gebhart/patrepeval huggingface dataset:
Endothelin receptor blockers reduce I/R-induced intestinal mucosal injury: role of blood flow (2002)

The aim of the present study was to assess the role of endothelin (ET) in ischemia-reperfusion (I/R)-induced mucosal injury. Mucosal permeability ((51)Cr-EDTA clearance) and tissue myeloperoxidase (MPO) activity were significantly increased after 30 min of ischemia followed by 30 min of reperfusion. The I/R-induced increases in mucosal permeability and polymorphonuclear leukocyte (PMN) infiltration were significantly attenuated by pretreatments with ET(A) (BQ-485) and/or ET(B) (BQ-788) receptor antagonists. Monoclonal antibody (MAb) directed against intercellular adhesion molecule-1 (ICAM-1; MAb 1A29) and superoxide dismutase (SOD) pretreatments significantly attenuated the increased mucosal permeability and PMN infiltration in a similar manner as with ET receptor antagonists. Superior mesenteric artery blood flow was significantly reduced during the reperfusion period. Both ET receptor antagonists caused a significant rise in blood flow compared with an untreated I/R group. In conclusion, our data suggest that ET(A) and/or ET(B) receptors, ICAM-1, and superoxide play an important role in I/R-induced mucosal dysfunction and PMN infiltration. Furthermore, ET is involved in the pathogenesis of post-reperfusion-induced damage and beneficial effects of ET receptor antagonism are related to an improvement of disturbed blood flow during the reperfusion period.
Delaminated zeolite‐catalysed synthesis of high‐molecular weight polycarbosilane as a low shrinkage SiC precursor (2007)

Abstract A polycarbosilane (PCS) with a higher number–average molecular weight (2710 vs. 1570), and hence with a higher ceramic yield (74 vs. 68%), compared to a commercial Nipusi type S PCS has been synthesized via the catalytic decomposition of polydimethylsilane at 400 °C using H‐ITQ‐2, a delaminated zeolite with a very high external surface area, as a solid acid. The silicon carbide film fabricated using this PCS was found to show a much lower level (16 vs. 39%) of shrinkage than the commercial PCS‐derived film, together with better mechanical properties, suggesting the potential of its preceramic polymer to produce robust ceramic coatings. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 725–732, 2008
Flux Analysis Uncovers Key Role of Functional Redundancy in Formaldehyde Metabolism (2004)

Genome-scale analysis of predicted metabolic pathways has revealed the common occurrence of apparent redundancy for specific functional units, or metabolic modules. In many cases, mutation analysis does not resolve function, and instead, direct experimental analysis of metabolic flux under changing conditions is necessary. In order to use genome sequences to build models of cellular function, it is important to define function for such apparently redundant systems. Here we describe direct flux measurements to determine the role of redundancy in three modules involved in formaldehyde assimilation and dissimilation in a bacterium growing on methanol. A combination of deuterium and (14)C labeling was used to measure the flux through each of the branches of metabolism for growth on methanol during transitions into and out of methylotrophy. The cells were found to differentially partition formaldehyde among the three modules depending on the flux of methanol into the cell. A dynamic mathematical model demonstrated that the kinetic constants of the enzymes involved are sufficient to account for this phenomenon. We demonstrate the role of redundancy in formaldehyde metabolism and have uncovered a new paradigm for coping with toxic, high-flux metabolic intermediates: a dynamic, interconnected metabolic loop.
Extending and Simplifying Transfer Function Design in Medical Volume Rendering Using Local Histograms (2005)

Direct Volume Rendering (DVR) is known to be of diagnostic value in the analysis of medical data sets. However, its deployment in everyday clinical use has so far been limited. Two major challenges are that the current methods for Transfer Function (TF) construction are too complex and that the tissue separation abilities of the TF need to be extended. In this paper we propose the use of histogram analysis in local neighborhoods to address both these conflicting problems. To reduce TF construction difficulty, we introduce Partial Range Histograms in an automatic tissue detection scheme, which in connection with Adaptive Trapezoids enable efficient TF design. To separate tissues with overlapping intensity ranges, we propose a fuzzy classification based on local histograms as a second TF dimension. This increases the power of the TF, while retaining intuitive presentation and interaction.
Macrophage‐secreted prostaglandin E2 potentiates immune complex‐induced B cell unresponsiveness (1990)

