gebhart/patrepeval huggingface dataset:
NSOM/QD-Based Direct Visualization of CD3-Induced and CD28-Enhanced Nanospatial Coclustering of TCR and Coreceptor in Nanodomains in T Cell Activation (2009)

Direct molecular imaging of nano-spatial relationship between T cell receptor (TCR)/CD3 and CD4 or CD8 co-receptor before and after activation of a primary T cell has not been reported. We have recently innovated application of near-field scanning optical microscopy (NSOM) and immune-labeling quantum dots (QD) to image Ag-specific TCR response during in vivo clonal expansion, and now up-graded the NSOM/QD-based nanotechnology through dipole-polarization and dual-color imaging. Using this imaging system scanning cell-membrane molecules at a best-optical lateral resolution, we demonstrated that CD3, CD4 or CD8 molecules were distinctly distributed as single QD-bound molecules or nano-clusters equivalent to 2-4 QD fluorescence-intensity/size on cell-membrane of un-stimulated primary T cells, and approximately 6-10% of CD3 were co-clustering with CD4 or CD8 as 70-110 nm nano-clusters without forming nano-domains. The ligation of TCR/CD3 on CD4 or CD8 T cells led to CD3 nanoscale co-clustering or interaction with CD4 or CD8 co-receptors forming 200-500 nm nano-domains or >500 nm micro-domains. Such nano-spatial co-clustering of CD3 and CD4 or CD3 and CD8 appeared to be an intrinsic event of TCR/CD3 ligation, not purely limited to MHC engagement, and be driven by Lck phosphorylation. Importantly, CD28 co-stimulation remarkably enhanced TCR/CD3 nanoscale co-clustering or interaction with CD4 co-receptor within nano- or micro-domains on the membrane. In contrast, CD28 co-stimulation did not enhance CD8 clustering or CD3-CD8 co-clustering in nano-domains although it increased molecular number and density of CD3 clustering in the enlarged nano-domains. These nanoscale findings provide new insights into TCR/CD3 interaction with CD4 or CD8 co-receptor in T-cell activation.
Toolkit for shared hypermedia on a distributed object oriented architecture (1993)

We present a toolkit and architecture for supporting networked shared (multi-user) hypermedia applications. The toolkit supports a rich set of media types: text, graphics, pictures, live and pre-recorded sound, and live and pre-recorded video. Hypermedia links can be anchored to any media type and refer to nodes which contain media items. Nodes provide for abstractions such as pages, cards and general information networks. Media information can be accessed and changed by several users. The toolkit is realised as a class library on a distributed object oriented language based on C. The concurrent and distributed features of the underlying architecture provide for multi-users. Issues of sharing, version management and access control are addressed by considering database extensions to the object oriented architecture. Support for networking of continuous media streams is provided by extensions to the underlying runtime system. The toolkit has been used to develop and support conference and groupware applications.
Chemical Derivatization as a Strategy to Study Structure-Activity Relationships of Glycosaminoglycans (2002)

Sulfated glycosaminoglycans (GAGs) are amenable to a number of chemical modifications that modulate their biological activity. N-sulfate groups can be exposed and N-acylated (usually N-acetylated), specific O-sulfate groups can be removed, and free hydroxyl groups (either preexisting in the original GAG or exposed by desulfation) can be sulfated. Heparin/heparan sulfate, chondroitin sulfate, and dermatan sulfate have been variously desulfated or sulfated to afford novel GAGs with protein binding and associated biological properties different from those of the original GAGs. Regiospecific sulfation of N-acetyl heparosan ( E. coli K5 polysaccharide) afforded a number of derivatives, some endowed with antithrombotic activity and others with antimetastatic properties. Most of the activities could be correlated with typical sulfation patterns along each GAG backbone. Glycol splitting of nonsulfated glucuronic residues (including a critical residue in the pentasaccharide sequence of the active site for antithrombin) leads to substantial loss of anticoagulant activity of heparin. Partial removal of sulfate groups at position 2 of iduronic acid residues followed by glycol splitting of all nonsulfated uronic acid residues afforded nonanticoagulant, antiangiogenic heparins.
AlN Microresonator-Based Filters With Multiple Bandwidths at Low Intermediate Frequencies (2013)

