 50, 12418–12419Publication Date (Web):December 17, 1997Publication History Received30 September 1997Published online17 December 1997Published inissue 17 December 1997https://pubs.acs.org/doi/10.1021/ja9734096https://doi.org/10.1021/ja9734096rapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views842Altmetric-Citations137LEARN 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:Iron,Metals,Monomers,Peptides and proteins,Zinc Get e-Alerts
Adaptive Multiagent System for Network Traffic Monitoring (2009)

An application of agent-based data mining for near-real time detection of attacks against the computer networks and connected hosts is based on processing network traffic statistics provided by high-speed network monitoring cards and using a set of known anomaly-detection techniques to identify the anomalous behavior. The individual anomaly-detection methods have relatively high error rates that make them unfit for most practical deployments. Using the agent-based trust modeling technique, the Camnep system fuses the data provided by anomaly-detection methods and progressively builds a better classification with an acceptable error rate. The system uses agent-based self-adaptation techniques to dynamically align its structure with the changes in network traffic structure and attacks.
Comment on “Electrospun hybrid organic/inorganic semiconductor Schottky nanodiode” [Appl. Phys. Lett. 89, 033505 (2006)] (2006)

First Page
Nepal—an algorithm for solving the volume integral equation (1993)

Abstract A new algorithm is proposed to solve the volume integral equation whereby the scatterer is first divided into N subscatterers. Smaller problems are nested within larger problems using the Huygens equivalence principle. The resultant algorithm has reduced computational complexity whose CPU time is proportional to N 1.5 . © 1993 John Wiley &amp; sons, Inc.
Proto‐oncogene amplification and homogeneously staining regions in human breast carcinomas (1990)

Cytogenetic studies on fresh human breast cancers revealed that homogeneously staining regions (HSRs), which are assumed to represent DNA amplification, are observed in almost half of the cases. To search for a possible relationship between HSRs and proto-oncogene amplification, 16 proto-oncogenes, including ERBB2, were studied by Southern blot analysis in four tumors with two or three HSRs, and in three tumors without HSRs. Only four proto-oncogenes were found to be amplified in at least one tumor each: HST and INT2 (x3), MYC (x2-3), and FES (x greater than 10). The large sizes of the HSRs, which each corresponded to several percent of the haploid genome, were hardly compatible with the low rate of amplification, except for FES and then only if a large adjacent segment was co-amplified. This incomplete correlation was demonstrated by in situ hybridization, using biotinylated probes, which showed fluorescent spots on only one HSR for FES in one tumor and for INT2 in another one. Our results indicate that most of the large amplifications corresponding to HSRs do not involve the proto-oncogenes usually studied in breast cancer. The large amplification of FES, detected in one tumor, may be coincidental.
Following cell fate in the living mouse embryo (1997)

It has been difficult to follow many of the dramatic changes in cell fate and cell migration during mouse development. This is because there has been no enduring marker that would allow cells to be recognised in the living embryo. We believe that we have overcome this problem by developing a novel form of green fluorescent protein, named MmGFP, that proves to be easily visible and non toxic to mouse cells and does not perturb embryogenesis. We show that synthetic mRNA encoding MmGFP can be injected into blastomeres to follow the fate of their progeny during preimplantation development. We have made a stable embryonic stem cell line that expresses MmGFP and introduced these fluorescent cells into mouse embryos. For the first time, we have been able to follow the fate of embryonic stem cells in living embryos and to observe directly the contribution of these cells to distinct lineages of the postimplantation embryo. This approach should lead to a more complete description of the dynamics of cell fate in the mouse.
Aluminum-Maltolate Induces Apoptosis and Necrosis in Neuro-2a Cells: Potential Role for p53 Signaling (2004)

Aluminum maltolate (Al-malt) causes neurodegeneration following in vivo exposure, and apoptosis plays a prominent role. The objective of this study was to define the form of cell death induced by Al-malt and to establish an in vitro model system amenable to mechanistic investigations of Al-malt-induced cell death. Neuro-2a cells, a murine neuroblastoma cell line, were treated with Al-malt for 24 h, following which mode of cell death and alterations in apoptosis-related gene expression were studied. Al-malt concentration-dependently increased cell death. The mode of cell death was a combination of apoptosis and necrosis. Treatment with Al-malt resulted in caspase 3 activation and the externalization of phosphatidyl serine, both indicative of apoptosis. In addition, nuclear condensation and fragmentation were evident. Interestingly, pretreatment with cycloheximide (CHX), a potent protein synthesis inhibitor markedly reduced Al-malt-induced apoptosis, indicating that altered gene expression was critical for this form of cell death. Pretreatment with CHX had no effect on necrosis induced by Al-malt. Analysis of gene expression showed that p53 mRNA was increased following treatment with Al-malt. This increase was accompanied by a marked inhibition of Bcl2 expression and an increase in BAX expression, a pattern of gene expression suggestive of a pro-apoptotic shift. Results show for the first time that p53 is induced by Al in neuron-like cells and suggest that the p53-dependent intrinsic pathway may be responsible for Al-induced apoptosis. Future studies investigating the role of p53 in Al neurotoxicity both in vivo and in vitro are warranted.
The Desmoteplase in Acute Ischemic Stroke Trial (DIAS) (2004)

