gebhart/patrepeval huggingface dataset:
Lysyl tRNA synthetase is required for the translocation of calreticulin to the cell surface in immunogenic death (2010)

In response to immunogenic cell death inducers, calreticulin (CRT) translocates from its orthotopic localization in the lumen of the endoplasmic reticulum (ER) to the surface of the plasma membrane where it serves as an engulfment signal for antigen-presenting cells.(1) Here, we report that yet another ER protein, the lysyl-tRNA synthetase (KARS), was exposed on the surface of stressed cells, on which KARS co-localized with CRT in lipid rafts. Depletion of KARS with small interfering RNAs suppressed CRT exposure induced by anthracyclines or UVC light. In contrast to CRT, KARS was also found in the supernatant of stressed cells. Recombinant KARS protein was unable to influence the binding of recombinant CRT to the cell surface. Moreover, recombinant KARS protein was unable to stimulate macrophages in vitro. These results underscore the contribution of KARS to the emission of (one of) the principal signal(s) of immunogenic cell death, CRT exposure.
Growth Phase-Dependent Regulation of Target Gene Promoters for Binding of the Essential Orphan Response Regulator HP1043 of Helicobacter pylori (2002)

Helicobacter pylori encodes three two-component systems and two orphan response regulators (RRs) that are predicted to be involved in transcriptional regulation. The HP1043 gene encodes an essential OmpR-like RR, 1043RR, for which no histidine kinase has been identified. Gel filtration and cross-linking experiments on the purified 1043RR protein reveals that this protein is a dimer and in vivo dimerization assays localize the dimerization to the N-terminal regulatory domain. DNA-binding studies have revealed two targets for specific binding of the 1043RR protein and moreover, phosphorylation of the protein was not needed for the activation of binding. Footprinting analysis demonstrated that the 1043RR protein binds to its own promoter, P(1043), overlapping the -35 promoter element from positions -17 to -45, suggesting that this protein is autoregulatory. In addition, it binds at a similar location, spanning nucleotides from positions -22 to -51 at the promoter of the methyl-accepting chemotaxis tlpB gene, P(tlpB). A possible inverted repeat was identified in the binding sites of both promoters. In an attempt to overexpress 1043RR in H. pylori, the 10-fold induction in transcription of a second copy of HP1043 with use of an inducible promoter failed to increase cellular levels of the RR protein, suggesting that 1043RR is tightly regulated at a posttranscriptional level. The P(1043) and P(tlpB) promoters were demonstrated to be coordinately regulated in response to growth phase in H. pylori. The essential role of HP1043 in encoding a cell cycle regulator is discussed.
Supplementary Table S2 from Engineered anti-CD70 antibody-drug conjugate with increased therapeutic index (2023)

Supplementary Table S2 from Engineered anti-CD70 antibody-drug conjugate with increased therapeutic index
Immunologically relevant peptide antigen exists on the presenting cell in a manner accessible to macromolecules in solution. (1986)

Although studies of the association of antigen with APC have been complicated by antigen-processing requirements, recent studies have suggested that immunologically relevant antigen should be present on the APC surface. Nevertheless, blocking of antigen presentation with antibody to the antigen has not been demonstrable in most systems. To study this problem we developed a system using avidin to block presentation of amino-terminal biotinylated synthetic peptide 132-146 of sperm whale myoglobin (B132) to a murine T cell clone specific for this site in association with I-Ed. greater than 95% specific inhibition was observed with doses of B132 equipotent to unmodified peptide. Specific blocking could be observed: (a) after pulsing APC with antigen, washing, and incubating for a chase period of 8-16 h before addition of avidin and T cells to assure adequate time for intracellular trafficking and maximal display of antigen on the cell surface, or (b) when monensin is present during the antigen pulse to inhibit such traffic. Therefore, the inhibition appeared to be occurring at the cell surface unless dissociation and reassociation were constantly occurring. To distinguish these, B10.GD APC (I-Ed-negative) were pulsed with antigen and cocultured with B10.D2 APC (I-Ed-positive). No detectable antigen presentation resulted. Thus, minimal dissociation and reassociation between antigen and APC occurs and, consequently, blocking by extracellular solution-phase binding of avidin to antigen is unlikely. Taken together, these data suggest that the blocking is occurring at the cell surface. Thus, under physiologic conditions, immunologically relevant antigen necessary for T cell activation appears to be present on the APC surface and is freely accessible to macromolecules the size of avidin. These findings hold specific implications for models of antigen presentation for T cell recognition.
Measurement of Solids Distribution in Suspension Flows using Electrical Resistance Tomography (2008)