Immune complexes (IC) are potent modulators of immune responses. In this report, we used an in vitro murine model system to investigate how two types of accessory cells pulsed with IC regulated B cell function. We demonstrate that IC-pulsed macrophages (M phi) induce hapten-specific B cell unresponsiveness, whereas IC-pulsed splenic lymphoid dendritic cells (LDC) and and LDC-like tumor line caused an augmentation of the antibody response. The mechanism by which IC-pulsed M phi diminished antibody production required two signals. The first was an antigen-specific signal supplied by the IC, and the second a nonspecific co-factor which was a product of M phi cyclo-oxygenase metabolism. Specifically, it was shown that prostaglandin E2 (PGE2) could function at this co-factor. Interestingly, other prostanoids, such as PGF2 alpha, did not function in this fashion. Purified fluorescein (FL+)-specific B cells pulsed with IC exhibited a similar pattern of hapten-specific unresponsiveness. Treatment of accessory cell-free, FL+B cells with PGE2 rendered them sensitive to subtolerogenic doses of soluble IC. Overall, our results suggest that one mechanism by which unresponsiveness can be induced involves both IC and PGE2, and that elevated levels of PGE2 sensitize B lymphocytes to antigen-specific tolerogenic signals.
Chiral Discotic Molecules: Expression and Amplification of Chirality (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Noise enhanced coupling between two oscillators with long-term plasticity (2015)

Spike timing-dependent plasticity is a fundamental adaptation mechanism of the nervous system. It induces structural changes of synaptic connectivity by regulation of coupling strengths between individual cells depending on their spiking behavior. As a biophysical process its functioning is constantly subjected to natural fluctuations. We study theoretically the influence of noise on a microscopic level by considering only two coupled neurons. Adopting a phase description for the neurons we derive a two-dimensional system which describes the averaged dynamics of the coupling strengths. We show that a multistability of several coupling configurations is possible, where some configurations are not found in systems without noise. Intriguingly, it is possible that a strong bidirectional coupling, which is not present in the noise-free situation, can be stabilized by the noise. This means that increased noise, which is normally expected to desynchronize the neurons, can be the reason for an antagonistic response of the system, which organizes itself into a state of stronger coupling and counteracts the impact of noise. This mechanism, as well as a high potential for multistability, is also demonstrated numerically for a coupled pair of Hodgkin-Huxley neurons.
Recombinant Spider Silk Bioinks for Continuous Protein Release by Encapsulated Producer Cells (2022)

Targeted therapies using biopharmaceuticals are of growing clinical importance in disease treatment. Currently, there are several limitations of protein-based therapeutics (biologicals), including suboptimal biodistribution, lack of stability, and systemic side effects. A promising approach to overcoming these limitations could be a therapeutic cell-loaded 3D construct consisting of a suitable matrix component that harbors producer cells continuously secreting the biological of interest. Here, the recombinant spider silk proteins eADF4(C16), eADF4(C16)-RGD, and eADF4(C16)-RGE have been processed together with HEK293 producer cells stably secreting the highly traceable reporter biological TNFR2-Fc-GpL, a fusion protein consisting of the extracellular domain of TNFR2, the Fc domain of human IgG1, and the luciferase of <i>Gaussia princeps</i> as a reporter domain. eADF4(C16) and eADF4(C16)-RGD hydrogels provide structural and mechanical support, promote HEK293 cell growth, and allow fusion protein production by the latter. Bioink-captured HEK293 producer cells continuously release functional TNFR2-Fc-GpL over 14 days. Thus, the combination of biocompatible, printable spider silk bioinks with drug-producing cells is promising for generating implantable 3D constructs for continuous targeted therapy.
Near-infrared optical tomography: endoscopic imaging approach (2007)