Filters with various bandwidths at low intermediate frequency (IF) have been demonstrated using aluminum nitride (AlN) microresonator technology. Specifically, at 13 MHz, 6 kHz, and 25 kHz bandwidth filters were implemented using a single resonator topology, and 250 kHz and 500 kHz bandwidth filters were constructed via the parallel lattice topology using four sub-resonators and L-matching networks. The bandwidths of these filters are from 0.046% to 3.8%, and particularly the 500 kHz bandwidth filter at 13 MHz is wider than that of the resonator kt <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> limit (40 kHz). The 100x variations in filter percent bandwidth were realized in a 1700 nm-thick aluminum nitride film on the same wafer through CMOS-compatible fabrication processes. Changes in the filter termination for proper filter matching were implemented in the Agilent Genesys RF and microwave design simulation software using actual measured filter responses with 50 Ω termination. The great flexibility in filter bandwidths and resonant frequencies, as well as other benefits such as size, manufacturing cost, isolation, and insertion loss provided by AlN microresonators will enable next generation multi-band, multi-waveform, and cognitive radios for defense and consumer wireless applications.
Gender preselection in mammals: an overview. (1996)

Recent advances in the separation of X and Y chromosome bearing spermatozoa have led to the availability of a method (Beltsville Sperm Sexing Technology) to preselect the sex in several mammals. Progeny using this procedure have been produced in cattle, sheep, swine and laboratory animals. Mammalian sperm are inherently different in that the X sperm carries from 2.8 to 7.5% more DNA than the Y sperm. Individual sperm DNA can be determined and used as the differentiating characteristic with flow cytometry and cell sorting instrumentation especially modified to measure small amounts of DNA in sperm. The process utilizes the fluorochrome Hoechst 33342 to bind to the DNA. The relative DNA is measured by passing the living sperm through a laser beam and collecting the light energy from the individual sperm. Data is acquired and used to select the particular sperm for deflection into collection tubes. The proportions of sorted X and Y sperm in each tube can be validated by reanalyzing an aliquot for DNA content. This value is then used to predict the outcome of fertilization and subsequent gestation. The sorted sperm are used to inseminate eggs via in vitro fertilization (IVF) or by surgical insemination into the oviduct or the uterus of appropriate females. Sperm are sorted at the rate of 0.5 million per hour for most species with the expectation of 90% or greater of one sex or the other being born. Progeny in cattle using IVF have been produced at greater than 90% accuracy. Rabbits have produced greater than 90% females using this process. Progeny produced from pigs average 85% for one sex or the other. All progeny produced (N = or > 300) have exhibited completely normal morphological appearance and normal reproductive function. Because of the inability to obtain large numbers of sorted sperm in a short amount of time, the technologies use for regular artificial insemination would not be practical in most domestic species. This sexing technology however is very applicable where IVF, intrauterine or intratubal insemination are convenient means for producing offspring. In addition, the recent advent of ultrasound guided insemination in cattle may provide and opportunity to use this technology for much lower numbers of sperm per insemination than previously thought possible. Using less than 2 x 10 sorted X or Y sperm would move the technology one step closer to practicality.
Chemical modification of an ecotropic murine leukemia virus results in redirection of its target cell specificity (1991)