Neutrally buoyant particles in low Reynolds number, pressure-driven suspension flows migrate from regions of high to low shear. When the particle density differs from the suspending fluid, buoyancy forces affect this particle migration. The ratio between the buoyancy and viscous forces, as quantified by a dimensionless buoyancy number, determines the phase distribution of the fully developed suspension. Electrical resistance tomography (ERT) was used to visualize and quantify particle migration in low Reynolds number pressure-driven pipe flows of dense and light particles suspended in a viscous fluid. The measured phase distributions are compared to the predictions of a modified suspension balance model. Les particules à flottabilité nulle dans les écoulements de suspensions entraînées par la pression et à faible nombre de Reynolds, migrent des régions de cisaillement élevé à celles de cisaillement faible. Lorsque la masse volumique des particules diffère de celle du fluide en suspension, les forces de flottabilité influent sur cette migration des particules. Le rapport entre la flottabilité et les forces visqueuses, tel que quantifié par un nombre de flottabilité adimensionnel, détermine la distribution de phase de la suspension pleinement développée. On a fait appel à la tomographie à résistance électrique (ERT) pour visualiser et quantifier la migration des particules dans les écoulements en conduites induits par la pression et à faible nombre de Reynolds pour des particules denses et légères suspendues dans un fluide visqueux. Les distributions de phases mesurées sont comparées aux prédictions d'un modèle d'équilibre de suspension modifié.
Faculty Opinions recommendation of Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. (2013)

Clustered regularly interspaced short palindromic repeats (CRISPR) are hypervariable loci widely distributed in prokaryotes that provide acquired immunity against foreign genetic elements. Here, we characterize a novel Streptococcus thermophilus locus, CRISPR3, and experimentally demonstrate its ability to integrate novel spacers in response to bacteriophage. Also, we analyze CRISPR diversity and activity across three distinct CRISPR loci in several S. thermophilus strains. We show that both CRISPR repeats and cas genes are locus specific and functionally coupled. A total of 124 strains were studied, and 109 unique spacer arrangements were observed across the three CRISPR loci. Overall, 3,626 spacers were analyzed, including 2,829 for CRISPR1 (782 unique), 173 for CRISPR2 (16 unique), and 624 for CRISPR3 (154 unique). Sequence analysis of the spacers revealed homology and identity to phage sequences (77%), plasmid sequences (16%), and S. thermophilus chromosomal sequences (7%). Polymorphisms were observed for the CRISPR repeats, CRISPR spacers, cas genes, CRISPR motif, locus architecture, and specific sequence content. Interestingly, CRISPR loci evolved both via polarized addition of novel spacers after exposure to foreign genetic elements and via internal deletion of spacers. We hypothesize that the level of diversity is correlated with relative CRISPR activity and propose that the activity is highest for CRISPR1, followed by CRISPR3, while CRISPR2 may be degenerate. Globally, the dynamic nature of CRISPR loci might prove valuable for typing and comparative analyses of strains and microbial populations. Also, CRISPRs provide critical insights into the relationships between prokaryotes and their environments, notably the coevolution of host and viral genomes.
The NLR-related protein NWD1 is associated with prostate cancer and modulates androgen receptor signaling (2014)

Prostate cancer (PCa) is among the leading causes of cancer-related death in men. Androgen receptor (AR) signaling plays a seminal role in prostate development and homeostasis, and dysregulation of this pathway is intimately linked to prostate cancer pathogenesis and progression. Here, we identify the cytosolic NLR-related protein NWD1 as a novel modulator of AR signaling. We determined that expression of NWD1 becomes elevated during prostate cancer progression, based on analysis of primary tumor specimens. Experiments with cultured cells showed that NWD1 expression is up-regulated by the sex-determining region Y (SRY) family proteins. Gene silencing procedures, in conjunction with transcriptional profiling, showed that NWD1 is required for expression of PDEF (prostate-derived Ets factor), which is known to bind and co-regulate AR. Of note, NWD1 modulates AR protein levels. Depleting NWD1 in PCa cell lines reduces AR levels and suppresses activity of androgen-driven reporter genes. NWD1 knockdown potently suppressed growth of androgen-dependent LNCaP prostate cancer cells, thus showing its functional importance in an AR-dependent tumor cell model. Proteomic analysis suggested that NWD1 associates with various molecular chaperones commonly related to AR complexes. Altogether, these data suggest a role for tumor-associated over-expression of NWD1 in dysregulation of AR signaling in PCa.
Antibody penetration of tumor GS-7 xenografts in nude mice: a model for mucinous adenocarcinoma of the colon. (1996)