Near-infrared optical tomography is an interesting technique of imaging with high blood-based contrast. Unfortunately non-invasive NIR tomographic imaging has been restricted to specific organs like breast that can be transilluminated externally. In this paper, we demonstrate that near-infrared (NIR) optical tomography can be employed at the endoscope-scale, and implemented at a rapid sampling speed that allows translation to in vivo use. A spread-spectral-encoding technique based on a broadband light source is combined with light delivery by linear-to-circular fiber bundle, to provide endoscopic probing of multiple source/detector fibers for tomographic imaging as well as parallel sampling of all source-detector pairs for rapid data acquisition. Endoscopic NIR tomography is demonstrated by use of a 12mm diameter probe housing 8 sources and 8 detectors at 8 Hz frame rate. Transrectal NIR optical tomography by use of tissue specimen is also presented. This novel approach provides the key feasibility studies to allow this blood-based contrast imaging technology to be tried in cancer detection of internal organs via endoscopic interrogation.
Overexpression of Cyclin A Inhibits Augmentation of Recombinant Adeno-Associated Virus Transduction by the Adenovirus E4orf6 Protein (1999)

The 34-kDa product of adenovirus E4 region open reading frame 6 (E4orf6) dramatically enhances transduction by recombinant adeno-associated virus vectors (rAAV). This is achieved by promoting the conversion of incoming single-stranded viral genomes into transcriptionally competent duplex molecules. The molecular mechanism for enhancing second-strand synthesis is not fully understood. In this study, we analyzed the cellular consequences of E4orf6 expression and the requirements for efficient rAAV transduction mediated by E4orf6. Expression of E4orf6 in 293 cells led to an inhibition of cell cycle progression and an accumulation of cells in S phase. This was preceded by specific degradation of cyclin A and p53, while the levels of other proteins involved in cell cycle control remained unchanged. In addition, the kinase activity of cdc2 was inhibited. We further showed that p53 expression is not necessary or inhibitory for augmentation of rAAV transduction by E4orf6. However, overexpression of cyclin A inhibited E4orf6-mediated enhancement of rAAV transduction. A cyclin A mutant incapable of recruiting protein substrates for cdk2 was unable to inhibit E4orf6-mediated augmentation. In addition, we created an E4orf6 mutant that is selectively defective in rAAV augmentation of transduction. Based on these findings, we suggest that cyclin A degradation represents a viral mechanism to disrupt cell cycle progression, resulting in enhanced viral transduction. Understanding the cellular pathways used during transduction will increase the utility of rAAV vectors in a wide range of gene therapy applications.
Kinetics of Free Radical Polymerization of Spacerless Dendronized Macromonomers in Supercritical Carbon Dioxide (2011)

The kinetics of the free radical polymerization in supercritical carbon dioxide of third (G3) and fourth (G4) generation spacerless dendronized macromonomers, bearing a methacrylate group at the focal point, is experimentally investigated. Conversions up to 90% could be achieved in few hours for both monomers, with degrees of polymerization on the order of thousands of monomer units for G3 and 100–200 for G4. Experimental data are interpreted using a conventional free radical kinetic scheme. Within this frame, chain termination is dominated by chain transfer to monomer and the extremely high reactivity of the macromonomers when polymerized in supercritical carbon dioxide is reflecting reduced termination rate at increasing dendron generation.
Molecular Dynamics Simulation on Longitudinal Optical Phonon Mode Decay and Heat Transport in a Silicon Nano-Structure Covered with Oxide Films (2011)

A series of molecular dynamics (MD) simulations have been conducted to investigate the heat transport in terms of the phonon dynamics in nanoscale silicon (Si). This work is motivated by a concern over the stagnation of heat at the drain region of nanoscopic transistors, owing to this, a large amount of optical phonons with a low group velocity are emitted from hot electrons, which are ballistically transferred through channel region. The point of this work is the explicit inclusion of the SiO 2 film in the MD simulation of the Si lattice. The calculation results show that longitudinal optical (LO) phonons decay faster as Si lattice thickness decreases and turn into acoustic phonons. In contrast, thermal diffusion rate decreases with Si lattice thickness. Both the decay rate of LO phonons and thermal diffusion rate are not governed by oxide thickness. These results imply that the phonon scattering at the SiO 2 /Si interface is enhanced by thinning the Si layer. In nanoscopic devices, a thin Si layer is effective in diminishing the optical phonons with a low group velocity, but it hinders the subsequent heat transport.
EFFECTS OF LEFLUNOMIDE AND DEOXYSPERGUALIN IN THE GUINEA PIG???RAT CARDIAC MODEL OF DELAYED XENOGRAFT REJECTION (1997)

