gebhart/patrepeval huggingface dataset:
Screening for in vivo protein-protein interactions. (1993)

We describe an in vivo approach for the isolation of proteins interacting with a protein of interest. The protein of interest is "tagged" with a portion of the biotin carboxylase carrier protein (BCCP), encoded on a specially constructed plasmid, so that it becomes biotinylated in vivo. The "query" proteins (e.g., those in a cDNA library) are tagged by fusing them to the 3' end of the lacZ gene on a lambda vector in such a way that the beta-galactosidase activity is not disrupted. These phage are transfected into cells containing the plasmid encoding the BCCP-tagged protein. The infection lyses the cells and exposes the protein complexes. The BCCP-tagged protein and any associated protein(s) are "captured" by using avidin, streptavidin, or anti-biotin antibody-coated filters. The detection of bound protein is accomplished by directly assaying for beta-galactosidase activity on the filters. Positive plaques can be plaque-purified for DNA sequencing. We have tested this approach by using c-Fos and c-Jun as our model system. We show that avidin, streptavidin, or polyclonal anti-biotin (but not a monoclonal anti-biotin) antibody is capable of specifically capturing in vivo biotinylated beta-galactosidase and c-Jun and that this capture is dependent upon the presence of both avidin and the BCCP moiety. Further, complexes containing c-Jun and c-Fos can also be isolated in this manner, and the isolation of this complex is dependent on the presence of c-Fos, c-Jun, avidin, and the BCCP moiety. We discuss the possible uses and limitations of this technique for isolating proteins that interact with a known protein.
Mechanisms of resistance to quinolones: target alterations, decreased accumulation and DNA gyrase protection (2003)

Quinolones are broad-spectrum antibacterial agents, commonly used in both clinical and veterinary medicine. Their extensive use has resulted in bacteria rapidly developing resistance to these agents. Two mechanisms of quinolone resistance have been established to date: alterations in the targets of quinolones, and decreased accumulation due to impermeability of the membrane and/or an overexpression of efflux pump systems. Recently, mobile elements have also been described, carrying the qnr gene, which confers resistance to quinolones.
Evidence fordx2−y2Pairing from the Magnetic Field Modulation of YBa2Cu3O7-Pb Josephson Junctions (1995)

We have measured the magnetic field modulation of the critical current of YBCO-Au-Pb Josephson junctions fabricated on the $a$ and $b$ edges and straddling the $a\ensuremath{-}b$ corners of YBCO single crystals. In corner junctions, the critical current drops sharply at zero applied field and increases as the field is increased in either direction, in sharp contrast to the Fraunhofer diffraction patterns observed for single edge junctions. This behavior signifies a sign change of the order parameter between the $a$ and $b$ directions, strong direct evidence that the superconducting pairing state of YBCO has ${d}_{{x}^{2}\ensuremath{-}{y}^{2}}$ symmetry.
Smart Charging for Electric Vehicles: A Survey From the Algorithmic Perspective (2016)

Smart interactions among the smart grid, aggregators, and EVs can bring various benefits to all parties involved, e.g., improved reliability and safety for the smart gird, increased profits for the aggregators, as well as enhanced self benefit for EV customers. This survey focuses on viewing this smart interactions from an algorithmic perspective. In particular, important dominating factors for coordinated charging from three different perspectives are studied, in terms of smart grid oriented, aggregator-oriented, and customer-oriented smart charging. Firstly, for smart grid oriented EV charging, we summarize various formulations proposed for load flattening, frequency regulation, and voltage regulation, then explore the nature and substantial similarity among them. Secondly, for aggregator-oriented EV charging, we categorize the algorithmic approaches proposed by research works sharing this perspective as direct and indirect coordinated control, and investigate these approaches in detail. Thirdly, for customer-oriented EV charging, based on a commonly shared objective of reducing charging cost, we generalize different formulations proposed by studied research works. Moreover, various uncertainty issues, e.g., EV fleet uncertainty, electricity price uncertainty, regulation demand uncertainty, etc., have been discussed according to the three perspectives classified. At last, we discuss challenging issues that are commonly confronted during modeling the smart interactions, and outline some future research topics in this exciting area.
The opioid receptors as targets for drug abuse medication (2015)

