gebhart/patrepeval huggingface dataset:
Synthesis and characterization of a novel chitosan-based network prepared using naturally occurring crosslinker (2000)

Novel chitosan-based polymeric networks were synthesized and characterized by FTIR, UV and C13 NMR. A naturally occurring crosslinking reagent—genipin, which has been used in herbal medicine and in the fabrication of food dyes, was used to prepare crosslinked chitosan hydrogel. The heterocyclic compound of genipin crosslinked chitosan was formed by a nucleophilic attack by amino group on the olefinic carbon atom at C-3 of deoxyloganin aglycone, followed by opening of the dihydropyran ring and attack by the secondary amine group on the intermediate aldehyde group. Additional, secondary amide linkages could be established in the genipin crosslinked chitosan network by the reaction of ester group of genipin with amino group of chitosan. This bifunctional linkages of genipin with amino group of chitosan leads to form crosslinked networks. Genipin reacted with nucleophilic reagent such as chitosan could further go through a polymerization to form oligomer-bridge in the crosslinked network. The finally formed chitosan networks are blue color, elastic and exhibits pH-dependent swelling characteristics. The swelling ratio of the chitosan hydrogel increased at pH lower than 3 and higher than 11 due to the hydrolysis of amide linkage in the genipin crosslinked chitosan network by acid or alkaline, followed by the protonation of amine group or ionization of carboxyl acid group in the network. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 2804–2814, 2000
Protein microcrystals and the design of a microdiffractometer: current experience and plans at EMBL and ESRF/ID13 (1999)

There is a growing demand for the examination of protein microcrystals at third-generation synchrotron sources. After successful pilot experiments at EMBL/ESRF, which proved that protein microcrystals are often suitable for data collection, operation of the microfocus beamline ID13 was made more user-friendly and suitable for macromolecular crystallography experiments. Given the excellent quality of the beamline microfocusing optics, the key element for successful experiments becomes the handling and visualization of microcrystals. To address this, a microdiffractometer has been designed to allow maximum precision combined with ease of usage and is currently under construction.
Finite Element Analysis of Schwarz P Surface Pore Geometries for Tissue‐Engineered Scaffolds (2012)

Tissue engineering scaffolds provide temporary mechanical support for tissue regeneration. To regenerate tissues more efficiently, an ideal structure of scaffolds should have appropriate porosity and pore structure. In this paper, we generate the Schwarz primitive (P) surface with various volume fractions using a phase‐field model. The phase‐field model enables us to design various surface‐to‐volume ratio structures with high porosity and mechanical properties. Comparing the Schwarz P surface′s von Mises stress with that of triply periodic cylinders and cubes, we draw conclusions about the mechanical properties of the Schwarz P surface.
Histone-like DNA binding protein of Streptococcus intermedius induces the expression of pro-inflammatory cytokines in human monocytes via activation of ERK1/2 and JNK pathways (2007)

Streptococcus intermedius is a commensal associated with serious, deep-seated purulent infections in major organs, such as the brain and liver. Histone-like DNA binding protein (HLP) is an accessory architectural protein in a variety of bacterial cellular processes. In this study, we investigated the mechanisms of pro-inflammatory cytokine inductions in THP-1 cells by stimulation with recombinant HLP of S. intermedius (rSi-HLP). rSi-HLP stimulation-induced production of pro-inflammatory cytokines (IL-8, IL-1 beta and TNF-alpha) occurred in a time- and dose-dependent manner. In contrast with the heat-stable activity of DNA binding, the induction activity of rSi-HLP was heat-unstable. In subsequent studies, rSi-HLP acted cooperatively with lipoteichoic acid, the synthetic Toll-like receptor 2 agonist, Pam3CSK4, and the cytosolic nucleotide binding oligomerization domain 2 receptor agonist, muramyldipeptide. Furthermore, Western blot and blocking assays with specific inhibitors showed that rSi-HLP stimulation induced the activation of cell signal transduction pathways, extracellular signal-regulated kinase 1/2 (ERK1/2) and c-Jun N-terminal kinase (JNK). In addition to its physiological role in bacterial growth through DNA binding, these results indicate that Si-HLP can trigger a cascade of events that induce pro-inflammatory responses via ERK1/2 and JNK signal pathways, and suggest that bacterial HLP may contribute to the activation of host innate immunity during bacterial infection.
Human Action Recognition by Representing 3D Skeletons as Points in a Lie Group (2014)