LEF or DSG along with CVF can result in the longest prolongation of xenograft survival yet reported in this model, in conjunction with a dampening of host mononuclear cell responses, including suppression of B cell activation. However, the persistent influx of MO in this model, despite lack of C-, Fc receptor- or apparent chemokine-dependent mechanisms, suggests the presence of additional mechanisms for cell recruitment and activation. It was of importance that, in this regard, although MO depletion is technically difficult and can lead to undesired effects, the demonstration of rapid MO lectin induction postxenografting indicates opportunities for blockade of MO recruitment and functions during DXR by use of anti-MO lectin monoclonal antibodies or administration of competing sugars.
Wide‐field color imaging of scatter‐based tissue contrast using both high spatial frequency illumination and cross‐polarization gating (2017)

This study characterizes the scatter-specific tissue contrast that can be obtained by high spatial frequency (HSF) domain imaging and cross-polarization (CP) imaging, using a standard color imaging system, and how combining them may be beneficial. Both HSF and CP approaches are known to modulate the sensitivity of epi-illumination reflectance images between diffuse multiply scattered and superficially backscattered photons, providing enhanced contrast from microstructure and composition than what is achieved by standard wide-field imaging. Measurements in tissue-simulating optical phantoms show that CP imaging returns localized assessments of both scattering and absorption effects, while HSF has uniquely specific sensitivity to scatter-only contrast, with a strong suppression of visible contrast from blood. The combination of CP and HSF imaging provided an expanded sensitivity to scatter compared with CP imaging, while rejecting specular reflections detected by HSF imaging. ex vivo imaging of an atlas of dissected rodent organs/tissues demonstrated the scatter-based contrast achieved with HSF, CP and HSF-CP imaging, with the white light spectral signal returned by each approach translated to a color image for intuitive encoding of scatter-based contrast within images of tissue. The results suggest that visible CP-HSF imaging could have the potential to aid diagnostic imaging of lesions in skin or mucosal tissues and organs, where just CP is currently the standard practice imaging modality.
The "lazy" NK cells of Chediak-Higashi syndrome. (1983)

Natural killer (NK) function, measured in a short-term (4-hr) 51Cr-release assay, is profoundly depressed in circulating PBL of donors with Chediak-Higashi syndrome (CHS). In this study, we demonstrate that CHS NK cells can express relatively normal lytic function after prolonged exposure in vitro to high levels of activating as well as cytotoxic stimuli. After activation with the human cloned interferon (B1) for 24 hr, CHS NK cells have lytic activity comparable to unactivated normals in a 4-hr 51Cr-release assay. In addition, after 5 days of activation with mitomycin C-treated B cell lines, CHS NK cells have levels of activity similar to those of activated normals but are defective in generating cytotoxic cells capable of lysing the stimulator B cell. Even though CHS NK cells are defective in a 4-hr 51Cr-release assay, after 16 hr they enhance their killing capability 200 to 400-fold. In fact, after 16 hr of interaction with K562 target cells, CHS NK cells are capable of releasing NK soluble cytotoxic factors. These results are consistent with the hypothesis that CHS NK cells have all the necessary cellular structures and molecules required for them to function as lytic effector cells, but their lack of cytotoxic function is due to a relative refractoriness in initiating the post-binding lytic mechanism.
Low-Loss Plasmonic Titanium Nitride Strip Waveguides (2014)

In this work we report low-loss insulator-metal-insulator plasmonic interconnects using the CMOS-compatible material titanium nitride. The mode profile shows the characteristic exponential decay of the plasmonic regime, with propagation losses as low as 0.79 dB/mm.
Microresonator-Based Scanning Comb Spectroscopy (2017)

We demonstrate mode-hop-free tuning of a modelocked silicon microresonator frequency comb over 60 GHz. Gas-phase spectroscopy of acetylene is performed with high-spectral-resolution (&lt; 80 MHz) over a bandwidth of 40 THz.
Enantioselective Synthesis of (R)- and (S)-1-2H-1-Octanol and Their Corresponding Amines (2011)

