gebhart/patrepeval huggingface dataset:
cis-acting sequences required for inducible interleukin-2 enhancer function bind a novel Ets-related protein, Elf-1. (1992)

The recent definition of a consensus DNA binding sequence for the Ets family of transcription factors has allowed the identification of potential Ets binding sites in the promoters and enhancers of many inducible T-cell genes. In the studies described in this report, we have identified two potential Ets binding sites, EBS1 and EBS2, which are conserved in both the human and murine interleukin-2 enhancers. Within the human enhancer, these two sites are located within the previously defined DNase I footprints, NFAT-1 and NFIL-2B, respectively. Electrophoretic mobility shift and methylation interference analyses demonstrated that EBS1 and EBS2 are essential for the formation of the NFAT-1 and NFIL-2B nuclear protein complexes. Furthermore, in vitro mutagenesis experiments demonstrated that inducible interleukin-2 enhancer function requires the presence of either EBS1 or EBS2. Two well-characterized Ets family members, Ets-1 and Ets-2, are reciprocally expressed during T-cell activation. Surprisingly, however, neither of these proteins bound in vitro to EBS1 or EBS2. We therefore screened a T-cell cDNA library under low-stringency conditions with a probe from the DNA binding domain of Ets-1 and isolated a novel Ets family member, Elf-1. Elf-1 contains a DNA binding domain that is nearly identical to that of E74, the ecdysone-inducible Drosophila transcription factor required for metamorphosis (hence the name Elf-1, for E74-like factor 1). Elf-1 bound specifically to both EBS1 and EBS2 in electrophoretic mobility shift assays. It also bound to the purine-rich CD3R element from the human immunodeficiency virus type 2 long terminal repeat, which is required for inducible virus expression in response to signalling through the T-cell receptor. Taken together, these results demonstrate that multiple Ets family members with apparently distinct DNA binding specificities regulate differential gene expression in resting and activated T cells.
Synthesis and transannular Diels–Alder reaction of a cis–trans–trans and a trans–cis–cis 13-membered macrocyclic trienone (1989)

The synthesis of the cis–trans–trans5 and trans–cis–cis6 macrocyclic trienones from cyclohexene is described. Upon heating at 300 °C, trienone 5 underwent 1,5-H shift and transannular Diels–Alder reaction to give adducts 33, 34, and 35 while trienone 6 provided tricyclic ketone 37. Keywords: transannular Diels–Alder reaction.
The steady state kinetic parameters and non-processivity of Escherichia coli deoxyribonucleic acid polymerase I (1975)

A steady state kinetic study of Escherichia coli DNA polymerase I has been carried out using poly[d(A-T)] as the template-primer substrate. The results of substrate saturation and product inhibition kinetic studies suggest an altered Ordered Bi Bi mechanism for the enzyme. The Michaelis constants for polymer, d-atp, and dTTP are 5 nM (3'-OH ends), 1 muM, and 2 muM, respectively. The apparent equilibrium constant for the reaction, Keq equals [PPi]/[dNTP], was estimated as greater than or equal to 500. No quaternary complex of enzyme, template, and both deoxynucleoside triphosphates was detected. Single turnover experiments at 4 degrees indicated that the enzyme functions non-processively under the specified conditions, that is, dissociates after each catalytic step. The results at higher temperature were consistent with dissociation within 30 steps. Furthermore, at 4 degrees a burst of incorporation stoichiometric with the amount of enzyme was observed upon initiation of the reaction, indicating that the rate-limiting step in the steady state occurs after phosphodiester bond formation. There is a linear Arrhenius dependence of the initial reaction on temperature in the range 4-40 degrees, with an apparent Ea equals 17 kcal/mol. The rate equations appropriate for template-dependent polymerases which dissociate after each catalytic step have been derived.
Issues in the haptic display of tool use (2002)

Our group is interested in using haptic display for training tool use. Applications include training doctors to use tools during surgery, and training astronauts to use tools during EVA. This paper describes some of the challenges of creating realistic haptic perceptions of tool use. Many of these challenges stem from the importance of unilateral constraints during tool use. Unilateral constraints occur whenever rigid bodies collide, resisting the interpenetration of the bodies, but not holding the bodies together. To identify unilateral constraints, a tool/environment simulation must perform collision detection. To respond properly to a collision, the simulation must estimate the forces that ensue, and integrate the equations of motion. All of these computations must occur in real time, and the simulation as a whole must be stable (to ensure the user's safety). Approaches to these problems are described.
Transfection of cells with custom-made calcium phosphate nanoparticles coated with DNA (2004)