A new cell line derived from a human adenocarcinoma of the colon, GS-7, was propagated as a s.c. tumor in nude mice. This tumor histologically is a mucinous adenocarcinoma (also designated mucoid or colloid) with characteristic large mucin pools that are not lined by an epithelial layer but may contain scattered, randomly distributed cancer cells. Ten to 20% of human colorectal adenocarcinomas are of this histological type, but rapidly growing xenografts with this histology have been rarely used experimentally. This tumor, therefore, constitutes a useful model for similar human tumors. The mucin pools contain large amounts of carcinoembryonic antigen and tumor-associated glycoprotein 72, and the cells express epithelial glycoprotein 2 on their surface. The ability of antibodies injected i.v. to penetrate this tumor was investigated, using both biotinylated and radioiodinated antibodies (Abs). The results demonstrate that Abs can effectively penetrate the mucin pools, and that large amounts of Ab can localize there. This tumor type may have advantages as a target for certain forms of experimental immunotherapy.
Proteomic differences in hippocampus and cortex of sudden unexplained death in childhood (2022)

Sudden unexplained death in childhood (SUDC) is death of a child over 1 year of age that is unexplained after review of clinical history, circumstances of death, and complete autopsy with ancillary testing. Multiple etiologies may cause SUDC. SUDC and sudden unexpected death in epilepsy (SUDEP) share clinical and pathological features, suggesting some similarities in mechanism of death and possible abnormalities in hippocampus and cortex. To identify molecular signaling pathways, we performed label-free quantitative mass spectrometry on microdissected frontal cortex, hippocampal dentate gyrus (DG), and cornu ammonis (CA1-3) in SUDC (n = 19) and pediatric control cases (n = 19) with an explained cause of death. At a 5% false discovery rate (FDR), we found differential expression of 660 proteins in frontal cortex, 170 in DG, and 57 in CA1-3. Pathway analysis of altered proteins identified top signaling pathways associated with activated oxidative phosphorylation (p = 6.3 × 10<sup>-15</sup>, z = 4.08) and inhibited EIF2 signaling (p = 2.0 × 10<sup>-21</sup>, z = - 2.56) in frontal cortex, and activated acute phase response in DG (p = 8.5 × 10<sup>-6</sup>, z = 2.65) and CA1-3 (p = 4.7 × 10<sup>-6</sup>, z = 2.00). Weighted gene correlation network analysis (WGCNA) of clinical history indicated that SUDC-positive post-mortem virology (n = 4/17) had the most significant module in each brain region, with the top most significant associated with decreased mRNA metabolic processes (p = 2.8 × 10<sup>-5</sup>) in frontal cortex. Additional modules were associated with clinical history, including fever within 24 h of death (top: increased mitochondrial fission in DG, p = 1.8 × 10<sup>-3</sup>) and febrile seizure history (top: decreased small molecule metabolic processes in frontal cortex, p = 8.8 × 10<sup>-5</sup>) in all brain regions, neuropathological hippocampal findings in the DG (top: decreased focal adhesion, p = 1.9 × 10<sup>-3</sup>). Overall, cortical and hippocampal protein changes were present in SUDC cases and some correlated with clinical features. Our studies support that proteomic studies of SUDC cohorts can advance our understanding of the pathogenesis of these tragedies and may inform the development of preventive strategies.
Additional Applications in Thermal Spray (2013)

Abstract This article reviews the use of thermal spray polymer coatings as a replacement for paints. It discusses the applications of the thermal spray forming process. The article also provides information on the applications of thermal spray in metal processing, textile and plastics, and ceramic and glass manufacturing industries.
Tunable Microcellular Morphologies from Poly(ferrocenylsilane) Ceramic Precursors Foamed in Supercritical CO2 (2004)

