gebhart/patrepeval huggingface dataset:
The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. (1996)

We have developed a novel technique for combined immunofluorescence/in situ hybridization on fixed budding yeast cells that maintains the three-dimensional structure of the nucleus as monitored by focal sections of cells labeled with fluorescent probes and by staining with a nuclear pore antibody. Within the resolution of these immunodetection techniques, we show that proteins encoded by the SIR3, SIR4, and RAP1 genes colocalize in a statistically significant manner with Y' telomere-associated DNA sequences. In wild-type cells the Y' in situ hybridization signals can be resolved by light microscopy into fewer than ten foci per diploid nucleus. This suggests that telomeres are clustered in vegetatively growing cells, and that proteins essential for telomeric silencing are concentrated at their sites of action, i.e., at telomeres and/or subtelomeric regions. As observed for Rap1, the Sir4p staining is diffuse in a sir3- strain, and similarly, Sir3p staining is no longer punctate in a sir4- strain, although the derivatized Y' probe continues to label discrete sites in these strains. Nonetheless, the Y' FISH is altered in a qualitative manner in sir3 and sir4 mutant strains, consistent with the previously reported phenotypes of shortened telomeric repeats and loss of telomeric silencing.
Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms (1998)

Traditional and molecular typing schemes for the characterization of pathogenic microorganisms are poorly portable because they index variation that is difficult to compare among laboratories. To overcome these problems, we propose multilocus sequence typing (MLST), which exploits the unambiguous nature and electronic portability of nucleotide sequence data for the characterization of microorganisms. To evaluate MLST, we determined the sequences of approximately 470-bp fragments from 11 housekeeping genes in a reference set of 107 isolates of Neisseria meningitidis from invasive disease and healthy carriers. For each locus, alleles were assigned arbitrary numbers and dendrograms were constructed from the pairwise differences in multilocus allelic profiles by cluster analysis. The strain associations obtained were consistent with clonal groupings previously determined by multilocus enzyme electrophoresis. A subset of six gene fragments was chosen that retained the resolution and congruence achieved by using all 11 loci. Most isolates from hyper-virulent lineages of serogroups A, B, and C meningococci were identical for all loci or differed from the majority type at only a single locus. MLST using six loci therefore reliably identified the major meningococcal lineages associated with invasive disease. MLST can be applied to almost all bacterial species and other haploid organisms, including those that are difficult to cultivate. The overwhelming advantage of MLST over other molecular typing methods is that sequence data are truly portable between laboratories, permitting one expanding global database per species to be placed on a World-Wide Web site, thus enabling exchange of molecular typing data for global epidemiology via the Internet.
Enhanced luminescence in top-gate-type organic light-emitting transistors (2004)

We have studied the structure and operating characteristics of top-gate-type organic light-emitting transistors (OLETs). The OLET is composed of an anode (source), organic layers including an organic electroluminescent (EL) layer, a cathode (drain) being opposed to the anode, and a gate, formed outside of the region between the anode and the cathode. EL characteristics of the OLET show that the luminescent intensity from the organic layers can be balanced by applying the bias voltage of the gate electrode.
Specific complexation of saccharides with dimeric phenylboronic acid that can be detected by circular dichroism (1993)

Abstract For the development of new receptor molecules that can recognize sugar molecules, we synthesized 2,2′-dimethoxydiphenylmethane-5,5′-diboronic acid (1) and diphenyl-3,3′-diboronic acid (2). It was shown that in the presence of 1, some mono- and disaccharides result in a CD band at 275 nm. It was also shown that 2 forms 1:1 complexes with several disaccharides and gives the characteristic exciton coupling in CD spectroscopy owing to immobilization of the two phenyl rings. The results indicate that the CD spectroscopic method using 1 or 2 as receptor molecules serves as a new sensory system for sugar molecules, and the absolute configuration of disaccharides was successfully predicted from the sign of the exciton coupling of the CD spectrum by using 2.
830 nm laser irradiation induces varicosity formation, reduces mitochondrial membrane potential and blocks fast axonal flow in small and medium diameter rat dorsal root ganglion neurons: implications for the analgesic effects of 830 nm laser (2007)

