gebhart/patrepeval huggingface dataset:
Effects of Phosphorylation by CAK on Cyclin Binding by CDC2 and CDK2 (1995)

The cyclin-dependent protein kinases (CDKs) are activated by association with cyclins and by phosphorylation at a conserved threonine residue by the CDK-activating kinase (CAK). We have studied the binding of various human CDK and cyclin subunits in vitro, using purified proteins derived from baculovirus-infected insect cells. We find that most CDK-cyclin complexes known to exist in human cells (CDC2-cyclin B, CDK2-cyclin A, and CDK2-cyclin E) form with high affinity in the absence of phosphorylation or other cellular components. One complex (CDC2-cyclin A) forms with high affinity only after CAK-mediated phosphorylation of CDC2 at the activating threonine residue. CDC2 does not bind with high affinity to cyclin E in vitro, even after phosphorylation of the CDC2 subunit. Thus, phosphorylation is of varying importance in the formation of high-affinity CDK-cyclin complexes.
Tumor-Derived Microvesicles Induce Proangiogenic Phenotype in Endothelial Cells via Endocytosis (2012)

We for the first time showed that endocytosis of TMV contributes to tumor angiogenesis. These findings offer new insights into cancer therapies and the crosstalk between tumor and endothelial cells mediated by TMV in the tumor microenvironment.
In vivo and in vitro characterization of long-term repopulating primitive hematopoietic cells isolated by sequential Hoechst 33342-rhodamine 123 FACS selection. (1993)

Subpopulations of very primitive hematopoietic cells were isolated by fluorescence-activated cell sorter (FACS) selection of density gradient-enriched, lineage-depleted marrow cells with blast cell light scatter characteristics that bound low levels of the DNA binding dye, Hoechst 33342 (Hö) and retained differential amounts of the mitochondrial binding dye, rhodamine 123 (Rh-123). The dyes were used sequentially in a single sorting operation. The subfractions of cells that stained most weakly with both dyes were highly coenriched for long-term repopulating cells (LTRC) and for in vitro high proliferative potential colony-forming cells (HPP-CFC). Furthermore, as populations of cells were progressively selected on the basis of decreasing Hö and Rh-123 fluorescence, first the CFU-S-8, then the CFU-S-12 diminished or disappeared entirely in the lowest Rh-123 fraction. In these low fluorescent populations, plating efficiency for HPP-CFC was very high when cultured in the combined presence of recombinant rat stem cell factor (rrSCF), recombinant human interleukin-1 (rhIL-1), recombinant murine interleukin-3 (rmIL-3) and recombinant human colony-stimulating factor-1 (rhCSF-1), apparently reaching 100% in some instances. When 20 male donor cells from this lowest fluorescent Hö/Rh-123 fraction were injected into lethally irradiated female recipients, along with a "compromised" marrow cell population (3x previously transplanted nonsorted female bone marrow cells), the sorted male donor cells were able to completely and exclusively repopulate the myeloid and the lymphoid B and T cell compartments of the recipients for at least 10 months posttransplant. Assays of cell fractions that were relatively more Rh-123 fluorescent demonstrated the presence of cell with progressively less repopulating capacity. When descendants of transplanted low fluorescent Rh-123 selected cells, as found in 12-day spleen colonies, were assayed for the capacity to provide long-term survival in secondary recipients, they were able to do so in a high proportion of lethally irradiated recipients. However, spleen colonies derived from the mid-high fluorescence fraction were completely unable to do so. In summary, we have demonstrated with a sequential Hö/Rh-123 sorting system that a subset of HPP-CFC cofractionate with LTRC with high frequency. Using this system, the enrichment of LTRC in the lowest Rh-123 compartment of the sequentially Hö/Rh-123 selected cells appears to be the greatest demonstrated thus far. In addition, this study further supports previous ones that identify a compartment of LTRC that are largely distinct from CFU-S-12.
A microRNA-regulated lentiviral vector mediates stable correction of hemophilia B mice (2007)