Abstract Both enantiomers of 1-2H-1-octanol were obtained by the enzymatic reduction of deuterated octanal in the presence of alcohol dehydrogenases (ADH) (ADH-T or ADH-LB) as the biocatalyst in good yield, purity, and enantiomeric excess (>95%). The cofactor nicotinamide adenine dinucleotide phosphate was regenerated by the addition of isopropanol. To simplify the synthetic route, the direct reduction of octanal using the same enzymes and the same cofactor but adding deuterated isopropanol was evaluated. This provided a one-step procedure from a commercially available starting compound to both enantiomers of 1-2H-1-octanol in good yields (>80%) and good enantiomeric excess (∼97%). The (S)-alcohols were converted to their corresponding (R)-amines, which showed ee's around 90%.
5013 An Experimental Investigation of NO_x Emission in High Air Temperature Combustion in Cylindrical Furnace (2006)

An experimental investigation of the effect of the distance between the fuel and air nozzles on NO_x emission at different temperatures and oxygen concentrations of the oxidizer in high air temperature combustion cylindrical furnace was conducted. Highly preheated oxidizer (air and nitrogen) was injected in the furnace through an oxidizer nozzle positioned at the center of the base of the cylindrical furnace. Propane was injected through three different sets of fuel nozzles, one set working at a time. As a result, the emission of NO_x decreased as the distance between the fuel nozzles and the oxidizer nozzle increased. At lower preheating temperatures and lower O2 concentrations of the oxidizer, the emission of NO_x tends to become lower.
Nonunion After Periprosthetic Femoral Fracture Associated with Total Hip Arthroplasty* (1999)

Nonunion of a femoral fracture associated with a total hip prosthesis is an infrequent problem. Treatment is difficult, with a high rate of complications and relatively poor functional outcomes. The data from this series must be interpreted with caution, as patients were managed over a period of three decades and many did not have the advantage of modern techniques of revision hip arthroplasty. Prevention of nonunion by optimum treatment of the initial fracture is most important. Treatment of a femoral nonunion about a total hip implant should be implemented on the basis of the status of the fixation of the prosthesis and the quality of the surrounding bone.
Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire (2012)

Idiosyncratic adverse drug reactions are unpredictable, dose-independent and potentially life threatening; this makes them a major factor contributing to the cost and uncertainty of drug development. Clinical data suggest that many such reactions involve immune mechanisms, and genetic association studies have identified strong linkages between drug hypersensitivity reactions to several drugs and specific HLA alleles. One of the strongest such genetic associations found has been for the antiviral drug abacavir, which causes severe adverse reactions exclusively in patients expressing the HLA molecular variant B*57:01. Abacavir adverse reactions were recently shown to be driven by drug-specific activation of cytokine-producing, cytotoxic CD8(+) T cells that required HLA-B*57:01 molecules for their function; however, the mechanism by which abacavir induces this pathologic T-cell response remains unclear. Here we show that abacavir can bind within the F pocket of the peptide-binding groove of HLA-B*57:01, thereby altering its specificity. This provides an explanation for HLA-linked idiosyncratic adverse drug reactions, namely that drugs can alter the repertoire of self-peptides presented to T cells, thus causing the equivalent of an alloreactive T-cell response. Indeed, we identified specific self-peptides that are presented only in the presence of abacavir and that were recognized by T cells of hypersensitive patients. The assays that we have established can be applied to test additional compounds with suspected HLA-linked hypersensitivities in vitro. Where successful, these assays could speed up the discovery and mechanistic understanding of HLA-linked hypersensitivities, and guide the development of safer drugs.
Supplementary Figure 1 from Capivasertib, an AKT Kinase Inhibitor, as Monotherapy or in Combination with Fulvestrant in Patients with <i>AKT1</i><sup>E17K</sup>-Mutant, ER-Positive Metastatic Breast Cancer (2023)

&lt;p&gt;Supplementary Figure 1. Participant Flow Diagram&lt;/p&gt;
Third International Havemeyer Workshop on Equine Herpesvirus type 1 (2012)

Supplementary item 1 Scientific questions for future investigation of EHV-1, with unknown factors and potential approaches. 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.
Supplementary Figure 2 from XPO1 (CRM1) Inhibition Represses STAT3 Activation to Drive a Survivin-Dependent Oncogenic Switch in Triple-Negative Breast Cancer (2023)

&lt;p&gt;PDF file - 53K, Serum levels of KPT-330 in mice.&lt;/p&gt;