gebhart/patrepeval huggingface dataset:
The Immunomodulatory Functions of Mesenchymal Stromal/Stem Cells Mediated via Paracrine Activity (2019)

Mesenchymal stromal/stem cells (MSCs) exist in almost all tissues, possessing the potential to differentiate into specialized cell types and exert immunomodulatory functions. Thus, they have attracted much attention as a promising therapeutic candidate. Recent studies have demonstrated that paracrine signaling is mainly responsible for the involvement of MSCs in the modulation of immune responses and the progression of diseases. Through release of secretome consisting of a diverse range of cytokines, chemokines, and extracellular vesicles (EVs), MSCs convey regulatory messages to recipient immune cells in the microenvironment. In this review, we focus on the recent advances in how MSCs contribute to immunomodulation through the secretion of paracrine factors. The further improved understanding of the molecular mechanism underlying the interactions between MSCs and immune cells highlights the paracrine biology of MSCs in the modulation of the immune microenvironment and promotes the clinical application of MSCs in regenerative medicine and immune diseases.
Beneficial effects of the active principle component of Korean cabbage kimchi via increasing nitric oxide production and suppressing inflammation in the aorta of apoE knockout mice (2012)

The present study investigated the effects of 3'-(4'-hydroxyl-3',5'-dimethoxyphenyl)propionic acid (HDMPPA), the active principle compound of kimchi, on vascular damage in the experimental atherosclerotic animal. HDMPPA was administrated by an intraperitoneal injection of 10 mg/kg per d for 8 weeks to apoE knockout (KO) mice with an atherogenic diet containing 1 % cholesterol, and its effects were compared with vehicle-treated control mice. HDMPPA increased NO content in the aorta, accompanied by a decrease in reactive oxygen species (ROS) concentration. Furthermore, in the HDMPPA-treated group, aortic endothelial NO synthase (eNOS) expression was up-regulated compared with the control group. These results suggested that HDMPPA could maintain NO bioavailability through an increasing eNOS expression and preventing NO degradation by ROS. Furthermore, HDMPPA treatment in apoE KO mice inhibited eNOS uncoupling through an increase in vascular tetrahydrobiopterin content and a decrease in serum asymmetric dimethylarginine levels. Moreover, HDMPPA ameliorates inflammatory-related protein expression in the aorta of apoE KO mice. Therefore, the present study suggests that HDMPPA, the active compound of kimchi, a Korean functional food, may exert its vascular protective effect through the preservation of NO bioavailability and suppression of the inflammatory response.
Characterization of dynamic and steady‐state protein phosphorylation using a fluorescent phosphoprotein gel stain and mass spectrometry (2004)

Protein phosphorylation plays a vital role in the regulation of most aspects of cellular activity, being key to propagating messages within signal transduction pathways and to modulating protein function. Pro-Q Diamond phosphoprotein gel stain is suitable for the fluorescence detection of phosphoserine-, phosphothreonine-, and phosphotyrosine-containing proteins directly in sodium dodecyl sulfate (SDS)-polyacrylamide gels. The technology is especially appropriate for profiling steady-state and dynamic phosphorylation on a proteome-wide scale, as demonstrated through detection of the native phosphorylation of cardiac mitochondrial phosphoproteins and changes in this profile arising from the activity of a protein kinase. For example, Pro-Q Diamond phosphoprotein gel stain was employed to demonstrate that among the 46 subunits of the mitochondrial respiratory chain complex, NADH:ubiquinone oxidoreductase (complex I), a 42 kDa subunit is phosphorylated in the steady-state. However, exposure of mitochondria to cAMP-dependent protein kinase increases phosphorylation of this 42 kDa subunit and results in de novo phosphorylation of an 18 kDa subunit as well. Since Pro-Q Diamond dye binds to phosphorylated residues noncovalently, the staining technology is fully compatible with modern microchemical analysis procedures, such as peptide mass profiling by matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry and post-source decay analysis of peptide phosphorylation.
Supplementary Methods, Figures 1-5 from mTOR Kinase Inhibition Causes Feedback-Dependent Biphasic Regulation of AKT Signaling (2023)