Abstract Summary: Poly(ferrocenylmethylphenylsilane) (PFMPS) and poly[ferrocenylmethyl(phenylacetylido)silane] (PFMPAS) homopolymers are organometallic polymers that can serve as precursors to magnetically‐active ceramics. In this work, PFMPS and PFMPAS films ranging in thickness from 30 to 220 μm have been exposed to scCO 2 over a broad range of saturation pressures, temperatures and times to produce surface‐constrained microcellular polymeric foams. Electron microscopy identifies viable foaming windows and reveals that foams with submicron cell sizes can be generated by judicious selection of exposure conditions. Cell shape anisotropy can likewise be varied from being nearly spherical to vertically elongated. Curvature in the films and non‐negligible surface roughness create paths that facilitate CO 2 diffusion, resulting in the formation of “V‐directional” cells oriented at approximately 30° to the film surface. The development of bimodal cell size distributions is attributed to temperature variation during depressurization and/or stepwise homogeneous and heterogeneous nucleation. These results are prerequisite for the production of magnetically‐active porous ceramics from pyrolyzed PFS foams. SEM image of a PFMPS foam generated in scCO 2 illustrating considerable cell anisotropy: the cells are tilted with respect to the film surface. magnified image SEM image of a PFMPS foam generated in scCO 2 illustrating considerable cell anisotropy: the cells are tilted with respect to the film surface.
Boron–Carbon Atomic Ratio Dependence on the Hardness and Oxidation Resistance of Solid Solutions of Perovskite-Type Borocarbide YRh3BxC1-x(0≦x≦1) (2002)

Solid solutions of the quaternary borocarbide system YRh3BxC1-x have been synthesized and studied from the viewpoints of their microhardness and oxidation resistance. Perovskite-type YRh3B and YRh3C form a continuous solid solution in the range of 0≦x≦1 with a cubic structure (space group: Pm3m, Z=1). The microhardness of YRh3BxC1-x increases with increasing boron content. The oxidation onset temperature also increases with boron content. Thus, it is indicated that the chemical stability of solid-solution YRh3BxC1-x is strongly dependent on the boron content.
Characterization of Neutralizing Profiles in HIV-1 Infected Patients from whom the HJ16, HGN194 and HK20 mAbs were Obtained (2011)

Several new human monoclonal antibodies (mAbs) with a neutralizing potential across different subtypes have recently been described. Three mAbs, HJ16, HGN194 and HK20, were obtained from patients within the HIV-1 cohort of the Institute of Tropical Medicine (ITM). Our aim was to generate immunization antibodies equivalent to those seen in plasma. Here, we describe the selection and characterization of patient plasma and their mAbs, using a range of neutralization assays, including several peripheral blood mononuclear cell (PBMC) based assays and replicating primary viruses as well as cell line based assays and pseudoviruses (PV). The principal criterion for selection of patient plasma was the activity in an 'extended incubation phase' PBMC assay. Neutralizing Abs, derived from their memory B cells, were then selected by ELISA with envelope proteins as solid phase. MAbs were subsequently tested in a high-throughput HOS-PV assay to assess functional neutralization. The present study indicates that the strong profiles in the patients' plasma were not solely due to antibodies represented by the newly isolated mAbs. Although results from the various assays were divergent, they by and large indicate that neutralizing Abs to other epitopes of the HIV-1 envelope are present in the plasma and synergy between Abs may be important. Thus, the spectrum of the obtained mAbs does not cover the range of cross-reactivity seen in plasma in these carefully selected patients irrespective of which neutralization assay is used. Nevertheless, these mAbs are relevant for immunogen discovery because they bind to the recombinant glycoproteins to which the immune response needs to be targeted in vivo. Our observations illustrate the remaining challenges required for successful immunogen design and development.
ZnO NWs-TiO2 NPs Hybrid Structure for Dye-Sensitized Solar Cell Applications (2009)

Abstract not Available.
SARM1 depletion rescues NMNAT1-dependent photoreceptor cell death and retinal degeneration (2020)

Leber congenital amaurosis type nine is an autosomal recessive retinopathy caused by mutations of the NAD<sup>+</sup> synthesis enzyme NMNAT1. Despite the ubiquitous expression of NMNAT1, patients do not manifest pathologies other than retinal degeneration. Here we demonstrate that widespread NMNAT1 depletion in adult mice mirrors the human pathology, with selective loss of photoreceptors highlighting the exquisite vulnerability of these cells to NMNAT1 loss. Conditional deletion demonstrates that NMNAT1 is required within the photoreceptor. Mechanistically, loss of NMNAT1 activates the NADase SARM1, the central executioner of axon degeneration, to trigger photoreceptor death and vision loss. Hence, the essential function of NMNAT1 in photoreceptors is to inhibit SARM1, highlighting an unexpected shared mechanism between axonal degeneration and photoreceptor neurodegeneration. These results define a novel SARM1-dependent photoreceptor cell death pathway and identifies SARM1 as a therapeutic candidate for retinopathies.
Overview of diffraction gratings technologies for spaceflight satellites and ground-based telescopes (2017)