An ecotropic virus was chemically modified in order to determine whether its target cell specificity could be altered. We hypothesized that chemical coupling of galactose residues to a virus might permit specific infection of hepatocytes mediated by asialoglycoprotein receptors unique to these cells. To test this hypothesis, we took advantage of the fact that: 1) artificial asialoglycoproteins can be created by chemical coupling of lactose to proteins; and 2) viruses that are ecotropic have a narrow species specificity. An ecotropic, rodent-specific, replication-defective murine leukemia virus containing the gene for beta-galactosidase was chemically modified with lactose to contain 5.9 mumol of lactose per mg of viral RNA. Modified and unmodified viruses were incubated for 5 days with HepG2, a human hepatoma line that possesses asialoglycoprotein receptors, and SK Hep1, a human cell line that does not. As expected from the ecotropism, unmodified virus did not produce beta-galactosidase activity in either cell type. Modified virus did not produce beta-galactosidase activity in SK Hep1 cells. However, modified virus did produce beta-galactosidase activity, 71.2 units/mg of cell protein, in the human receptor (+) HepG2 cells. Interestingly, modification of the virus also resulted in decreased enzyme activity in previously susceptible host rodent cells. Competition with modified virus by an excess of an asialoglycoprotein completely prevented development of enzymatic activity in HepG2 cells. Histochemical treatment of cells with 5-bromo-4-chloro-3-indoyl beta-D-galactoside to detect in situ beta-galactosidase activity demonstrated that only HepG2 cells treated with modified virus were positive and that 36% of these cells were stained after 5 days. These data indicate that chemical modification of a virus can result in a redirection of the infectivity of the virus toward hepatocyte-derived cells mediated by the presence of asialoglycoprotein receptors.
C2‐Symmetrical Thiodigalactoside Bis‐Benzamido Derivatives as High‐Affinity Inhibitors of Galectin‐3: Efficient Lectin Inhibition through Double Arginine–Arene Interactions (2005)

Inhibitors of galectin-3, which has been implicated in cancer- and immunity-related processes, can be synthesized from thiodigalactoside derivatives with aromatic amide substituents at both C3 positions (see structure). Dissociation constant (Kd) values as low as 33 nM have been obtained. Computer modeling suggests that such high affinity stems from double arginine–arene stacking interactions. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z500627_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Telomeric and rDNA Silencing in Saccharomyces cerevisiae Are Dependent on a Nuclear NAD+ Salvage Pathway (2002)

The Sir2 protein is an NAD(+)-dependent protein deacetylase that is required for silencing at the silent mating-type loci, telomeres, and the ribosomal DNA (rDNA). Mutations in the NAD(+) salvage gene NPT1 weaken all three forms of silencing and also cause a reduction in the intracellular NAD(+) level. We now show that mutation of a highly conserved histidine residue in Npt1p results in a silencing defect, indicating that Npt1p enzymatic activity is required for silencing. Deletion of another NAD(+) salvage pathway gene called PNC1 caused a less severe silencing defect and did not significantly reduce the intracellular NAD(+) concentration. However, silencing in the absence of PNC1 was completely dependent on the import of nicotinic acid from the growth medium. Deletion of a gene in the de novo NAD(+) synthesis pathway BNA1 resulted in a significant rDNA silencing defect only on medium deficient in nicotinic acid, an NAD(+) precursor. By immunofluorescence microscopy, Myc-tagged Bna1p was localized throughout the whole cell in an asynchronously growing population. In contrast, Myc-tagged Npt1p was highly concentrated in the nucleus in approximately 40% of the cells, indicating that NAD(+) salvage occurs in the nucleus in a significant fraction of cells. We propose a model in which two components of the NAD(+) salvage pathway, Pnc1p and Npt1p, function together in recycling the nuclear nicotinamide generated by Sir2p deacetylase activity back into NAD(+).
Oligomer Diversity during the Aggregation of the Repeat Region of Tau (2018)