Supplementary Methods, Figures 1-5 from mTOR Kinase Inhibition Causes Feedback-Dependent Biphasic Regulation of AKT Signaling
Dynamic Appearance Modeling for Human Tracking (2006)

Dynamic appearance is one of the most important cues for tracking and identifying moving people. However, direct modeling spatio-temporal variations of such appearance is often a difficult problem due to their high dimensionality and nonlinearities. In this paper we present a human tracking system that uses a dynamic appearance and motion modeling framework based on the use of robust system dynamics identification and nonlinear dimensionality reduction techniques. The proposed system learns dynamic appearance and motion models from a small set of initial frames and does not require prior knowledge such as gender or type of activity. The advantages of the proposed tracking system are illustrated with several examples where the learned dynamics accurately predict the location and appearance of the targets in future frames, preventing tracking failures due to model drifting, target occlusion and scene clutter.
Chapter 1. C-glycosylation invented by Pr Lubineau's team: a key-reaction for innovation in cosmetics (2014)

The aim of this chapter is to provide a brief description of why and how the Research Group of L'Oreal, a leading company in cosmetics, has developed on an industrial scale the C-glycosylation reaction invented by Pr. Lubineau's team. This first example of industrial development in the world comes from the compliance of this technology with the principles of green chemistry and the access to original structures of high interest for skin anti-ageing. From various C-6 and C-5 saccharides, original C-glycosyl derivatives were synthesized for evaluating their potential role as activators of the biosynthesis of glycosylaminoglycans, polysaccharides that are essential to maintain the mechanical properties of skin. A β-C-xylosyl derivative combined the highest activity in vitro with confirmation in vivo. This eco-designed compound was developed using the calculation of green indicators and further marketed under the name of Pro-Xylane™.
Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains (2020)

Streptomyces venezuelae is well known to produce various secondary metabolites, including chloramphenicol, jadomycin, and pikromycin. Although many strains have been classified as S. venezuelae species, only a limited number of strains have been explored extensively for their genomic contents. Moreover, genomic differences and diversity in secondary metabolite production between the strains have never been compared. Here, we report complete genome sequences of three S. venezuelae strains (ATCC 10712, ATCC 10595, and ATCC 21113) harboring chloramphenicol and jadomycin biosynthetic gene clusters (BGC). With these high-quality genome sequences, we revealed that the three strains share more than 85% of total genes and most of the secondary metabolite biosynthetic gene clusters (smBGC). Despite such conservation, the strains produced different amounts of chloramphenicol and jadomycin, indicating differential regulation of secondary metabolite production at the strain level. Interestingly, antagonistic production of chloramphenicol and jadomycin was observed in these strains. Through comparison of the chloramphenicol and jadomycin BGCs among the three strains, we found sequence variations in many genes, the non-coding RNA coding regions, and binding sites of regulators, which affect the production of the secondary metabolites. We anticipate that these genome sequences of closely related strains would serve as useful resources for understanding the complex secondary metabolism and for designing an optimal production process using Streptomyces strains.
An Optical-Electrical Sub-Sampling Receiver Employing Continuous-Time ΔΣ Modulation (2006)

An optical-electrical sub-sampling down-conversion receiver architecture leveraging low-jitter optical sampling is described. A simple interface between the optical and electrical domains is accomplished by combining a photodiode with a second-order continuous-time ΔΣ modulator. A prototype system implemented in 0.18 mum CMOS achieving 36.4 dB SNR in a 2 MHz BW with an OSR of 250 is demonstrated.
Fading characterization in a semi-anechoic chamber with artificial scatterers for Mean Effective Gain measurements of wireless handheld terminals (2008)