We report the formation of 830 nm (cw) laser-induced, reversible axonal varicosities, using immunostaining with beta-tubulin, in small and medium diameter, TRPV-1 positive, cultured rat DRG neurons. Laser also induced a progressive and statistically significant decrease (p<0.005) in MMP in mitochondria in and between static axonal varicosities. In cell bodies of the neuron, the decrease in MMP was also statistically significant (p<0.05), but the decrease occurred more slowly. Importantly we also report for the first time that 830 nm (cw) laser blocked fast axonal flow, imaged in real time using confocal laser microscopy and JC-1 as mitotracker. Control neurons in parallel cultures remained unaffected with no varicosity formation and no change in MMP. Mitochondrial movement was continuous and measured along the axons at a rate of 0.8 microm/s (range 0.5-2 microm/s), consistent with fast axonal flow. Photoacceptors in the mitochondrial membrane absorb laser and mediate the transduction of laser energy into electrochemical changes, initiating a secondary cascade of intracellular events. In neurons, this results in a decrease in MMP with a concurrent decrease in available ATP required for nerve function, including maintenance of microtubules and molecular motors, dyneins and kinesins, responsible for fast axonal flow. Laser-induced neural blockade is a consequence of such changes and provide a mechanism for a neural basis of laser-induced pain relief. The repeated application of laser in a clinical setting modulates nociception and reduces pain. The application of laser therapy for chronic pain may provide a non-drug alternative for the management of chronic pain.
Establishing Optimal Wave Communication Channels Automatically (2013)

We show how multiple optimal orthogonal channels for communicating or interconnecting with waves between two objects can be aligned and optimized automatically using controllable beamsplitters, detectors and simple local feedback loops, without moving parts, without device calibration, without fundamental beam splitting loss, and without calculations. Optical applications include multiple simultaneous orthogonal spatial communication channels in free space or multimode optical fibers, automatically focused power delivery with waves, multiple channel communication through scattering or lossy media, and real-time-optimized focused channels to and from multiple moving objects. The approach physically implements automatic singular value decomposition of the wave coupling between the objects, and is equivalent in its effect to the beam forming in a laser resonator with phase-conjugate mirrors with the additional benefits of allowing multiple orthogonal channels to be formed simultaneously and avoiding the need for any nonlinear optical materials.
Mutations affecting antigen processing impair class II-restricted allorecognition (1991)

Both exogenously derived and endogenously derived Ag generally require processing for their optimal binding and presentation by class I and class II major histocompatibility proteins. It is not known whether steps involved in Ag processing also affect the recognition of alloreactive T cells. We have recently described B cell mutants which have general defects in the processing and presentation of a variety of exogenous Ag to class II restricted T cells. In this report we have studied the ability of these processing mutants to stimulate a set of anti-DR3-specific alloreactive T cells clones. These processing/presentation mutants express normal MHC class II molecules, both in terms of primary sequence and cell surface abundance, but they appear unable to generate effective peptide-MHC complexes. When tested for their ability to stimulate MHC class II alloreactive T cell clones, only one of four T cell clones was stimulated by these mutants; the other three alloreactive T cell clones were not stimulated by either of two different mutants. Both of these mutants express normal levels of the accessory molecules, LFA-3 and ICAM-1. The inability of these mutants to stimulate three of four alloreactive clones indicates that the capacity to be recognized by many alloreactive T cells is linked to the Ag processing capacity of a stimulator cell.
New developments of computer-aided crystallographic analysis in transmission electron microscopy (2000)