The molecular mechanism of protein aggregation is of both fundamental and clinical importance as amyloid aggregates are linked to a number of neurodegenerative disorders. Such protein aggregates include macroscopic insoluble fibrils as well as small soluble oligomeric species. Time-dependent resolution of these species is prerequisite for a detailed quantitative understanding of protein aggregation; this remains challenging due to the lack of methods for detecting and characterizing transient and heterogeneous protein oligomers. Here we have used single molecule fluorescence techniques combined with mechanistic modeling to study the heparin-induced aggregation of the repeat region of tau, which forms the core region of neurofibrillary tangles found in Alzheimer's disease. We distinguish several subpopulations of oligomers with different stability and follow their evolution during aggregation reactions as a function of temperature and concentration. Employment of techniques from chemical kinetics reveals that the two largest populations are structurally distinct from fibrils and are both kinetically and thermodynamically unstable. The first population is in rapid exchange with monomers and held together by electrostatic interactions; the second is kinetically more stable, dominates at later times, and is probably off-pathway to fibril formation. These more stable oligomers may contribute to other oligomer induced effects in the cellular environment, for example, by overloading protein quality control systems. We also show that the shortest growing filaments remain suspended in aqueous buffer and thus comprise a third, smaller population of transient oligomers with cross-β structure. Overall our data show that a diverse population of oligomers of different structures and half-lives are formed during the aggregation reaction with the great majority of oligomers formed not going on to form fibrils.
Granulocyte-Macrophage Colony-Stimulating Factor and Interleukin-2 Fusion cDNA for Cancer Gene Immunotherapy (2004)

Genetic engineering of tumor cells to express both granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin (IL)-2 can induce synergistic immune antitumor effects. Paradoxically, the combination has also been reported to down-regulate certain immune functions, highlighting the unpredictability of dual cytokine use. We hypothesized that a GM-CSF and IL-2 fusion transgene (GIFT) could circumvent such limitations yet preserve synergistic features. We designed a fusion cDNA of murine GM-CSF and IL-2. Protein structure computer modeling of GIFT protein predicted for intact ligand binding domains for both cytokines. B16 mouse melanoma cells were gene modified to express GIFT (B16GIFT), and these cells were unable to form tumors in C57bl/6 mice. Irradiated B16GIFT whole-cell tumor vaccine could also induce absolute protective immunity against challenge by live B16 cells. In mice with established melanoma, B16GIFT therapeutic cellular vaccine significantly improved tumor-free survival when compared with B16 expressing both IL-2 and GM-CSF. We show that GIFT induced a significantly greater tumor site recruitment of macrophages than combined GM-CSF and IL-2 and that macrophage recruitment arises from novel chemotactic feature of GIFT. In contrast to suppression by GM-CSF of natural killer (NK) cell recruitment despite coexpression of IL-2, GIFT leads to significant functional NK cell infiltration as confirmed in NK-defective beige mice. In conclusion, we demonstrated that a fusion between GM-CSF and IL-2 can invoke greater antitumor effect than both cytokines in combination, and novel immunobiological properties can arise from such chimeric constructs.
Fermentative Production of Plant Benzylisoquinoline Alkaloids in Microbes (2013)

Higher plants produce diverse chemicals, including alkaloids, terpenoids, and phenolic compounds (phenylpropanoids and flavonoids) as secondary metabolites. These chemicals are widely used for human health and nutrition. Alkaloids, for example, are valued in medicine due to their high biological activities, but most of these metabolites accumulate at low levels in plant cells, resulting in poor extraction yields. Increasingly, attention is devoted to the production of plant metabolites by reconstructing plant biosynthetic pathways in microorganisms. This technology has been aided by advances in synthetic biology and metabolic engineering. Here, the review a fermentation platform for low-cost production of numerous alkaloids using bioengineered Escherichia coli and/or Saccharomyces cerevisiae.
On the impact of carbon-doping on the dynamic Ron and off-state leakage current of 650V GaN power devices (2015)

A strong positive correlation between dynamic Ron and the ionization of buffer traps by injection of electrons from the Si substrate is presented. By exploring different Carbon doping profiles in the epi layers, the substrate buffer leakage is substantially reduced, which in turns results in lower dynamic Ron. The traps in the epi structure are characterized by different electrical techniques such as drain current transient, on-the-fly trapping and ramped back-gating experiments.
New Waveguide Fabrication Techniques for Next-generation PLCs (2005)

New waveguide fabrication techniques will be needed to make highly functional next-generation planar lightwave circuits (PLCs). After first reviewing the basic PLC fabrication process, this article describes recent progress in waveguide fabrication techniques. In particular, it describes a fabrication technique designed to make an ultralow loss waveguide for large-scale optical circuits, a fabrication technique that can produce ultra-compact optical circuits for high-density integration, and a laser direct writing waveguide fabrication technique whose goal is flexible waveguide formation and high-density integration.
Oral Immunization with a Recombinant Bacterial Antigen Produced in Transgenic Plants (1995)