This paper presents the methodology and corresponding analysis of the scattered field measurements in a semi- anechoic ferrite-lined chamber. The focus is on recreating a Rayleigh fading environment with realistic cross-polarization ratio (XPR) with the purpose of measuring the mean effective gain (MEG) of mobile handheld terminal operating in the 900 MHz GSM band. The emulated XPR was similar in each of the studied scenarios and approximately equal to 12 dB. The Rayleigh fading hypothesis for the statistics of the envelope of the measured signals could not be rejected in most cases at the 95% level with the Kolmogorov goodness-of-fit test.
Dichroic Fourier Transform Infrared Spectroscopy Characterization of the β-Sheet Orientation in Spider Silk Films on Silicon Substrates (2021)

Orientation analysis of the β-sheet structure within films of the established recombinant spider silk protein eADF4(C16) was performed using a concept based on dichroic transmission- and attenuated total reflection-Fourier transform infrared spectroscopy, lineshape analysis, assignment of amide I components to specific vibration modes, and transition dipole moment directions of β-sheet structures. Based on the experimental dichroic ratio <i>R</i>, the order parameter <i>S</i> of β-sheet structures was calculated with respect to uniaxial orientation. Films of eADF4(C16) were deposited on untexturized (Si) and unidirectionally scratched silicon substrates (Si-sc) and post-treated with MeOH vapor. Freshly cast thin and thick eADF4(C16) films out of hexafluoroisopropanol featured β-sheet contents of ≈6%, which increased to >30% after MeOH post-treatment in dependence of time. Pseudo-first order folding kinetics were obtained, suggesting a transition from an unfolded to a folded state. In MeOH post-treated thin films with diameters in the nanometer range, a significant orientation of β-sheets was obtained regardless of the texturization of the silicon substrate (Si, Si-sc). This was rationalized by dichroic ratios of the amide I component at 1696 cm<sup>-1</sup> assigned to the (0, π) mode of antiparallel β-sheet structures, whose transition dipole moment <i>M</i> is located in parallel to both β-sheet plane and chain direction. The calculated high molecular order parameter <i>S</i> ≈ 0.40 suggested vertically (out-of-plane) oriented antiparallel β-sheet stacks with tilt angles of γ ≈ 39° to the surface normal. Microscale (thick) films, in contrast, revealed low order parameters <i>S</i> ≈ 0. Scanning force microscopy on thin eADF4 films at silicon substrates showed dewetted polymer film structures rather at the micro-scale. These findings give new insights in the role of the β-sheet crystallite orientation for the mechanical properties of spider silk materials.
Interconnection of post-transcriptional regulation: The RNA-binding protein Hfq is a novel target of the Lon protease in Pseudomonas aeruginosa (2016)

Besides being a major opportunistic human pathogen, Pseudomonas aeruginosa can be found in a wide range of environments. This versatility is linked to complex regulation, which is achieved through the action of transcriptional regulators, and post-transcriptional regulation by intracellular proteases including Lon. Indeed, lon mutants in this species show defects in motility, biofilm formation, pathogenicity and fluoroquinolone resistance. Here, the proteomic approach stable isotope labeling by amino acids in cell culture (SILAC) was used to search for novel proteolytic targets. One of the proteins that accumulated in the lon mutant was the RNA-binding protein Hfq. Further experiments demonstrated the ability of Lon to degrade Hfq in vitro. Also, overexpression of the hfq gene in the wild-type strain led to partial inhibition of swarming, swimming and twitching motilities, indicating that Hfq accumulation could contribute to the phenotypes displayed by Lon mutants. Hfq overexpression also led to the upregulation of the small regulatory RNA PhrS. Analysis of the phenotypes of strains lacking or overexpressing this sRNA indicated that the Lon protease might be indirectly regulating the levels and activity of sRNAs via Hfq. Overall, this study revealed new links in the complex regulatory chain that controls multicellular behaviours in P. aeruginosa.
Realizing Super-Resolution with Superimposed Projection (2007)

We consider the problem of rendering high-resolution images on a display composed of multiple superimposed lower-resolution projectors. A theoretical analysis of this problem in the literature previously concluded that the multi-projector superimposition of low resolution projectors cannot produce high resolution images. In our recent work, we showed to the contrary that super-resolution via multiple superimposed projectors is indeed theoretically achievable. This paper derives practical algorithms for real multi-projector systems that account for the intra- and inter-projector variations and that render high-quality, high-resolution content at real-time interactive frame rates. A camera is used to estimate the geometric, photometric, and color properties of each component projector in a calibration step. Given this parameter information, we demonstrate novel methods for efficiently generating optimal sub-frames so that the resulting projected image is as close as possible to the given high resolution images.
Stress, Heat Shock Proteins, and Autoimmunity (2007)