Recently introduced cost-effective depth sensors coupled with the real-time skeleton estimation algorithm of Shotton et al. [16] have generated a renewed interest in skeleton-based human action recognition. Most of the existing skeleton-based approaches use either the joint locations or the joint angles to represent a human skeleton. In this paper, we propose a new skeletal representation that explicitly models the 3D geometric relationships between various body parts using rotations and translations in 3D space. Since 3D rigid body motions are members of the special Euclidean group SE(3), the proposed skeletal representation lies in the Lie group SE(3)×.. .×SE(3), which is a curved manifold. Using the proposed representation, human actions can be modeled as curves in this Lie group. Since classification of curves in this Lie group is not an easy task, we map the action curves from the Lie group to its Lie algebra, which is a vector space. We then perform classification using a combination of dynamic time warping, Fourier temporal pyramid representation and linear SVM. Experimental results on three action datasets show that the proposed representation performs better than many existing skeletal representations. The proposed approach also outperforms various state-of-the-art skeleton-based human action recognition approaches.
Technology for advanced high-performance microprocessors (1998)

This paper describes the development of logic technologies that meet the density, performance, power, and manufacturing requirements for advanced high-performance microprocessors. Aggressive scaling of MOS transistor dimensions along with reduced power supply provide devices with high performance, low power, and good reliability. Multiple layers of planarized aluminum interconnect with high aspect ratios are used to address the increasing importance of interconnect density and performance. Static RAM test vehicles with small 6-transistor cell sizes are used to develop these logic technologies and to provide early demonstrations of yield and performance capabilities. The manufacturing strategy includes development group ownership of the technology from inception to early manufacturing ramp, extensive reuse of prior generation process equipment and modules, and a "copy exactly" methodology to ensure successful process startup and ramp in multiple facilities.
Electrical Stimulation Induces the Level of TGF-β1 mRNA in Osteoblastic Cells by a Mechanism Involving Calcium/Calmodulin Pathway (1997)

It is well-known that electrical stimulation can prompt healing of bone fractures. However, the mechanism involved is less clear. In this study, we found that capacitively coupled electric field-induced proliferation of osteoblastic cells (MC3T3-E1) accompanied increased levels of transforming growth factor-beta 1 (TGF-beta1) mRNA determined by quantitative reverse transcription/polymerase chain reaction. Previous reports have shown that verapamil and W-7, both of which block voltage gated calcium channels and inhibit the activation of cytosolic calmodulin, respectively, blocked capacitively coupled electric field-induced proliferation of the osteoblast cells. Interestingly, we found that verapamil and W-7 can also block capacitively coupled electric field-induced elevation of TGF-beta1 mRNA. This result suggested that electrical stimulation induces the level of TGF-beta1 mRNA in osteoblastic cells by a mechanism involving calcium/calmodulin pathway. The potential roles of TGF-beta in the electrical signal-induced osteogenesis was discussed.
Antiviral and protein-inducing activities of recombinant human leukocyte interferons and their hybrids (1984)

The antiviral activities of recombinant human leukocyte interferons IFN-alpha A and IFN-alpha D as well as five hybrids of these interferons against retroviruses, vesicular stomatitis virus, and encephalomyocarditis virus were studied in feline, human, and murine cells. Although these interferon species had widely different potencies, their activities against these viruses were, in general, proportional. The IFN-alpha A/D (Bgl) hybrid was the most potent species, and the IFN-alpha D/A (Bgl) hybrid was the least potent. However, the latter species did not interfere with the action of the former species. Like natural human leukocyte interferon, each of the seven species of recombinant interferons induced the synthesis of at least five proteins in human fibroblasts, whereas induction of only one such protein was readily detected in a feline fibroblast line in which these interferon species inhibited the replication of all three viruses.
The automated reproduction of pictures with nonreproducible colors (1984)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1984.
KrF excimer laser annealed TFT with very high field-effect mobility of 329 cm/sup 2//V-s (1992)