The binding subunit of Escherichia coli heat-labile enterotoxin (LT-B) is a highly active oral immunogen. Transgenic tobacco and potato plants were made with the use of genes encoding LT-B or an LT-B fusion protein with a microsomal retention sequence. The plants expressed the foreign peptides, both of which formed oligomers that bound the natural ligand. Mice immunized by gavage produced serum and gut mucosal anti-LT-B immunoglobulins that neutralized the enterotoxin in cell protection assays. Feeding mice fresh transgenic potato tubers also caused oral immunization.
NKB1: a natural killer cell receptor involved in the recognition of polymorphic HLA-B molecules. (1994)

Natural killer (NK) cells kill normal and transformed hematopoietic cells that lack expression of major histocompatibility complex (MHC) class I antigens. Lysis of HLA-negative Epstein Barr virus-transformed B lymphoblastoid cell lines (B-LCL) by human NK cell clones can be inhibited by transfection of the target cells with certain HLA-A, -B, or -C alleles. NK cell clones established from an individual demonstrate clonal heterogeneity in HLA recognition and a single NK clone can recognize multiple alleles. We describe a potential human NK cell receptor (NKB1) for certain HLA-B alleles (e.g., HLA-B*5101 and-B*5801) identified by the mAb DX9. NKB1 is a 70-kD glycoprotein that is expressed on a subset of NK cells and NK cell clones. DX9 monoclonal antibody (mAb) specifically inhibits the interaction between NK cell clones and B-LCL targets transfected with certain HLA-B alleles, but does not affect recognition of HLA-A or HLA-C antigens. An individual NK cell clone can independently recognize B-LCL targets transfected with HLA-B or HLA-C antigens; however, DX9 mAb only affects interaction with transfectants expressing certain HLA-B alleles. These findings demonstrate the existence of NK cell receptors involved in the recognition of HLA-B and imply the presence of multiple receptors for MHC on an individual NK clone.
Quantitative Comparison of Long-wavelength Alexa Fluor Dyes to Cy Dyes: Fluorescence of the Dyes and Their Bioconjugates (2003)

Amine-reactive N-hydroxysuccinimidyl esters of Alexa Fluor fluorescent dyes with principal absorption maxima at about 555 nm, 633 nm, 647 nm, 660 nm, 680 nm, 700 nm, and 750 nm were conjugated to antibodies and other selected proteins. These conjugates were compared with spectrally similar protein conjugates of the Cy3, Cy5, Cy5.5, Cy7, DY-630, DY-635, DY-680, and Atto 565 dyes. As N-hydroxysuccinimidyl ester dyes, the Alexa Fluor 555 dye was similar to the Cy3 dye, and the Alexa Fluor 647 dye was similar to the Cy5 dye with respect to absorption maxima, emission maxima, Stokes shifts, and extinction coefficients. However, both Alexa Fluor dyes were significantly more resistant to photobleaching than were their Cy dye counterparts. Absorption spectra of protein conjugates prepared from these dyes showed prominent blue-shifted shoulder peaks for conjugates of the Cy dyes but only minor shoulder peaks for conjugates of the Alexa Fluor dyes. The anomalous peaks, previously observed for protein conjugates of the Cy5 dye, are presumably due to the formation of dye aggregates. Absorption of light by the dye aggregates does not result in fluorescence, thereby diminishing the fluorescence of the conjugates. The Alexa Fluor 555 and the Alexa Fluor 647 dyes in protein conjugates exhibited significantly less of this self-quenching, and therefore the protein conjugates of Alexa Fluor dyes were significantly more fluorescent than those of the Cy dyes, especially at high degrees of labeling. The results from our flow cytometry, immunocytochemistry, and immunohistochemistry experiments demonstrate that protein-conjugated, long-wavelength Alexa Fluor dyes have advantages compared to the Cy dyes and other long-wavelength dyes in typical fluorescence-based cell labeling applications.