A new computer program for on-line crystallographic analysis in transmission electron microscopy (TEM) is presented. The program is based on the fast on-line determination of single-crystal orientations from Kikuchi and spot patterns. Spot patterns, which are particularly useful in the case of highly deformed metals, are analyzed by a new digital image processing procedure. This procedure improves the precision and ease of the orientation measurement. The program permits the on-line measurement of glide systems characterized by the Burgers vector and the crystallographic line direction of dislocations and their glide planes. The determination of twin systems, based on the misorientation calculation for any crystal structure, is included as well. The possibility of determining the foil thickness permits the complete crystallographic characterization of interfaces. Finally, the program facilitates the discrimination of phases and includes the fit of the lattice parameters a , b and c from diffraction patterns. The new procedures are described in detail. Application examples are given for all functions.
Bactericidal/permeability-increasing protein (BPI) and lipopolysaccharide-binding protein (LBP): structure, function and regulation in host defence against Gram-negative bacteria (2003)

Lipopolysaccharide-binding protein (LBP) and bactericidal/permeability-increasing protein (BPI) are closely related endotoxin-binding proteins that function in a co-ordinated manner to facilitate an integrated host response to invading Gram-negative bacteria. Differences in the structure and function of BPI and LBP, as well as differences in their mobilization, permit highly sensitive pro-inflammatory responses to small numbers of bacteria at the onset of bacterial invasion and, later, efficient elimination of viable bacteria and their remnants and of endotoxin-driven inflammation.
A Real-Time Convolutional Neural Network for Super-Resolution on FPGA With Applications to 4K UHD 60 fps Video Services (2018)

In this paper, we present a novel hardware-friendly super-resolution (SR) method based on a convolutional neural network (CNN) and its dedicated hardware (HW) on field programmable gate array (FPGA). Although CNN-based SR methods have shown very promising results for SR, their computational complexities are prohibitive for hardware implementation. To the best of our knowledge, we are the first to implement a real-time CNN-based SR HW that upscales 2K full high-definition video to 4K ultra high-definition (UHD) video at 60 frames per second (fps). In our dedicated CNN-based SR HW, low-resolution input frames are processed line-by-line, and the number of convolutional filter parameters is reduced significantly by incorporating depth-wise separable convolutions with a residual connection. Our CNN-based SR HW incorporates a cascade of 1D convolutions having large receptive fields along horizontal lines while keeping vertical receptive fields minimal, which allows us to save required line memory space in achieving comparable SR performance against full 2D convolution operations. For efficient HW implementation, we use a simple and effective quantization method with little peak signal-to-noise ratio (PSNR) degradation. Also, we propose a compression method to efficiently store intermediate feature map data to reduce the number of line memories used in HW. Our HW implementation on the FPGA generates 4K UHD frames of higher PSNR values at 60 fps and shows better visual quality, compared with conventional CNN-based SR methods that are trained and tested in software.
Expression of Guanylyl Cyclase-A/Atrial Natriuretic Peptide Receptor Blocks the Activation of Protein Kinase C in Vascular Smooth Muscle Cells (1997)

To understand the molecular mechanisms of cellular signaling of atrial natriuretic peptide (ANP), we have studied its effect on the enzymatic activity of endogenous and overexpressed protein kinase C (PKC) in rat thoracic aortic vascular smooth muscle (RTASM) cells. Angiotensin II (ANG II), endothelin-1 (ET-1), and 12-O-tetradecanoylphorbol 13-acetate (TPA) stimulated fourfold to fivefold PKC activity in PKC-alpha cDNA-transfected RTASM cells. However, pretreatment of these cells with ANP significantly inhibited the agonist-stimulated PKC activity in a dose-dependent manner. The inhibitory effect of ANP was more effective if cells were transfected with both PKC-alpha and guanylyl cyclase-A/atrial natriuretic peptide receptor (Npra) cDNAs. The agonist-stimulated PKC activity was also inhibited if RTASM cells were pretreated with cGMP analog 8-bromo-cGMP; however, the treatment of cells with a cAMP analog, dibutyryl-cAMP, did not show any discernible effect. The pretreatment of cells with Npra antagonist A-71915, significantly blocked the production of cGMP as well as the inhibitory effect of ANP on PKC activity. To further examine whether the antagonistic action of ANP and 8-bromo-cGMP on agonist-stimulated PKC activity were mediated through cGMP-dependent protein kinase (PKG), cells were treated with ANP or 8-bromo-cGMP and activators of PKC in the presence of KT-5823, a specific inhibitor of PKG. The treatment of cells with KT-5823 significantly attenuated the inhibitory effects of both ANP and 8-bromo-cGMP on agonist-stimulated PKC activity. The results from these studies provide strong evidence that ANP antagonizes the activation of PKC in RTASM cells, involving guanylyl cyclase-A receptor Npra and second messenger cGMP. Our data further support the notion that ANP acts as a negative mediator of signaling cross-talks between Npra and PKC in a cGMP-dependent manner, probably involving cGMP-dependent protein kinase in this process.
Oral but Not Parenteral Interleukin (IL)-12 Redirects T Helper 2 (Th2)-type Responses to an Oral Vaccine Without Altering Mucosal IgA Responses (1997)