The diffraction gratings are widely used in Space-flight satellites for spectrograph instruments or in ground-based telescopes in astronomy. The diffraction gratings are one of the key optical components of such systems and have to exhibit very high optical performances. HORIBA Jobin Yvon S.A.S. (part of HORIBA Group) is in the forefront of such gratings development for more than 40 years. During the past decades, HORIBA Jobin Yvon (HJY) has developed a unique expertise in diffraction grating design and manufacturing processes for holographic, ruled or etched gratings. We will present in this paper an overview of diffraction grating technologies especially designed for space and astronomy applications. We will firstly review the heritage of the company in this field with the space qualification of different grating types. Then, we will describe several key grating technologies developed for specific space or astronomy projects: ruled blazed low groove density plane reflection grating, high-groove density holographic toroidal and spherical grating, and finally transmission Fused Silica Etched (FSE) grism-assembled grating. We will not present the Volume Phase Holographic (VPHG) grating type which is used in Astronomy.
Influence of a transverse hypersonic inhomogeneity on the spectrum formed as a result of stimulated Brillouin scattering in single-mode fiber waveguides (1989)

Quartz glass fiber waveguides suffer not only from a transverse optical inhomogeneity but also from a transverse inhomogeneity of a hypersonic wave responsible for stimulated Brillouin scattering (STBS). Experiments on such waveguides revealed a considerable broadening of the STBS spectrum (compared with a homogeneous nonwaveguide medium) in the case of a single-mode waveguide characterized by antiwaveguide propagation of hypersound, i.e., when the velocity of hypersound in the core was higher than the velocity in the cladding. The width of the STBS spectrum depended weakly on the duration of the pump pulses and was governed by the nature of the transverse hypersonic inhomogeneity. The best agreement between the experimental results on the width of the spectrum and theoretical calculations was obtained for a waveguide with a central dip in the refractive index profile. Determination not only of the width but also of the profile of the STBS line yielded more detailed information on the refractive index profile.
CD40 Expression by Human Bronchial Epithelial Cells (1999)

CD40 is a 50-kDa protein expressed on B cells, dendritic cells, monocytes and epithelial cells, but the distribution of CD40 expression in humans is not completely known. It binds to a ligand (CD40L) which is expressed essentially on activated T cells. The interaction between CD40 and CD40L plays important roles in immune responses. CD40 expression was investigated on bronchial tissues and human bronchial cell lines using immunohistochemistry, immunofluorescence staining and analysis with a cytometer, respectively. Constitutive CD40 expression, but not that of CD40L, was slightly detectable on normal human bronchial epithelial cells (HBEC) in situ and on an adult lung adenocarcinoma (SKLU1) cell line, while another cell line, a bronchial transformed SV40 cell line (WI26VA4), was negative for CD40. Among the various cytokines tested, only interferon (IFN)-gamma was found to induce CD40 expression on WI26VA4. Tumour necrosis factor (TNF)-alpha was the best cytokine able to up-regulate CD40 in SKLU1 cells. A combination of IFN-gamma and TNF-alpha was slightly more effective than the cytokine alone at up-regulating CD40 expression on both cell lines. We further investigated the functional consequences of CD40 ligation on both cell lines. These bronchial cells expressed CD40, HLADR and CD54 under basal conditions or when stimulated by cytokines. Stimulation through CD40 did not affect cell-surface-antigen expression on either cell line. The production of cytokines such as interleukin (IL)-6 and granulocyte macrophage-colony stimulating factor (GM-CSF) by HBEC has been described. SKLU1 and WI26VA4 cells released IL-6 and GM-CSF spontaneously. Whatever the case, CD40 engagement did not modulate spontaneous or TNF-alpha-induced production of these two cytokines. These data indicate for the first time that normal HBEC express CD40 in situ. Further investigations are required in order to determine the role of CD40 on normal HBEC.