A longstanding goal for the treatment of hemophilia B is the development of a gene transfer strategy that can maintain sustained production of clotting factor IX (F.IX) in the absence of an immune response. To this end, we have sought to use lentiviral vectors (LVs) as a means for systemic gene transfer. Unfortunately, initial evaluation of LVs expressing F.IX from hepatocyte-specific promoters failed to achieve sustained F.IX expression in hemophilia B mice due to the induction of an anti-F.IX cellular immune response. Further analysis suggested that this may be a result of off-target transgene expression in hematopoietic-lineage cells of the spleen. In order to overcome this problem, we modified our vector to contain a target sequence for the hematopoietic-specific microRNA, miR-142-3p. This eliminated off-target expression in hematopoietic cells, and enabled sustained gene transfer in hemophilia B mice for more than 280 days after injection. Treated mice had more than 10% normal F.IX activity, no detectable anti-F.IX antibodies, and were unresponsive to F.IX immunization. Importantly, the mice survived tail-clip challenge, thus demonstrating phenotypic correction of their bleeding diathesis. This work, which is among the first applications to exploit the microRNA regulatory pathway, provides the basis for a promising new therapy for the treatment of hemophilia B.
Heavy and Light Chain Variable Single Domains of an Anti-DNA Binding Antibody Hydrolyze Both Double- and Single-stranded DNAs without Sequence Specificity (2006)

Anti-DNA antibodies (Abs) are of biomedical interest because they are associated with autoimmune diseases in human and mice. Previously we isolated an anti-DNA monoclonal Ab 3D8 from an autoimmune-prone MRL-lpr/lpr mouse. Here we have characterized DNA binding kinetics and hydrolyzing activities of the recombinant single chain variable fragment (scFv) and the single variable domains of heavy chain (VH) and light chain (VL) using various single-stranded (ss) and double-stranded (ds) DNA substrates. All the Abs bound to both ds- and ssDNAs without significant preferential sequence specificity showing scFv higher affinities (KD = approximately 17-74 nm) than VH (KD = approximately 2.4-8.4 microm) and VL (KD = approximately 3.2-72 microm), and efficiently hydrolyzed both ds- and ssDNAs without sequence specificity in a Mg2+-dependent manner, except for the poor activity of 3D8 scFv for ss-(dT)40. Elucidated crystal structure-based His to Ala mutations on the complementarity determining regions of VH (His-H35 --> Ala) and/or VL (His-L94 --> Ala) of 3D8 scFv significantly inhibited the catalytic activities, indicating that the His residues are involved in the catalytic mechanism of 3D8 scFv. However, the DNA hydrolyzing activities of single domain VH and VL were not affected by the mutations, indicative of their different catalytic mechanisms from that of 3D8 scFv. Our results demonstrate single domain Abs with DNase activities for the first time, which might provide new insights into substrate recognition and catalytic mechanisms of anti-DNA Abs.
Detection and sequencing of phosphopeptides (2000)

Consecutive enzymatic reactions of analytes which are affinity bound to immobilized metal ion beads with subsequent direct analysis of the products by matrix-assisted laser desorption/ionization mass spectrometry have been used for detecting phosphorylation sites. The usefulness of this method was demonstrated by analyzing two commercially available phosphoproteins, beta-casein and alpha-casein, as well as one phosphopeptide from a kinase reaction mixture. Agarose loaded with either Fe3+ or Ga3+ was used to isolate phosphopeptides from the protein digest. Results from using either metal ion were complementary. Less overall suppression effect was achieved when Ga3+-loaded agarose was used to isolate phosphopeptides. The selectivity for monophosphorylated peptides, however, was better with Fe3+-loaded agarose. This technique is easy to use and has the ability to analyze extremely complicated phosphopeptide mixtures. Moreover, it eliminates the need for prior high-performance liquid chromatography separation or radiolabeling, thus greatly simplifying the sample preparation.
The Nuclear Receptor Superfamily (2009)

Acting principally to control patterns of gene expression, nuclear receptors play vital roles during embryonic development and in the regulation of metabolic and reproductive functions in adult life, which proves this superfamily of ligand-activated transcription factors to be a crucial part of biological life. In The Nuclear Receptor Superfamily: Methods and Protocols, expert researchers describe a range of molecular, structural and cell biological techniques currently used to investigate the structure-function of nuclear receptors, together with experimental approaches that may lead to new therapeutic strategies for treating nuclear receptor-associated diseases. Written in the highly successful Methods in Molecular Biology™ series format, the chapters in this volume contain brief introductions to the topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, as well as notes from the experts to highlight tips on troubleshooting and avoiding known pitfalls. Cutting-edge and easy to use, The Nuclear Receptor Superfamily: Methods and Protocols provides beneficial and time-saving guidance for all those undertaking research in this ever-growing field of study
Purification and Properties of Human Factor IXa (1976)