Our past studies have shown that the mucosal adjuvant cholera toxin (CT) induces T helper type 2 (Th2) responses with systemic IgG1, IgE and mucosal secretory IgA (S-IgA) antibodies (Abs). In this study, recombinant murine IL-12 (rmIL-12) was given either parenterally or orally to mice orally immunized with tetanus toxoid (TT) and CT to determine whether this cytokine could redirect the CT-induced Th2-type responses and what effect this shift would have on S-IgA Ab responses. Intraperitoneal administration of rmIL-12 shifted TT-specific responses toward Th1-type and resulted in CD4+ T cells producing IFN-gamma and IL-2 with markedly reduced levels of Th2-type cytokines. This cytokine profile was accompanied by increased delayed-type hypersensitivity (DTH) and shifts in serum IgG1 to IgG2a and IgG3 anti-TT Ab responses. Further, serum IgE and S-IgA Ab responses were markedly reduced by parenteral IL-12. When IL-12 complexed to liposomes was given orally both shifts to IgG2a and IgG3 and low IgE Abs again occurred concomitant with enhanced serum IFN-gamma and DTH responses. Interestingly, oral rmIL-12 did not result in significant levels of serum IL-12 nor altered S-IgA Ab responses and resulted in higher levels of some Th2-type cytokines both in vitro and in vivo when compared with parenteral IL-12. Our results show that the shifts in systemic immune responses with intact S-IgA Abs which occur after oral delivery of IL-12-liposomes are due to cytokine effects in the Peyer's patches and suggest new strategies for the targeted manipulation of Th1- and Th2-type responses to mucosal vaccines.
In ovo transplantation of enteric nervous system precursors from vagal to sacral neural crest results in extensive hindgut colonisation (2002)

The enteric nervous system (ENS) is derived from vagal and sacral neural crest cells (NCC). Within the embryonic avian gut, vagal NCC migrate in a rostrocaudal direction to form the majority of neurons and glia along the entire length of the gastrointestinal tract, whereas sacral NCC migrate in an opposing caudorostral direction, initially forming the nerve of Remak, and contribute a smaller number of ENS cells primarily to the distal hindgut. In this study, we have investigated the ability of vagal NCC, transplanted to the sacral region of the neuraxis, to colonise the chick hindgut and form the ENS in an experimentally generated hypoganglionic hindgut in ovo model. Results showed that when the vagal NC was transplanted into the sacral region of the neuraxis, vagal-derived ENS precursors immediately migrated away from the neural tube along characteristic pathways, with numerous cells colonising the gut mesenchyme by embryonic day (E) 4. By E7, the colorectum was extensively colonised by transplanted vagal NCC and the migration front had advanced caudorostrally to the level of the umbilicus. By E10, the stage at which sacral NCC begin to colonise the hindgut in large numbers, myenteric and submucosal plexuses in the hindgut almost entirely composed of transplanted vagal NCC, while the migration front had progressed into the pre-umbilical intestine, midway between the stomach and umbilicus. Immunohistochemical staining with the pan-neuronal marker, ANNA-1, revealed that the transplanted vagal NCC differentiated into enteric neurons, and whole-mount staining with NADPH-diaphorase showed that myenteric and submucosal ganglia formed interconnecting plexuses, similar to control animals. Furthermore, using an anti-RET antibody, widespread immunostaining was observed throughout the ENS, within a subpopulation of sacral NC-derived ENS precursors, and in the majority of transplanted vagal-to-sacral NCC. Our results demonstrate that: (1) a cell autonomous difference exists between the migration/signalling mechanisms used by sacral and vagal NCC, as transplanted vagal cells migrated along pathways normally followed by sacral cells, but did so in much larger numbers, earlier in development; (2) vagal NCC transplanted into the sacral neuraxis extensively colonised the hindgut, migrated in a caudorostral direction, differentiated into neuronal phenotypes, and formed enteric plexuses; (3) RET immunostaining occurred in vagal crest-derived ENS cells, the nerve of Remak and a subpopulation of sacral NCC within hindgut enteric ganglia.
Development and evaluation of agents for targeting visceral amyloid. (2011)