Especially since the (re-)discovery of T cell subpopulations with specialized regulatory activities, mechanisms of anti-inflammatory T cell regulation are studied very actively and are expected to lead to the development of novel immunotherapeutic approaches, especially in chronic inflammatory diseases. Heat shock proteins (Hsp) are possible targets for regulatory T cells due to their enhanced expression in inflamed (stressed) tissues and the evidence that Hsp induce anti-inflammatory immunoregulatory T cell responses. Initial evidence for an immunoregulatory role of Hsp in chronic inflammation was obtained through analysis of T cell responses in the rat model of adjuvant arthritis and the findings that Hsp immunizations protected against the induction of various forms of autoimmune arthritis in rat and mouse models. Since then, immune reactivity to Hsp was found to result from inflammation in various disease models and human inflammatory conditions, such as rheumatoid arthritis (RA), type 1 diabetes, and atherosclerosis. Now, also in the light of a growing interest in T cell regulation, it is of interest to further explore the mechanisms through which Hsp can be utilized to trigger immunoregulatory pathways, capable of suppressing such a wide and diversified spectrum of inflammatory diseases.
Influence of protonic solvents on spin–spin coupling involving phosphorus directly bonded to hydrogen, fluorine, or another phosphorus atom in phosphoryl and thiophosphoryl molecules (1972)

The effect on the n.m.r. spectral parameters of dissolving five different phosphoryl and thiophosphoryl compounds in a series of organic solvents of varying protonic acidity was studied. For all five of these compounds, the absolute magnitudes of the coupling constants for the directly bonded magnetically active nuclei increased with solvent acidity, whilst there was also a concurrent small change in the chemical shift(s). These and related results are discussed in terms of association with the acidic solvent through hydrogen bonding at the phosphoryl oxygen atom (or thiophosphoryl sulphur atom). Some pertinent semi-empirical LCAO–MO–SCF calculations have been carried out for these molecules, with and without hydrogen bonding.
Surface D2 Autoreceptor Expression on Substantia Nigra Dopamine Neuron Dendrites (2021)

Abstract G-Protein coupled D2 receptors expressed on dopamine neurons, i.e. D2-autoreceptors (D2Rs), negatively regulate transmitter release and cell firing in axonal terminals and somatodendritic compartments. However, as the membrane distribution of D2Rs at somatodendritic signaling sites has not been fully characterized, functional mechanistic details remain uncertain. This study utilized a knockin mouse to examine surface D2Rs linked at the N-terminus to a superecliptic pHlourin green fluorescent protein epitope (SEP) in dopamine neurons of the substantia nigra. By incubating live slices with a highly specific anti-SEP antibody, the selective labeling of plasma membrane associated receptors was achieved. The SEP-D2Rs appeared as puncta like structures apposed to the surface of dendrites and soma of dopamine neurons. The percentage of D2R expression apposed to TH positive structures varied linearly with the density of TH fibers observed. TH-associated SEP-D2Rs displayed a cell surface density of 0.180 puncta per µm 2 , which corresponds to an average frequency of 1 punctum every 1.326 µm using nearest neighbor analysis. The distinct punctate appearance of the anti-SEP staining indicates there is a population of D2Rs organized in discrete clusters along the plasma membrane, an arrangement that can spatially localize signaling and influence GPCR efficacy. The results also indicate that D2Rs are spatially distributed on the plasma membrane at a frequency higher than previously reported.
Discovery of the Oxadiazine FRM-024: A Potent CNS-Penetrant Gamma Secretase Modulator (2021)