Functionalised nanoparticles of calcium phosphate were prepared by controlled precipitation from aqueous solution, followed by coating with DNA. A successful transfection of transformed human endothelial cells was accomplished by adding the dispersion of nanoparticles to the cell culture. The functionalised nanoparticles formed a stable colloid and did not lose their ability for cell transfection during 2–3 weeks of storage. The nanoparticles were approximately spherical with diameters of 10 to 20 nm and covered and stabilised by a hull of DNA.
HGF induces FAK activation and integrin-mediated adhesion in MTLn3 breast carcinoma cells (1999)

Expression of hepatocyte growth factor (HGF) and its tyrosine kinase receptor, c-Met, is positively correlated with breast carcinoma progression. We found that in invasive and metastatic MTLn3 breast carcinoma cells, HGF stimulated both initial adhesion to and motility on the extracellular matrix (ECM) ligands laminin 1, type I collagen, and fibronectin. Next, analysis with function-perturbing antibodies showed that adhesion to the different ECM proteins was mediated through specific beta1 integrins. In MTLn3 cells, HGF induced rapid tyrosine phosphorylation and activation of both c-Met and focal adhesion kinase (FAK). Cell anchorage and adhesion to the ECM substrates was required for HGF-induced FAK activation, since HGF failed to trigger tyrosine phosphorylation of FAK in suspended cells. Our results provide evidence that the 2 signaling pathways, integrin/ECM and c-Met/HGF, cooperate synergistically to induce FAK activation in an adhesion-dependent manner, leading to enhanced cell adhesion and motility. Moreover, we found that a FRNK (the FAK-related non-kinase)-like molecule is expressed in MTLn3 cells. Since FRNK acts as a competitive inhibitor of FAK function, our results suggest that a FRNK-like protein could facilitate disassembly of focal adhesions and likely be responsible for the HGF-induced scattering and motility of MTLn3 cells.
Hijacking power and bandwidth from the mobile phone's audio interface (2010)

We endow the mobile phone with a low-cost, open interface that can parasitically power external peripherals, and transfer data to and from them, using analog, digital, and serial signaling, using only the existing headset audio port. This interface, called HiJack, allows the mobile phone to easily integrate with a range of external sensors, opening the door to new phone-centric sensing applications. In this paper, we characterize the signaling and power delivery capability of the audio jack, design circuits and software to transfer data and harvest energy, and evaluate the performance of our designs. We also use the mobile phone's audio channel to create a layered communications stack that supports low-level, analog signaling and high-level, multiplexed data communications with external devices. Our design supports a single, bi-directional communications channel at a data rate of 8.82 kbps over a Manchester-encoded serial stream, using just a few discrete components and the hardware peripherals found in almost any microcontroller. Our harvester delivers 7.4 mW to a load with 47% efficiency using components that cost $2.34 in 10K volume. Integrating the pieces, we present a combined system for delivering data and power over audio, and demonstrate its use by turning an iPhone into an inexpensive oscilloscope.
Generation of an autocrine leukaemia using a retroviral expression vector carrying the interleukin-3 gene. (1986)

The growth factor-dependent, non-leukemogenic cell line FDC-P1, was converted to an interleukin-3 (IL-3) producing leukemogenic cell line using a retroviral expression vector carrying the IL-3 gene. The new cell line, FDC-P1-IL3 proliferated independently of exogenous IL-3 and its proliferation was inhibited by anti IL-3 antisera. This inhibition could be overcome by addition of GM-CSF to the cultures. The data indicate that insertion of the retroviral expression vector into the genome of FDC-P1 cells has established an autocrine loop involving constitutive secretion of IL-3 and that such a loop can play an important role in leukemogenesis.
A cmos chip for individual cell manipulation and detection (2003)

Manipulation of populations of living cells on an individual basis is essential for the investigation of complex interactions among cells. We present a new approach to the integration on silicon of dielectrophoretic actuators and optical sensors that allow us to carry out this task. The device presented in this paper is an 8×8 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> chip implemented in a two-poly three-metal 0.35-μm CMOS technology, featuring 102,400 actuation electrodes, arranged in an array of 320×320, 20 μm×20μm microsites each comprising addressing logic, an embedded memory for electrode programming, and an optical sensor. The chip enables software-controlled displacement of more than 10,000 individual living cells, allowing biologists to devise complex interaction protocols that are impossible to manage otherwise. The manipulation does not damage the viability of the cells, so that this approach could be a unique extension to the techniques already available to biologists.
Superquadrics Revisited: Learning 3D Shape Parsing Beyond Cuboids (2019)