Wall, JS, Solomon A, Kennel, SJ. Development and evaluation of agents for targeting visceral amyloid. Visceral amyloidosis is a rare disease characterized by the deposition in organs and tissues of protein fibrils, heparan sulfate proteoglycan as well as serum amyloid P component and other serum proteins. Imaging these pathologic deposits aids in the clinical management of patients with amyloidosis. Whole body scintigraphic imaging of amyloid load as well as organ specific anatomic imaging provides information that can inform prognosis and can be used to monitor disease progression or response to therapy. These capabilities are limited in the USA, which has led to our development and evaluation of two new reagents that specifically target amyloid <i>in vivo</i> and have been used to image visceral deposits in mice and patients with AL amyloidosis. The fibril-reactive mAb 11-1F4, when labeled with iodine-124 was shown to bind AL amyloid in patients by using PET/CT imaging. These studies were performed to support the evaluation of this reagent as a novel immunotherapy for AL patients. In addition, we have identified a heparin-binding peptide that co-localizes with murine AA amyloid <i>in vivo</i> and can be used to image the deposits. The interaction of this peptide, designated p5, with amyloid is dependent on the net positive charge and truncated forms that would be more desirable as clinical imaging agents were found to be significantly less efficient for amyloid imaging. The development and positive preclinical validation of these two reagents offers potential new therapeutic and diagnostic tools for patients with these devastating diseases.
Mammalian Male and Female Germ Cells Express a Germ Cell-Specific Y-Box Protein, MSY21 (1998)

Here we report the isolation and characterization of mouse testicular cDNAs encoding the mammalian homologue of the Xenopus germ cell-specific nucleic acid-binding protein FRGY2 (mRNP3+4), hereafter designated MSY2. MSY2 is a member of the Y box multigene family of proteins; it contains the cold shock domain that is highly conserved among all Y box proteins and four basic/aromatic islands that are closely related to the other known germline Y box proteins from Xenopus, FRGY2, and goldfish, GFYP2. Msy2 undergoes alternative splicing to yield alternate N-terminal regions upstream of the cold shock domain. Although MSY2 is a member of a large family of nucleic acid-binding proteins, Southern blotting detects only a limited number of genomic DNA fragments, suggesting that Msy2 is a single copy gene. By Northern blotting and immunoblotting, MSY2 appears to be a germ cell-specific protein in the testis. Analysis of Msy2 mRNA expression in prepubertal and adult mouse testes, and in isolated populations of germ cells, reveals maximal expression in postmeiotic round spermatids, a cell type with abundant amounts of stored messenger ribonucleoproteins. In the ovary, MSY2 is present exclusively in diplotene-stage and mature oocytes. MSY2 is maternally inherited in the one-cell-stage embryo but is not detected in the late two-cell-stage embryo. This loss of MSY2 is coincident with the bulk degradation of maternal mRNAs in the two-cell embryo.