The recent approval of aducanumab for Alzheimer's disease has heightened the interest in therapies targeting the amyloid hypothesis. Our research has focused on identification of novel compounds to improve amyloid processing by modulating gamma secretase activity, thereby addressing a significant biological deficit known to plague the familial form of the disease. Herein, we describe the design, synthesis, and optimization of new gamma secretase modulators (GSMs) based on previously reported oxadiazine <b>1</b>. Potency improvements with a focus on predicted and measured properties afforded high-quality compounds further differentiated via robust Aβ<sub>42</sub> reductions in both rodents and nonhuman primates. Extensive preclinical profiling, efficacy studies, and safety studies resulted in the nomination of FRM-024, (+)-<i>cis</i>-5-(4-chlorophenyl)-6-cyclopropyl-3-(6-methoxy-5-(4-methyl-1<i>H</i>-imidazole-1-yl)pyridin-2-yl)-5,6-dihydro-4<i>H</i>-1,2,4-oxadiazine, as a GSM preclinical candidate for familial Alzheimer's disease.
Cloak (2022)

The increased memory demands of workloads are putting high pressure on Last Level Caches (LLCs). In general, there is limited opportunity to increase the capacity of LLCs due to the area and power requirements of the underlying SRAM technology. Interestingly, emerging Non-Volatile Memory (NVM) technologies promise a feasible alternative to SRAM for LLCs due to their higher area density. However, NVMs have substantially higher read and write latencies, which offset their density benefit. Although researchers have proposed methods to tolerate NVM's higher write latency, little emphasis has been placed on the critical NVM read latency.
A Survey of Some Recent Advances in Step-Growth Polymerization (1996)

The field of step-growth polymers encompasses many polymer structures and polymerization reaction types. This chapter attempts to cover topics in step-growth polymerization outside of the areas reviewed in the other introductory chapters in this book, i.e., poly(aryl ethers), dendritic polymers, high-temperature polymers and transition-metal catalyzed polymerizations. Polyamides, polyesters, polycarbonates, poly(phenylene sulfides) and other important polymer systems are addressed. The chapter is not a comprehensive review but rather an overview of some of the more interesting recent research results reported for these step-growth polymers, including new polymerization chemistries and mechanistic studies. Aromatic Polyamides Aromatic polyamides (aramids) are important in the commercial fibers industry because of their high tensile strength and good flame resistance. The demand for these materials is increasing as new applications are found. One example is their use in composites where high-use temperatures, light weight, chemical resistance, and dimensional stability are crucial. The most widely employed synthetic route to
High-quality GaN on intentionally roughened c-sapphire (2003)

GaN films were grown using metal-organic chemical vapor deposition (MOCVD) on intentionally roughened c-sapphire in order to study the effect of the substrate roughness. Controlled substrate damage was achieved by exposing the substrate surfaces to controlled amounts of trimethylgallium followed by exposure to hydrogen at elevated temperature. The bulk film quality was studied by high-resolution X-ray diffraction and the surface topography was examined by atomic force microscopy. It was observed that mild substrate roughness (surface pit depth up to 30 nm) does not have a significant effect on the bulk film quality nor the GaN surface topography, and that recovery of the surface roughness is observed in very early stages of film growth. Cross sectional transmission electron microscopy confirmed that MOCVD GaN grown on inclined sidewalls etched in c-sapphire maintained the epitaxial relationship despite the substrate miscut of ca. 15° with respect to the c-axis.
Biomass‐Derived Porous Carbon Materials: Synthesis and Catalytic Applications (2015)

Abstract Novel biomass‐derived porous carbons are attractive candidates for the preparation of carbon‐supported catalysts with a wide range of catalytic applications. Such carbonaceous catalysts are environmentally benign and could provide a cost‐competitive advantage as compared to existing heterogeneous catalysts. Tunable surface properties of carbon materials and excellent physical properties (e.g., hydrophobicity, chemically inert nature, etc.) are compatible with diverse catalysis reactions including organic transformations, as well as electro‐ and photochemical processes in aqueous solutions. This contribution provides an overview on the utilization of different biomass feedstocks and/or biomass‐derived precursors for the synthesis of carbonaceous materials to design advanced catalytic systems and their emerging applications in catalysis.