The endogenous opioid system is largely expressed in the brain, and both endogenous opioid peptides and receptors are present in areas associated with reward and motivation. It is well known that this endogenous system plays a key role in many aspects of addictive behaviours. The present review summarizes the modifications of the opioid system induced by chronic treatment with drugs of abuse reported in preclinical and clinical studies, as well as the action of opioid antagonists and agonists on the reinforcing effects of drugs of abuse, with therapeutic perspectives. We have focused on the effects of chronic psychostimulants, alcohol and nicotine exposure. Taken together, the changes in both opioid peptides and opioid receptors in different brain structures following acute or chronic exposure to these drugs of abuse clearly identify the opioid system as a potential target for the development of effective pharmacotherapy for the treatment of addiction and the prevention of relapse.
Transcellular Delivery of an Insulin-Transferrin Conjugate in Enterocyte-like Caco-2 Cells (1996)

Insulin, acylated with dimethylmaleic anhydride, was conjugated to transferrin (Tf) via a disulfide linkage. The molar insulin: Tf ratio in the conjugate was 3:1. The insulin-Tf conjugate (insulin-Tf) was tested for the transport of insulin across enterocyte-like Caco-2 cell monolayers by the process of transferrin receptor (TfR)-mediated transcytosis. The uptake of insulin-Tf in Caco-2 cells was TfR-mediated but no insulin receptor-mediated. Transport studies showed that insulin-Tf transport was 5- to 15-fold higher than free insulin transport across Caco-2 cells in both apical-to-basal and basal-to-apical directions. Brefeldin A (BFA), an agent that we have previously shown to cause an increase in TfR transcytosis, further enhanced the transport of the conjugated insulin three-fold in both directions; thus, a combination of the conjugate and BFA can cause a net 45-fold increase in the apical-to-basolateral transport of insulin across Caco-2 cell monolayers. The transported conjugate was intact as indicated by elution on a Sephadex G-50 column. Insulin in the transcytosed conjugate, unlike the original dimethylmaleyl insulin, was capable of binding to anti-insulin antibodies, indicating that free amino groups of insulin were regenerated either during or after the transcytotic process. Because Caco-2 cell monolayers provide a good model for intestinal epithelium, the insulin-Tf conjugate in combination with BFA can be a rational approach to increase the oral absorption of insulin in vivo.
Nanorod‐Coated PNIPAM Microgels: Thermoresponsive Optical Properties (2007)

Nanoparticles and in particular gold nanorods have interesting optical properties arising from two well-differentiated plasmon modes. The frequency of such modes can be altered by their chemical environment and coupling with neighboring rods. This study investigates new composite materials made of gold nanorods adsorbed on thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) microgels. It is shown that the thermally induced collapse of the polymer network inside the particles leads to a red shift of the longitudinal plasmon band of the gold rods, which is found to be fully reversible.
Confinement-Dependent Below-Gap State in PbS Quantum Dot Films Probed by Continuous-Wave Photoinduced Absorption (2008)

We have measured continuous-wave (cw) photoinduced absorption (PA) spectra of PbS quantum dot (QD) films with four different sizes over a spectral range of 0.25-0.5 eV at T=10 K. The PA spectrum shows a strong asymmetric IR absorption peak (IR-PA). Both the peak position and shape of this IR-PA indicate distinct confinement dependence. Combining with results of interband transitions and Stokes shift, we assign this IR-PA to a transition from a well-defined below-gap state to the second excitonic level (1P). By measuring the frequency dependence of this IR-PA, we estimate the lifetime of this below-gap state to be around several microseconds. Possible interpretations of the origin of this below-gap state are given. This transition could potentially be used to monitor photogenerated charge transfer in such QD systems.
Site-specific vibrational dynamics of the CD3ζ membrane peptide using heterodyned two-dimensional infrared photon echo spectroscopy (2004)