A thin-film transistor (TFT) with a maximum field-effect mobility of 320 cm/sup 2//V-s, an on/off current ratio of 7.6*10/sup 7/, a threshold voltage of 6.7 V and a subthreshold slope of 0.37 V/decade was fabricated by using pulse laser annealing processes. Amorphous silicon films (a-Si:H) with a very low impurity concentration of 4*10/sup 18/ cm/sup -3/ for oxygen, 1.5*10/sup 18/ cm/sup -3/ for carbon, and 2*10/sup 17/ cm/sup -3/ for nitrogen were deposited by a plasma chemical vapor deposition (CVD) method and annealed by KrF excimer laser (wavelength of 248 nm). The Raman spectroscopy technique was a useful tool for optimizing laser annealing conditions. Experimental results show that two factors are very important for fabricating very-high mobility TFTs: (1) utilizing high-purity as-deposited a-Si:H film; and (2) performing whole laser annealing processes sequentially in a vacuum container and optimizing illumination conditions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The FGL2‐FcγRIIB pathway: A novel mechanism leading to immunosuppression (2008)

Fibrinogen-like protein 2 (FGL2) is a multifunctional protein, which has been implicated in the pathogenesis of allograft and xenograft rejection. Previously, FGL2 was shown to inhibit maturation of BM-derived DC and T-cell proliferation. The mechanism of the immunosuppressive activity of FGL2 remains poorly elucidated. Here, we focus on identification of FGL2-specific receptor(s) and their ability to modulate APC activity and allograft survival. Using flow cytometry and surface plasmon resonance analysis, we show that FGL2 binds specifically to Fc gamma receptor (FcgammaR)IIB and FcgammaRIII receptors, which are expressed on the surface of APC, including B lymphocytes, macrophages and DC. Antibody to FcgammaRIIB and FcgammaRIII, or deficiency of these receptors, abrogated FGL2 binding. FGL2 inhibited the maturation of BMDC from FcgammaRIIB+/+ mice but not from FcgammaRIIB(-/-) mice and induced apoptosis in the FcgammaRIIB+ mouse B-cell line (A20) but not the A20IIA1.6 cell line that does not express FcgammaRIIB. Recombinant FGL2 infused into FcgammaRIIB+/+ (C57BL/6J, H-2b) mice but not FcgammaRIIB(-/-) mice inhibited rejection of fully mismatched BALB/cJ (H-2d) skin allografts. The identification of specific receptor binding has important implications for the pathogenesis of immune-mediated disease and suggests a potential for targeted FGL2 therapy.
Improving immune function and controlling viral replication in HIV-1-infected patients with immune-based therapies. (2001)

Restoring and preserving immune function is a key component to successfully managing HIV-1 disease. Phase II/III studies have evaluated the safety and immunologic effects of immune-based therapies, including granulocyte-macrophage colony-stimulating factor, interleukin-2, and an inactivated HIV-1 immunogen, as adjuncts to antiretroviral therapy. Addition of each of these immune-based therapies to a background antiretroviral regimen enhanced, to varying degrees, immunologic function and suppression of viral replication in HIV-1-infected patients, suggesting a potential role for immune-based therapies in the treatment of HIV-1 disease. Further studies are needed to better characterize specific immunologic and virologic effects in different patient populations and to determine their impact on clinical outcomes.
Localization of the adenovirus early region 1B 55-kilodalton protein during lytic infection: association with nuclear viral inclusions requires the early region 4 34-kilodalton protein (1991)

The distribution of the adenovirus early region 1B 55-kDa protein (E1B-55kDa) in lytically infected HeLa cells was determined. At the time of infection, when the E1B-55kDa protein facilitates the cytoplasmic accumulation of viral mRNA while simultaneously restricting the accumulation of most cellular mRNA, five distinct intracellular localizations of the protein were observed. Only one of these was disrupted when cells were infected with a mutant virus that fails to produce a second viral protein encoded by early region 4 (E4-34kDa). This protein normally forms a complex with the E1B-55kDa polypeptide, enabling it to influence RNA metabolism. This key localization of the E1B protein was within and about the periphery of nuclear viral inclusion bodies believed to be the site of viral DNA replication and transcription. In the absence of the E4-34kDa protein, the coincidence of E1B-55kDa-specific immunofluorescence and phase-dense viral inclusions was reduced compared with that in a wild-type infection. Similarly, by immunoelectron microscopy, the relative number of E1B-55kDa-specific immunogold particles associated with the clear fibrillar inclusion bodies was reduced. However, the E4-34kDa protein was not required for the close association of the early region 2A DNA binding protein with the viral inclusions. We propose that the viral 55-kDa-34-kDa protein complex interacts with a cellular factor required for cytoplasmic accumulation of mRNAs and directs it to the periphery of the transcriptionally active viral inclusion bodies. This model provides an explanation for the ability of these viral proteins to simultaneously enhance accumulation of viral mRNAs and inhibit accumulation of cellular mRNAs.
A scalable lossy to lossless audio coder for MPEG-4 lossless audio coding (2004)