Summary Human factor IXa was purified 5,000-fold from serum by ion exchange chromatography. The preparation was free from other clotting factors. Both pH sensitivity and heat stability of purified factor IXa appeared to be different from those of factor IX in the plasma. The molecular weight of human factor IXa is 80,000 as estimated from gel-filtration experiments. Modification of seryl or histidyl side chains abolished the activity of factor IXa.
Multiring Fiducial Systems for Scalable Fiducial-Tracking Augmented Reality (2001)

In augmented reality (AR), a user can see a virtual world as well as the real world. To avoid registration problems between the virtual world and the real world, the user's viewing pose in both worlds should be kept the same. Fiducial-tracking AR is an attractive approach to the registration problem. However, most of the developed fiducialtracking AR systems have restricted workspaces. To provide a wide range of workspaces (from a small-scale desktop space to a large-scale space) and a wide range of views (from far views to detailed views), an AR system should have scalability. In this paper, we present multiring color fiducial systems and a real-time fiducial detection method for scalable fiducial-tracking AR. We analyze the optimal ring width and develop formulas to obtain the optimal fiducial set with applicationspecific inputs. We develop a real-time ring-detection method that converts the five-DOF ellipse-detection problem to a series of simple steps with a 1-D segmentfilter and multithreshold segmentation. The results lead to a simple and inexpensive means of achieving scalable-area tracking for AR and an approach that is suitable as an optical tracking method for VR as well.
Fleet Management Using Inmarsat-C And GP - A Norwegian Pilot Project (2005)

This paper briefly describes the satellite communication system INMARSAT-C and the satellite navigation system GPS (Global Positioning System) and describes some applications related to them. Emphasis is given on a Norwegian pilot project known as the Sties Project, where a fleet management system using INMARSAT-C and GPS was tested in a real-life transport environment.
Practical guidelines for process validation and process control of white cell‐reduced blood components: report of the Biomedical Excellence for Safer Transfusion (BEST) Working Party of the International Society of Blood Transfusion (ISBT) (1996)

Guidelines are presented for process validation, process control, and assessment of conformance in the production of WBC-reduced blood components. Policy makers retain the responsibility to establish, on the basis of the expected use of WBC-reduced components, requirements for the frequency of testing and for the proportion of prepared units that are expected with a stated degree of confidence to meet the standards. Facilities preparing WBC-reduced components can monitor key factors that influence the preparation of WBC-reduced blood, can periodically assess their conformance with the standards, and can intervene to correct adverse changes in the process. This approach can be used to ensure the consistent quality of WBC-reduced blood components.
The T to R transition in the copper(II)-substituted insulin hexamer. Anion complexes of the R-state species exhibiting type 1 and type 2 spectral characteristics (1992)

The R-state conformation of the Cu(II)-substituted insulin hexamer has been identified, and a number of its derivatives have been studied via 1H NMR, ESR, and UV-visible spectroscopy. This work establishes that the Cu(II)-substituted insulin hexamer undergoes an analogous T to R conformational transition in solution that has been identified previously for Zn(II)- and Co(II)-insulin hexamers [Roy, M., Brader, M.L., Lee, R. W.-K., Kaarsholm, N.C., Hansen, J., & Dunn, M.F. (1989) J. Biol. Chem. 264, 19081-19085]. The data indicate that each Cu(II) center of the R-state Cu(II)-insulin hexamer possesses a coordination site that is accessible to anions from solution. Both phenol and anionic ligands that coordinate to the Cu(II) ions are required to generate the necessary heterotropic interactions that stabilize the R-state structure. With phenylmethylthiolate (PMT), a Cu(II)-R6 adduct that displays the spectral features of blue (type 1) copper proteins is obtained. This complex is proposed to embody a pseudotetrahedral CuIIN3S(PMT) chromophore, in which N is HisB10 (imidazolyl). The remaining ligands examined gave rise to Cu(II)-R6 adducts that possessed the spectral characteristics of normal (type 2) Cu(II) proteins. Under reducing conditions, Cu(I)-T6 and Cu(I)-R6 hexamers have been identified.
Nucleotide Sequence of a Soybean (Glycine max L. Merr.) Ubiquitin Gene (1994)