Heterodyned two-dimensional infrared (2D IR) spectroscopy has been used to study the amide I vibrational dynamics of a 27-residue peptide in lipid vesicles that encompasses the transmembrane domain of the T-cell receptor CD3ζ. Using 1–13C=18O isotope labeling, the amide I mode of the 49-Leucine residue was spectroscopically isolated and the homogeneous and inhomogeneous linewidths of this mode were measured by fitting the 2D IR spectrum collected with a photon echo pulse sequence. The pure dephasing and inhomogeneous linewidths are 2 and 32 cm−1, respectively. The population relaxation time of the amide I band was measured with a transient grating, and it contributes 9 cm−1 to the linewidth. Comparison of the 49-Leucine amide I mode and the amide I band of the entire CD3ζ peptide reveals that the vibrational dynamics are not uniform along the length of the peptide. Possible origins for the large amount of inhomogeneity present at the 49-Leucine site are discussed.
Tetrahydrobiopterin Uptake in Supplemental Administration: Elevation of Tissue Tetrahydrobiopterin in Mice Following Uptake of the Exogenously Oxidized Product 7,8-Dihydrobiopterin and Subsequent Reduction by an Anti-folate-Sensitive Process (2004)

In order to increase the tissue level of tetrahydrobiopterin (BH4), supplementation with 6R-tetrahydrobiopterin (6RBH4) has been widely employed. In this work, the effectiveness of 6RBH4 was compared with 7,8-dihydrobiopterin (7,8BH2) and sepiapterin by administration to mice. Administration of 6RBH4 was the least effective in elevating tissue BH4 levels in mice while sepiapterin was the best. In all three cases, a dihydrobiopterin surge appeared in the blood. The appearance of the dihydrobiopterin surge after BH4 treatment suggested that systemic oxidation of the administered BH4 had occurred before accumulation of BH4 in the tissues. This idea was supported by the following evidences: 1) An increase in tissue BH4 was effectively inhibited by methotrexate, an inhibitor of dihydrofolate reductase which reduces 7,8BH2 to BH4. 2) When the unnatural diastereomer 6SBH4 was administered to mice, a large proportion of the recovered BH4 was in the form of the 6R-diastereomer, suggesting that this BH4 was the product of a dihydrofolate reductase process by which 7,8BH2 converts to 6RBH4. These results indicated that the exogenous BH4 was oxidized and the resultant 7,8BH2 circulated through the tissues, and then it was incorporated by various other tissues and organs through a pathway shared by the exogenous sepiapterin and 7,8BH2 in their uptake. It was demonstrated that maintaining endogenous tetrahydrobiopterin in tissues under ordinary conditions was also largely dependent on an methotrexate-sensitive process, suggesting that cellular tetrahydrobiopterin was maintained both by de novo synthesis and by salvage of extracellular dihydrobiopterin.
Sampling procedural shaders using affine arithmetic (1998)

Procedural shaders have become popular tools for describing surface reflectance functions and other material properties. In comparison to fixed resolution textures, they have the advantage of being resolution-independent and storage-efficient. While procedural shaders provide an interface for evaluating the shader at a single point, it is not easily possible to obtain an average value of the shader together with accurate error bounds over a finite area. Yet the ability to compute such error bounds is crucial for several interesting applications, most notably heirarchical area sampling for global illumination, using the finite element approach, and for generation of textures used in interactive computer graphics. Using affine arithmetic for evaluating the shader over a finite area yields a tight, conservative error interval for the shader function. Compilers can automatically generate code for utilizing affine arithmetic from within shaders implemented in a dedicated language such as the RenderMann shading language.
Molecular and Biochemical Characterization of Postharvest Senescence in Broccoli (2001)

Postharvest senescence in broccoli (Brassica oleracea L. var Italica) florets results in phenotypic changes similar to those seen in developmental leaf senescence. To compare these two processes in more detail, we investigated molecular and biochemical changes in broccoli florets stored at two different temperatures after harvest. We found that storage at cooler temperatures delayed the symptoms of senescence at both the biochemical and gene expression levels. Changes in key biochemical components (lipids, protein, and chlorophyll) and in gene expression patterns occurred in the harvested tissue well before any visible signs of senescence were detected. Using previously identified senescence-enhanced genes and also newly isolated, differentially expressed genes, we found that the majority of these showed a similar enhancement of expression in postharvest broccoli as in developmental leaf senescence. At the biochemical level, a rapid loss of membrane fatty acids was detected after harvest, when stored at room temperature. However, there was no corresponding increase in levels of lipid peroxidation products. This, together with an increased expression of protective antioxidant genes, indicated that, in the initial stages of postharvest senescence, an orderly dismantling of the cellular constituents occurs, using the available lipid as an energy source. Postharvest changes in broccoli florets, therefore, show many similarities to the processes of developmental leaf senescence.
Multiarchitectonic and stereotactic atlas of the human thalamus (1997)