Abstracting complex 3D shapes with parsimonious part-based representations has been a long standing goal in computer vision. This paper presents a learning-based solution to this problem which goes beyond the traditional 3D cuboid representation by exploiting superquadrics as atomic elements. We demonstrate that superquadrics lead to more expressive 3D scene parses while being easier to learn than 3D cuboid representations. Moreover, we provide an analytical solution to the Chamfer loss which avoids the need for computational expensive reinforcement learning or iterative prediction. Our model learns to parse 3D objects into consistent superquadric representations without supervision. Results on various ShapeNet categories as well as the SURREAL human body dataset demonstrate the flexibility of our model in capturing fine details and complex poses that could not have been modelled using cuboids.
Sacred Landscapes and the Conversion of Eighth-Century Hessia (2008)

The place-names of Hessia in central Germany are a valuable resource for the study of the early medieval conversion period. A number of them refer to pagan gods and sites of Christian and pagan worship which are unevidenced in the historical sources. These sites are discussed and interpreted in relation to one another, to the regional topography and to the relatively well-documented context of the Anglo-Saxon mission to Hessia in the eighth century.
In vivo cancer gene therapy by adenovirus-mediated transfer of a bifunctional yeast cytosine deaminase/uracil phosphoribosyltransferase fusion gene. (2000)

Direct transfer of prodrug activation systems into tumors was demonstrated to be an attractive method for the selective in vivo elimination of tumor cells. However, most current suicide gene therapy strategies are still handicapped by a poor efficiency of in vivo gene transfer and a limited bystander cell killing effect. In this study, we describe a novel and highly potent suicide gene derived from the Saccharomyces cerevisiae cytosine deaminase (FCY1) and uracil phosphoribosyltransferase genes (FUR1). This suicide gene, designated FCU1, encodes a bifunctional chimeric protein that combines the enzymatic activities of FCY1 and FUR1 and efficiently catalyzes the direct conversion of 5-FC, a nontoxic antifungal agent, into the toxic metabolites 5-fluorouracil and 5-fluorouridine-5'monophosphate, thus bypassing the natural resistance of certain human tumor cells to 5-fluorouracil. Unexpectedly, although the uracil phosphoribosyltransferase activity of FCU1 was equivalent to that encoded by FUR1, its cytosine deaminase activity was 100-fold higher than the one encoded by FCY1. As a consequence, tumor cells transduced with an adenovirus expressing FCU1 (Ad-FCU1) were sensitive to concentrations of 5-FC 1000-fold lower than the ones used for cells transduced with a vector expressing FCY1 (Ad-FCY1). Furthermore, bystander cell killing was also more effective in cells transduced with Ad-FCU1 than in cultures infected with Ad-FCY1 or Ad-FUR1, alone or in combination. Finally, intratumoral injections of Ad-FCU1 into allo- or xenogeneic tumors implanted s.c. into mice, with concomitant systemic administration of 5-FC, led to substantial delays in tumor growth. These unique properties make of the FCU1/5-FC prodrug activation system a novel and powerful candidate for cancer gene therapy strategies.
Monoclonal antibody to type F Clostridium botulinum toxin (1990)

Hybridomas synthesizing monoclonal antibodies (MAbs) against type F Clostridium botulinum toxin were developed. MAb from one stable hybridoma, hybridoma 223, consisted of kappa light chains and an immunoglobulin G subclass 2a heavy chain. This MAb was used in a double-sandwich enzyme-linked immunosorbent assay to detect type F toxin in foods, culture fluids, and purified toxin preparations. The sensitivity of the double-sandwich enzyme-linked immunosorbent assay was approximately 10 mouse lethal doses of toxin per ml of toxic fluid.
The Role of Metabotropic Glutamate Receptor in Drug Reward, Motivation and Dependence (2007)