Ubiquitin is a polypeptide consisting of 76 amino acid residues and is present in all eukaryotes studied so far. It is one of the most highly conserved proteins known, differing at only 4 of 76 positions in such diverse organisms as yeast, maize, and human (Callis and Vierstra, 1989). The protein has been implicated in many vital cellular processes, such as protein turnover (Hershko, 1988), cell cycle control (Rechsteiner, 1991), response to heat shock, and resistance to heavy metal (Bond and Schlesinger, 1986; Jungmann et al., 1993). We report here the isolation and sequence determination of a genomic DNA that encodes a polyubiquitin in soybean (Glycine max L. Merr.). Soybean leaf genomic DNA was partially digested with Sau3AI and used to construct a library in BamHI-digested XEMBL3. Putative positive clones containing ubiquitin genes were isolated from the genomic DNA library, using a 1.1-kb EcoRI/HindIII fragment of the soybean cDNA clone pUBS6 (Fortin et al., 1988) as a probe. Thirteen positive plaques were identified by plaque hybridization and, after DNA preparation, the inserts of the 13 clones were subcloned into plasmid vector Bluescript II SK+. On the basis of restriction maps and hybridization data, the 13 genome clones could be divided into three types (data not shown). One of the clones, pSUB38 (Table I), was sequenced by a modified version of the dideoxy-chain termination method using an Applied Biosystems model 370 Sequencer. This soybean genomic DNA clone contained an insert of 2309 bp, including a 915bp ORF. To analyze the promoter of the ubiquitin gene in the 5' noncoding region, the upstream fragment was also sequenced. The 915-bp ORF encoding polyubiquitin was arranged as three tandem, head-to-tail, 228-bp repeats and a fourth, terminal repeat containing 231 bp. This ORF encodes a polypeptide of 305 amino acid residues. The first three repeats contained 76 amino acid residues each, whereas the terminal repeat contained an additional Phe residue. This additional amino acid is presumably removed during processing of the polyubiquitin to the mature monomers (Chrislensen et al., 1992). The amino acid sequence deduced for soybean polyubi-
Calcium Dependence of Toxic Cell Death: A Final Common Pathway (1979)

Primary cultures of adult rat hepatocytes were treated in the presence or absence of extracellular calcium with ten different membrane-active toxins. In all cases more than half the cells were killed in 1 to 6 hours in the presence but not in the absence of extracellular calcium. An effect of calcium on the primary mechanism of membrane injury by any of the agents cannot be implicated. Viability, as determined by trypan blue exclusion correlated well with other indices of viability such as plating efficiency and the hydrolysis of fluorescein diacetate. It is concluded that the cells are killed by processes that involve at least two steps. In each type of injury, disruption of the integrity of the plasma membrane by widely differing mechanisms is followed by a common functional consequence involving extracellular calcium, and most likely representing an influx of calcium across the damaged plasma membrane and down a steep concentration gradient. This later step represents, or at least initiates, a final common pathway for the toxic death of these cells.
Dye-sensitized nanostructured and organic photovoltaic cells: technical review and preliminary tests (2002)

The solar electricity is presently a rapidly growing but often relatively expensive renewable energyform. Recently however, new molecular photovoltaic (PV) materials have been developed, whichcould enable a production of low-cost solar cells in the future.\nThe thesis begins with a discussion of the current status of the PV technology and a shortintroduction to the different PV technologies and to the basics of photovoltaics.\nThe dye-sensitized solar cell (DSSC) is an electrochemical solar cell where light absorption occursby dye molecules attached to a nanostructured TiO2 electrode. An introduction to the DSSC is givenincluding a short description of the operating principle of the cell and a discussion of the physicaland chemical processes behind it. A systematic literature review is done on the materials and mostessential preparation methods of the standard DSSC.\nThe performance of the DSSC is reviewed in terms of the energy conversion efficiency and the longtermstability. The important directions of development are the transition from glass substrates toplastic foils and from batch processing to continuous processing as well as the use of solid stateelectrolytes. The glass-based DSSC technology is on the verge of commercialization and themanufacturing cost estimates for the technology are close to the projected costs of other PVtechnologies.\nThe purely organic solar cells are discussed individually beginning with the discussion of thefundamentals of organic photovoltaics and an introduction of different types of organic photovoltaicmaterials including semiconducting polymers, dyes, pigments and liquid crystalline materials. Areview is done on the performance results of organic solar cells categorizing the cells by their devicearchitecture. The development of the organic PV materials is still at an early stage and no clearlyoutperforming materials or cell structures have yet emerged.\nExperimental results are reported including a demonstration of the dye-sensitization with a naturaldye as well as a preparation and testing of a series of ruthenium-dye based DSSCs. An efficiency of0.6% at about 600 W/m2 solar illumination was obtained for the DSSCs in outdoor measurements.
Non-Uniform and Large Distance Constellation Design for Hierarchical Modulation (2010)