To improve anatomical definition and stereotactic precision of thalamic targets in neurosurgical treatments of chronic functional disorders, a new atlas of the human thalamus has been developed. This atlas is based on multiarchitectonic parcellation in sections parallel or perpendicular to the standard intercommissural reference plane. The calcium-binding proteins parvalbumin (PV), calbindin D-28K (CB), and calretinin (CR) were used as neurochemical markers to further characterize thalamic nuclei and delimit subterritories of functional significance for stereotactic explorations. Their overall distribution reveals a subcompartmentalization of thalamic nuclei into several groups. Predominant PV immunostaining characterizes primary somatosensory, visual and auditory nuclei, the ventral lateral posterior nucleus, reticular nucleus (R), and to a lesser degree also, lateral part of the centre médian nucleus, and anterior, lateral, and inferior divisions of the pulvinar complex. In contrast, CB immunoreactivity is prevalent in medial thalamic nuclei (intralaminar and midline), the posterior complex, ventral posterior inferior nucleus, the ventral lateral anterior nucleus, ventral anterior, and ventral medial nuclei. The complementary distributions of PV and CB appear to correlate with distinct lemniscal and spinothalamic somatosensory pathways and to cerebellar and pallidal motor territories, respectively. Calretinin, while overlapping with CB in medial thalamic territories, is also expressed in R and limbic associated anterior group nuclei that contain little or no CB. Preliminary analysis indicates that interindividual nuclear variations cannot easily be taken into account by standardization procedures. Nevertheless, some corrections in anteroposterior coordinates in relation to different intercommissural distances are proposed. J. Comp. Neurol. 387:588–630, 1997. © 1997 Wiley-Liss, Inc.
Isolation and characterization of a cDNA and gene coding for a fourth CD1 molecule. (1989)

The CD1 locus encodes a family of major histocompatibility complex (MHC) antigen-like glycoproteins which associate with beta 2-microglobulin and are expressed on immature thymocytes and Langerhans cells. Three CD1 molecules have been identified by monoclonal antibodies and molecular cloning: CD1a, -b, and -c. We have isolated a cDNA coding for a fourth CD1 molecule from a human thymocyte library and termed this molecule CD1d. Reported here are the complete nucleotide sequence and genomic organization of CD1d. They predict that this molecule is related to the previously identified CD1a, -b, and -c molecules and to MHC class I molecules, with three external domains, a transmembrane domain, and a short cytoplasmic tail. The sequence of CD1d is the most divergent among the CD1 molecules in the membrane-distal alpha 1 and alpha 2 domains and in the 5' untranslated region. In contrast, all four CD1 molecules are highly homologous in the membrane-proximal alpha 3 domain, which is likely involved in beta 2-microglobulin binding. A comparison of CD1 and MHC class I sequences suggests that these molecules each evolved to interact with a distinct set of cell surface proteins.
Integrated Processing of Satellite Orbit and Satellite Gradiometry Data (1992)

A gravity gradiometry mission was proposed to reach progress in high resolution gravity field determination. It is well known that a low orbiter will be launched in the late nineties. ARISTOTELES will carry a payload consisting of a two-axis gradiometer and a GPS receiver. It is intended to place ARISTOTELES in a near polar orbit of about 200 km height.
Specific features of the catalytic behavior of supported palladium nanoparticles in heterogeneous catalytic reactions (2010)

Specific features of the catalytic behavior of supported palladium nanoparticles were analyzed in terms of both the size of the particles and their interaction with the support. The influence of these factors on the activity and selectivity of palladium nanoparticles in carbon-carbon bond hydrogenolysis, hydrogenation of aromatic compounds, olefins, and acetylenes, hydrodechlorination, as well as complete oxidation of organic compounds was discussed. It was shown that the optimal nanoparticle size depends on the type of the reaction and also such factors as the nature of interaction between the nanoparticles and support, absorptivity of the substrates and catalytic reaction products, and electronic and crystal structure of the nanoparticles.
The Pluses of Subtraction (1993)