Addiction to drugs of abuse is a disorder that involves dysfunctions in motivational processes. Both the primary rewarding effects of drugs, as well as the acquired motivational properties of stimuli associated with drug-seeking and -taking, contribute to the perpetuation of dependence on drugs of abuse. Metabotropic glutamate (mGlu) receptors, which mediate slow glutamate neurotransmission, are located throughout limbic and cortical brain sites implicated in drug addiction. Preclinical evidence suggests that mGlu receptors play a crucial role in regulating behavioral effects of drugs of abuse relevant to drug addiction. Specifically, antagonists at excitatory postsynaptic mGlu5 receptors decrease drug self-administration without affecting motor behaviors, cognition or the reward value of natural rewards, while agonists at inhibitory presynaptic mGlu2/3 receptor agonists prevent reinstatement to drug-seeking and -taking after a period of abstinence. These findings have increased our understanding of the neuropathological processes associated with aspects of dependence on drugs of abuse and have provided new targets for pharmacological approaches to the treatment of dysfunctions in motivational processes characterizing the various phases of drug addiction.
Proton NMR assignment and secondary structure of the calcium-free form of the amino-terminal epidermal growth factor like domain in coagulation factor X (1990)

Blood coagulation factor X is composed of discrete domains, two of which are homologous to the epidermal growth factor (EGF). The N-terminal EGF like domain in factor X (fX-EGFN), residues 45-86 of the intact protein, contains a beta-hydroxylated aspartic acid and has one Ca2(+)-binding site. Using 2D NMR techniques, we have made a full assignment of the 500-MHz 1H NMR spectrum of Ca2(+)-free fX-EGFN. On the basis of this assignment and complementary NOESY experiments, we have also determined the secondary structure of Ca2(+)-free fX-EGFN in water solution. Residues 45-49 are comparatively mobile, whereas residues 50-56 are constrained by two disulfide bonds to one side of an antiparallel beta-sheet involving residues 59-64 and 67-72. Another antiparallel beta-sheet involves residues 76-77 and 83-84. A small, parallel beta-sheet connects residues 80-81 and 55-56 and thereby orients the two antiparallel beta-sheets relative to each other. Four beta-turns are identified, involving residues 50-53, 56-59, 64-67, and 73-76. Residues 78-82 adopt an extended bend structure. On the basis of secondary structure and the location of the three disulfide bonds, we find that Asp 46, Asp 48, and Hya 63 are sufficiently close to each other to form a Ca2(+)-binding site. However, the amino terminus of the Ca2(+)-free form of fX-EGFN is not part of a triple-stranded beta-sheet as in other EGF like peptides. Differences and similarities between fX-EFGN and murine EGF with respect to secondary structure and conformational shifts are discussed.
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility (2009)

We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid-based docking method and a modification of the flexible sidechain technique.
Microfabricated suspensions for electrical connections on the tunable elastomer membrane (2004)

Electrical connections through microfabricated suspensions on a pneumatically pumped elastomer membrane were demonstrated. A method to fabricate the suspensions on the elastomer membrane was developed. The elastomer membrane was 1 mm in diameter and 120 μm in thickness. Resistances of the microfabricated suspensions measured across the elastomer membrane were within 1% difference when the membrane’s center deflection ranged from 0 to 100 μm, which corresponded to a numerical aperture change from 0 to 0.2 as well as a 2.6% elongation of the elastomer.
Phosphorylation of parathyroid hormone by human and bovine parathyroid glands. (1984)

Human and bovine parathyroid gland slices were incubated in vitro for varying time periods with inorganic 32P and [35S]methionine or [3H]serine. Tissue was then extracted with aqueous medium, and parathyroid hormone (PTH) purified. Incorporated 32P was found to coelute with immunoreactive PTH in multiple chromatographic systems, and a peak of phosphorylated material could be resolved from the nonphosphorylated hormone by reversed phase high pressure liquid chromatography. The amino acid composition of both the phosphorylated and the nonphosphorylated entities conformed to that of the major glandular species of PTH, and phosphorylated hormone accounted for 10-20% of the total. A time course revealed slow incorporation of 32P into hormone, and after a 4-h preincubation with inorganic 32P, co-elution of 32P with both PTH and its precursor was observed. Phosphoserine was identified in purified PTH labeled with [3H]serine. Additionally dilute acid hydrolysis of PTH, labeled with [35S]methionine and containing 32P, generated an 35S-labeled fragment with which 32P co-chromatographed. The results are consistent with in vitro phosphorylation of PTH on serine residues within the NH2-terminal region of the hormone by both human and bovine glands and suggest that phosphorylation of the prohormone occurs as well.
The Desk encyclopedia of microbiology (2004)