In this paper, we newly design a non-uniform QAM signal constellation, which could be appropriately applied for hierarchical modulation. This novel constellation is constructed by a certain number of equilateral triangles and hierarchically divided into two layers; one for MSB and the other for LSB. The advantage of using this constellation compared to uniform rectangular QAM constellation is that the MED for LSB is constantly maintained whereas the MED for MSB is remarkably increased. To this end, we evaluate the performance in terms of SER by means of link level simulation. Consequently, the newly designed constellation does not compromise the modulation performance between MSB and LSB, and the SNR gain of MSB as opposed to uniform rectangular QAM constellation reaches 0.5~0.8dB but without sacrificing the performance of LSB.
Born Again Neural Networks (2018)

Knowledge Distillation (KD) consists of transferring “knowledge” from one machine learning model (the teacher) to another (the student). Commonly, the teacher is a high-capacity model with formidable performance, while the student is more compact. By transferring knowledge, one hopes to benefit from the student’s compactness, without sacrificing too much performance. We study KD from a new perspective: rather than compressing models, we train students parameterized identically to their teachers. Surprisingly, these Born-Again Networks (BANs), outperform their teachers significantly, both on computer vision and language modeling tasks. Our experiments with BANs based on DenseNets demonstrate state-of-the-art performance on the CIFAR-10 (3.5%) and CIFAR-100 (15.5%) datasets, by validation error. Additional experiments explore two distillation objectives: (i) Confidence-Weighted by Teacher Max (CWTM) and (ii) Dark Knowledge with Permuted Predictions (DKPP). Both methods elucidate the essential components of KD, demonstrating the effect of the teacher outputs on both predicted and non-predicted classes.
DNA-Templated Carbon Nanotube Field-Effect Transistor (2003)

The combination of their electronic properties and dimensions makes carbon nanotubes ideal building blocks for molecular electronics. However, the advancement of carbon nanotube-based electronics requires assembly strategies that allow their precise localization and interconnection. Using a scheme based on recognition between molecular building blocks, we report the realization of a self-assembled carbon nanotube field-effect transistor operating at room temperature. A DNA scaffold molecule provides the address for precise localization of a semiconducting single-wall carbon nanotube as well as the template for the extended metallic wires contacting it.
Electrochemical Investigations into the Binding of Some Nonredox Active Metal Ions to Surface-Bound Glutamic Acid Conjugates (2007)

A number of ferrocene glutamic acid cystamine conjugates suitable for the preparation of thin film on gold were prepared and fully characterized electrochemically and spectroscopically. In this study, we evaluate the interactions of nonelectroactive metal ions such as Ca2+ and Tb3+ ions using a combined electrochemical and spectroscopic approach. Cyclic voltammetry studies show a reversible one-electron redox behavior associated with the ferrocene group. These peptide interfaces exhibit a considerable affinity to bind Ca2+ and Tb3+ ions from aqueous solutions with log K ∼ 3. In the presence of metal ion, the charge associated with oxidation of the ferrocene group decreases in line with a blockage of the formation of Fc+/ClO4- ion pair by the formation of an overlayer on top of the film, which essentially shuts down the oxidation of the Fc group. The resulting increase in the film thickness is monitored by X-ray photoelectron spectroscopy (XPS) and by a decrease in the capacitance as monitored by electrochemical impedance spectroscopy. XPS measurements show that the metal ions bind exclusively to the carboxylic acid and that the amide group is not involved in metal binding.