A general problem in genetics is the identification of specific DNA sequence differences underlying phenotypic variation. These differences can be foreign DNA segments from an infecting pathogen that integrate into a host genome, spontaneously arising DNA rearrangements or point mutations that cause cancer in somatic tissues, or a wide variety of induced and naturally occurring mutations that are transmitted from generation to generation, often resulting in genetic diseases in humans. Each of these situations requires a somewhat different approach to identify the particular DNA difference in the genomes of the unaffected and the affected cell or organism that causes the phenotype. But, as a rule for all of these cases, the larger the genome or the smaller the DNA difference, the more difficult it is to find. In this issue of Science, Lisitsyn and co-workers (1) describe a new method, based on the principles of subtractive hybridization, for cloning even the smallest DNA differences between two or more complex genomes that shows great promise for speeding up this rate-limiting step in genetic analysis.
Cell-Penetrant, Nanomolar O-GlcNAcase Inhibitors Selective against Lysosomal Hexosaminidases (2010)

Posttranslational modification of metazoan nucleocytoplasmic proteins with N-acetylglucosamine (O-GlcNAc) is essential, dynamic, and inducible and can compete with protein phosphorylation in signal transduction. Inhibitors of O-GlcNAcase, the enzyme removing O-GlcNAc, are useful tools for studying the role of O-GlcNAc in a range of cellular processes. We report the discovery of nanomolar OGA inhibitors that are up to 900,000-fold selective over the related lysosomal hexosaminidases. When applied at nanomolar concentrations on live cells, these cell-penetrant molecules shift the O-GlcNAc equilibrium toward hyper-O-GlcNAcylation with EC₅₀ values down to 3 nM and are thus invaluable tools for the study of O-GlcNAc cell biology.
Sphingosine Kinase-1 as a Chemotherapy Sensor in Prostate Adenocarcinoma Cell and Mouse Models (2005)

Systemic chemotherapy was considered of modest efficacy in prostate cancer until the recent introduction of taxanes. We took advantage of the known differential effect of camptothecin and docetaxel on human PC-3 and LNCaP prostate cancer cells to determine their effect on sphingosine kinase-1 (SphK1) activity and subsequent ceramide/sphingosine 1-phosphate (S1P) balance in relation with cell survival. In vitro, docetaxel and camptothecin induced strong inhibition of SphK1 and elevation of the ceramide/S1P ratio only in cell lines sensitive to these drugs. SphK1 overexpression in both cell lines impaired the efficacy of chemotherapy by decreasing the ceramide/S1P ratio. Alternatively, silencing SphK1 by RNA interference or pharmacologic inhibition induced apoptosis coupled with ceramide elevation and loss of S1P. The differential effect of both chemotherapeutics was confirmed in an orthotopic PC-3/green fluorescent protein model established in nude mice. Docetaxel induced a stronger SphK1 inhibition and ceramide/S1P ratio elevation than camptothecin. This was accompanied by a smaller tumor volume and the reduced occurrence and number of metastases. SphK1-overexpressing PC-3 cells implanted in animals developed remarkably larger tumors and resistance to docetaxel treatment. These results provide the first in vivo demonstration of SphK1 as a sensor of chemotherapy.
Detection of tumor necrosis factor α but not tumor necrosis factor β in rheumatoid arthritis synovial fluid and serum (1988)

Synovial fluids from 6 of 12 patients with rheumatoid arthritis (RA) and from 3 of 11 patients with reactive arthritis contained measurable levels of tumor necrosis factor alpha (TNF alpha). Seven of 12 sera from RA patients contained TNF alpha, while only 1 of those from reactive arthritis patients was positive. Gamma-interferon was detected in the synovial fluids and sera of only the RA patients. Tumor necrosis factor beta was not detected in any sera or synovial fluids. RA patients with detectable TNF alpha had higher erythrocyte sedimentation rates and synovial fluid leukocyte counts.