Adhesion, Bacterial Agrobacterium and Plant Cell Transformation Antibiotic Resistance in Bacteria Antifungal Agents Antisense RNAs Antiviral Agents Archaea Attenuation, Transcriptional Bacillus subtilis, Genetics Bacteriophages Biocides: Nonpublic Health, Nonagricultural Antimicrobials Biofilms and Biofouling Biological Warfare Bioluminescence, Microbial Bioreactors Bioremedation Biosensors Cell Membrane: Structure and Function Cell Walls, Bacterial Chemotaxis Chromosome, Bacterial Conjugation, Bacterial Crystalline Bacterial Cell Surface Layers (S Layers) Culture Collections and Their Databases Developmental Processes in Bacteria Diversity, Microbial DNA Repair DNA Replication DNA Restriction and Modification DNA Sequencing and Genomics Ecology, Microbial Emerging Infections Energy Transduction Processes Enteropathogenic Bacteria Escherichia coli and Salmonella, Genetics Exotoxins Extremophiles Fimbriae, Pili Flagella Foodborne Illnesses Fungal Infections, Cutaneous Fungal Infections, Systemic Gastrointestinal Microbiology Genetically Modified Organisms: Guidelines and Regulations for Research Genomes, Mapping of Bacterial Germfree Animal Techniques Gram-Negative Anaerobic Pathogens Gram-Negative Cocci, Pathogenic Heat Stress Horizontal Transfer of Genes Between Microorganisms Human Immunodeficiency Virus (HIV) Identification of Bacteria, Computerized Industrial Fermentation Processes Insects' Symbiotic Microorganisms Iron Metabolism Lipopolysaccharides Methanogenesis Methylotrophy Nitrogen Cycle Nitrogen Fixation Nodule Formation in Legumes Nutrition of Microorganisms Oral Microbiology Osmotic Stress Outer Membrane, Gram-Negative Bacteria Oxidative Stress pH Stress Plant Pathogens Plasmids, Bacterial Polymerase Chain Reaction (PCR) Prions Protein Secretion Quorum-Sensing in Gram-Negative Bacteria Recombinant DNA, Basic Procedures Sexually Transmitted Diseases Skin Microbiology Soil Microbiology SOS Response Space Flight, Effects on Microorganisms Sporulation Starvation, Bacterial Strain improvement Sulfur Cycle Transcriptional Regulation Transduction: Host DNA Transfer by Bacteriophages Transformation, Genetic Transposable Elements Two-Component Systems Vaccines, Bacterial Vaccines, Viral Viruses Viruses, Emerging Yeasts
The Characterization and Cycloaddition Reaction of 5,6-Dihydro-1,3-dimethyl-6-methylene-5-[(substituted amino)methylene]-2,4(1H,H)-pyrimidinediones (1990)

Abstract 5,6-Dihydro-1,3-dimethyl-6-methylene-5-[(substituted amino)methylene]-2,4(1H,3H)-pyrimidinedione intermediates (E) were characterized spectroscopically and chemically. The cycloaddition reaction of E with olefinic dienophiles was carried out in highly regio- and stereoselective manners to give quinazoline derivatives.
Interleukin-12: Biological Properties and Clinical Application (2007)

Interleukin-12 (IL-12) is a heterodimeric protein, first recovered from EBV-transformed B cell lines. It is a multifunctional cytokine, the properties of which bridge innate and adaptive immunity, acting as a key regulator of cell-mediated immune responses through the induction of T helper 1 differentiation. By promoting IFN-gamma production, proliferation, and cytolytic activity of natural killer and T cells, IL-12 induces cellular immunity. In addition, IL-12 induces an antiangiogenic program mediated by IFN-gamma-inducible genes and by lymphocyte-endothelial cell cross-talk. The immunomodulating and antiangiogenic functions of IL-12 have provided the rationale for exploiting this cytokine as an anticancer agent. In contrast with the significant antitumor and antimetastatic activity of IL-12, documented in several preclinical studies, clinical trials with IL-12, used as a single agent, or as a vaccine adjuvant, have shown limited efficacy in most instances. More effective application of this cytokine, and of newly identified IL-12 family members (IL-23 and IL-27), should be evaluated as therapeutic agents with considerable potential in cancer patients.