In this paper, we present Advanced Audio Zip (AAZ), a scalable lossless audio coding technology that was recently selected as the reference model for MPEG audio scalable lossless coding (SLS) work. AAZ provides excellent compression performance while delivering fine grain bit-rate scalability from lossy to lossless coding. Moreover, AAZ provides backward compatibility to the MPEG advanced audio coding (AAC) system by embedding an AAC compliant bit-stream into the lossless bit-stream. As a result, AAZ serves as a universal coding solution with functionalities that were previously offered by several distinct audio coding technologies such as lossless audio coding, perceptual audio coding, or scalable audio coding; and maximizes the interchangeability for digital audio contents migrating among these application domains.
Regulation of Telomere Structure and Functions by Subunits of the INO80 Chromatin Remodeling Complex (2007)

ATP-dependent chromatin remodeling complexes have been implicated in the regulation of transcription, replication, and more recently DNA double-strand break repair. Here we report that the Ies3p subunit of the Saccharomyces cerevisiae INO80 chromatin remodeling complex interacts with a conserved tetratricopeptide repeat domain of the telomerase protein Est1p. Deletion of IES3 and some other subunits of the complex induced telomere elongation and altered telomere position effect. In telomerase-negative mutants, loss of Ies3p delayed the emergence of recombinational survivors and stimulated the formation of extrachromosomal telomeric circles in survivors. Deletion of IES3 also resulted in heightened levels of telomere-telomere fusions in telomerase-deficient strains. In addition, a delay in survivor formation was observed in an Arp8p-deficient mutant. Because Arp8p is required for the chromatin remodeling activity of the INO80 complex, the complex may promote recombinational telomere maintenance by altering chromatin structure. Consistent with this notion, we observed preferential localization of multiple subunits of the INO80 complex to telomeres. Our results reveal novel functions for a subunit of the telomerase complex and the INO80 chromatin remodeling complex.
Two Cytoplasmic Loops of the Glucagon Receptor Are Required to Elevate cAMP or Intracellular Calcium (1999)

The glucagon receptor is a member of a distinct class of G protein-coupled receptors (GPCRs) sharing little amino acid sequence homology with the larger rhodopsin-like GPCR family. To identify the components of the glucagon receptor necessary for G-protein coupling, we replaced sequentially all or part of each intracellular loop (i1, i2, and i3) and the C-terminal tail of the glucagon receptor with the 11 amino acids comprising the first intracellular loop of the D4 dopamine receptor. When expressed in transiently transfected COS-1 cells, the mutant receptors fell into two different groups with respect to hormone-mediated signaling. The first group included the loop i1 mutants, which bound glucagon and signaled normally. The second group comprised the loop i2 and i3 chimeras, which caused no detectable adenylyl cyclase activation in COS-1 cells. However, when expressed in HEK 293T cells, the loop i2 or i3 chimeras caused very small glucagon-mediated increases in cAMP levels and intracellular calcium concentrations, with EC50 values nearly 100-fold higher than those measured for wild-type receptor. Replacement of both loops i2 and i3 simultaneously was required to completely abolish G protein signaling as measured by both cAMP accumulation and calcium flux assays. These results show that the i2 and i3 loops play a role in glucagon receptor signaling, consistent with recent models for the mechanism of activation of G proteins by rhodopsin-like GPCRs.
Inactivation of Glutathione Peroxidase by Nitric Oxide (1995)