Intravenous desmoteplase administered 3 to 9 hours after acute ischemic stroke in patients selected with perfusion/diffusion mismatch is associated with a higher rate of reperfusion and better clinical outcome compared with placebo. The sICH rate with desmoteplase was low, using doses up to 125 microg/kg.
Clinical significance of alterations of chromosome 8 detected by fluorescence in situ hybridization analysis in pathologic organ‐confined prostate cancer (2002)

Loss of 8p22 and gain of 8q24 are known to be common chromosomal alterations in prostate cancer. We have previously demonstrated that concurrent 8q24 overrepresentation and 8p22 loss were associated with a poor prognosis in patients with high-grade, locally advanced prostate cancer. We evaluated the alteration of 8p22 and 8q24 in a large cohort of pathologic organ-confined prostate cancer using fluorescence in situ hybridization (FISH) analysis. All 195 patients with Gleason scores > 5, pathologic stage T(2)N(0)M(0) (pT(2)N(0)M(0)) prostate cancer, who underwent a radical prostatectomy at the Mayo Clinic between 1987 and 1991, and for whom blocks were available, were selected for this study. The median follow-up period was 9.5 years, and endpoints of this study were biochemical and clinical disease progression. The latter includes local as well as systemic disease progression. FISH analysis using paraffin-embedded tissues was performed for 8p22 (LPL), centromere 8 (8cen), and 8q24 (MYC) and was successful for 156 tumors (80.0%). Of these tumors, 104 (66.6%) had one or more numeric alterations of the 3 loci evaluated. An increased copy number of 8q24 was observed in 66 (42.3%) tumors, of which 20 (12.8%) had an additional increase (AI) of 8q24, and 46 (29.5%) had a gain of 8q24 with an equivalent gain of 8cen. Losses and gains of 8p22 were detected in 81 (51.9%) and 20 (12.8%) tumors, respectively. An AI of 8q24 was significantly associated with the tumor Gleason score (P = 0.042). Univariate analysis indicated that loss of 8p22 was a significant predictor of biochemical and clinical disease progression (P = 0.025 and P = 0.011, respectively). Furthermore, the group with loss of 8p22 concurrent with an AI of 8q24 (Loss 8p22-any 8cen-AI 8q24) had an increased rate of biochemical disease progression (P = 0.052). Multivariate analysis demonstrated that neither individual nor the Loss-any-AI combination of alterations was a significant independent predictor of disease progression when adjusting for Gleason score, preoperative PSA levels, and DNA ploidy. These data suggest that loss of 8p22 is associated with a poor prognosis, specifically when it is accompanied by AI of 8q24 in pT(2)N(0)M(0) prostate cancer.
Single-Crystal Colloidal Multilayers of Controlled Thickness (1999)

Materials whose dielectric constant varies spatially with submicrometer periodicity exhibit diffractive optical properties which are potentially valuable in a number of existing and emerging applications. Here, such systems are fabricated by exploiting the spontaneous crystallization of monodisperse silica spheres into close-packed arrays. By reliance on a vertical deposition technique to pack the spherical colloids into close-packed silica−air arrays, high quality samples can be prepared with thicknesses up to 50 μm. These samples are planar and thus suitable for optical characterization. Scanning electron microscopy (SEM) of these materials illustrates the close-packed ordering of the spherical colloids in planes parallel to the substrate; cross-sectional SEM micrographs of the arrays as well as optical methods are used to measure sample thickness and uniformity. Normal-incidence transmission spectra in the visible and near-infrared regions show distinct peaks due to diffraction from the colloidal layers. While these basic optical characteristics are similar to thicker and polycrystalline gravity-sedimented colloidal crystals, the systematic control over the number of colloidal layers allows the effect of sample thickness on the optical spectrum to be studied for the first time.