S-nitro-N-acetyl-DL-penicillamine (SNAP), a nitric oxide (NO) donor, inactivated bovine glutathione peroxidase (GPx) in a dose- and time-dependent manner. The IC50 of SNAP for GPx was 2 microM at 1 h of incubation and was 20% of the IC50 for another thiol enzyme, glyceraldehyde-3-phosphate dehydrogenase, in which a specific cysteine residue is known to be nitrosylated. Incubation of the inactivated GPx with 5 mM dithiothreitol within 1 h restored about 50% of activity of the start of the SNAP incubation. A longer exposure to NO donors, however, irreversibly inactivated the enzyme. The similarity of the inactivation with SNAP and reactivation with dithiothreitol of GPx to that of glyceraldehyde-3-phosphate dehydrogenase, suggested that NO released from SNAP modified a cysteine-like essential residue on GPx. When U937 cells were incubated with 100 microM SNAP for 1 h, a significant decrease in GPx activity was observed although the change was less dramatic than that with the purified enzyme, and intracellular peroxide levels increased as judged by flow cytometric analysis using a peroxide-sensitive dye. Other major antioxidative enzymes, copper/zinc superoxide dismutase, manganese superoxide dismutase, and catalase, were not affected by SNAP, which suggested that the increased accumulation of peroxides in SNAP-treated cells was due to inhibition of GPx activity by NO. Moreover, stimulation with lipopolysaccharide significantly decreased intracellular GPx activity in RAW 264.7 cells, and this effect was blocked by NO synthase inhibitor N omega-methyl-L-arginine. This indicated that GPx was also inactivated by endogenous NO. This mechanism may at least in part explain the cytotoxic effects of NO on cells and NO-induced apoptotic cell death.
A Unique Paradigm for a Turn-ON Near-Infrared Cyanine-Based Probe: Noninvasive Intravital Optical Imaging of Hydrogen Peroxide (2011)

The development of highly sensitive fluorescent probes in combination with innovative optical techniques is a promising strategy for intravital noninvasive quantitative imaging. Cyanine fluorochromes belong to a superfamily of dyes that have attracted substantial attention in probe design for molecular imaging. We have developed a novel paradigm to introduce a Turn-ON mechanism in cyanine molecules, based on a distinctive change in their π-electrons system. Our new cyanine fluorochrome is synthesized through a simple two-step procedure and has an unprecedented high fluorescence quantum yield of 16% and large extinction coefficient of 52,000 M(-1)cm(-1). The synthetic strategy allows one to prepare probes for various analytes by introducing a specific triggering group on the probe molecule. The probe was equipped with a corresponding trigger and demonstrated efficient imaging of endogenous hydrogen peroxide, produced in an acute lipopolysaccharide-induced inflammation model in mice. This approach provides, for the first time, an available methodology to prepare modular molecular Turn-ON probes that can release an active cyanine fluorophore upon reaction with specific analyte.
Neuropilin 1 deficiency on CD4+Foxp3+ regulatory T cells impairs mouse melanoma growth (2012)

Infiltration of Foxp3(+) regulatory T (T reg) cells is considered to be a critical step during tumor development and progression. T reg cells supposedly suppress locally an effective anti-tumor immune response within tumor tissues, although the precise mechanism by which T reg cells infiltrate the tumor is still unclear. We provide evidence that Neuropilin 1 (Nrp-1), highly expressed by Foxp3(+) T reg cells, regulates the immunological anti-tumor control by guiding T reg cells into the tumor in response to tumor-derived vascular endothelial growth factor (VEGF). We demonstrate for the first time that T cell-specific ablation of Nrp-1 expression results in a significant breakdown in tumor immune escape in various transplantation models and in a spontaneous, endogenously driven melanoma model associated with strongly reduced tumor growth and prolonged tumor-free survival. Strikingly, numbers of tumor-infiltrating Foxp3(+) T reg cells were significantly reduced accompanied by enhanced activation of CD8(+) T cells within tumors of T cell-specific Nrp-1-deficient mice. This phenotype can be reversed by adoptive transfer of Nrp-1(+) T reg cells from wild-type mice. Thus, our data strongly suggest that Nrp-1 acts as a key mediator of Foxp3(+) T reg cell infiltration into the tumor site resulting in a dampened anti-tumor immune response and enhanced tumor progression.