gebhart/patrepeval huggingface dataset:
Engineering a Rugged Nanoscaffold To Enhance Plug-and-Display Vaccination (2018)

Nanoscale organization is crucial to stimulating an immune response. Using self-assembling proteins as multimerization platforms provides a safe and immunogenic system to vaccinate against otherwise weakly immunogenic antigens. Such multimerization platforms are generally based on icosahedral viruses and have led to vaccines given to millions of people. It is unclear whether synthetic protein nanoassemblies would show similar potency. Here we take the computationally designed porous dodecahedral i301 60-mer and rationally engineer this particle, giving a mutated i301 (mi3) with improved particle uniformity and stability. To simplify the conjugation of this nanoparticle, we employ a SpyCatcher fusion of mi3, such that an antigen of interest linked to the SpyTag peptide can spontaneously couple through isopeptide bond formation (Plug-and-Display). SpyCatcher-mi3 expressed solubly to high yields in Escherichia coli, giving more than 10-fold greater yield than a comparable phage-derived icosahedral nanoparticle, SpyCatcher-AP205. SpyCatcher-mi3 nanoparticles showed high stability to temperature, freeze-thaw, lyophilization, and storage over time. We demonstrate approximately 95% efficiency coupling to different transmission-blocking and blood-stage malaria antigens. Plasmodium falciparum CyRPA was conjugated to SpyCatcher-mi3 nanoparticles and elicited a high avidity antibody response, comparable to phage-derived virus-like particles despite their higher valency and RNA cargo. The simple production, precise derivatization, and exceptional ruggedness of this nanoscaffold should facilitate broad application for nanobiotechnology and vaccine development.
The Thyroid Hormone Receptor-β Agonist GC-1 Induces Cell Proliferation in Rat Liver and Pancreas (2006)

Thyroid hormones regulate cell growth, cell differentiation, and metabolic functions via interaction with the thyroid hormone nuclear receptors (TRs). Recently, a small class of halogen-free high-affinity thyroid hormone agonists has been developed that are highly selective for the TRbeta subtype. Because of the selective hyperthyroidism generated by one of these agonists, GC-1, this compound has the potential to be developed as a new therapeutic agent for the treatment of a variety of metabolic disturbances, including lipid disorders and obesity; thus, it becomes important to determine whether GC-1 has other unknown effects on potential target organs. The purpose of this study was to investigate the effect of GC-1 on cell proliferation in rat liver and pancreas. Rats treated with GC-1 (50 or 100 mug/100 g body weight) were killed at different time points. Hepatic and pancreatic cell proliferation was monitored by immunohistochemical determination of bromodeoxyuridine incorporation. The expression of cell cycle-related genes was analyzed by Northern and Western analysis. The results show that GC-1 strongly stimulates rat hepatocyte proliferation in the absence of tissue injury. Although GC-1-induced hepatocyte proliferation was associated with a rapid increase in cyclin D1 mRNA levels, no change in the expression of c-jun and c-fos was observed. GC-1 also induced massive pancreatic cell proliferation. The results indicate that the TRbeta-selective agonist GC-1 is a strong mitogen for hepatocytes and pancreatic acinar cells. Furthermore, they suggest that the TRbeta receptor is the mediator for the mitogenic activity of thyroid hormone and other thyromimetics.
The Naturally Processed CD95L Elicits a c-Yes/Calcium/PI3K-Driven Cell Migration Pathway (2011)

Patients affected by chronic inflammatory disorders display high amounts of soluble CD95L. This homotrimeric ligand arises from the cleavage by metalloproteases of its membrane-bound counterpart, a strong apoptotic inducer. In contrast, the naturally processed CD95L is viewed as an apoptotic antagonist competing with its membrane counterpart for binding to CD95. Recent reports pinpointed that activation of CD95 may attract myeloid and tumoral cells, which display resistance to the CD95-mediated apoptotic signal. However, all these studies were performed using chimeric CD95Ls (oligomerized forms), which behave as the membrane-bound ligand and not as the naturally processed CD95L. Herein, we examine the biological effects of the metalloprotease-cleaved CD95L on CD95-sensitive activated T-lymphocytes. We demonstrate that cleaved CD95L (cl-CD95L), found increased in sera of systemic lupus erythematosus (SLE) patients as compared to that of healthy individuals, promotes the formation of migrating pseudopods at the leading edge of which the death receptor CD95 is capped (confocal microscopy). Using different migration assays (wound healing/Boyden Chamber/endothelial transmigration), we uncover that cl-CD95L promotes cell migration through a c-yes/Ca²⁺/PI3K-driven signaling pathway, which relies on the formation of a CD95-containing complex designated the MISC for Motility-Inducing Signaling Complex. These findings revisit the role of the metalloprotease-cleaved CD95L and emphasize that the increase in cl-CD95L observed in patients affected by chronic inflammatory disorders may fuel the local or systemic tissue damage by promoting tissue-filtration of immune cells.
Protein kinase C-α mediates epidermal growth factor receptor transactivation in human prostate cancer cells (2005)

Progression of human prostate cancer to a malignancy that is refractory to androgen-ablation therapy renders the disease resistant to available treatment options and accounts for the high prostate cancer mortality rate. Epidermal growth factor receptor (EGFR) expression in human prostate cancer specimens increases with disease progression to androgen-refractory prostate cancer, and experimental models implicate EGFR-dependent signaling to Erk1/2 activation in the androgen-refractory prostate cancer phenotype. 12-O-Tetradecanoylphorbol-13-acetate (TPA)-induced Erk1/2 activation in human prostate cancer PC-3 cells is a paradigm of diacylglycerol-induced EGFR transactivation in androgen-independent prostate cancer. In this report, we establish an obligatory role for TPA-induced protein kinase C (PKC)-alpha activation in EGFR transactivation and signaling to Erk1/2 activation in PC-3 cells. TPA-regulated molecules include PKCs, PKDs, and Ras guanyl nucleotide-releasing proteins. The PKC-selective inhibitors GF109203X and Go6983 each blocked TPA-induced EGFR transactivation, indicating a requirement for PKC. PC-3 cells express four PKC isozymes. Prolonged bryostatin 1 treatment abrogated PKCalpha expression without altering expression levels of the other PKC isozymes. Pharmacologic PKCalpha "knockdown" abrogated TPA-induced Erk1/2 activation without affecting the EGF/EGFR-induced response, indicating that PKCalpha was required for EGFR transactivation but dispensable for signaling of ligand-activated EGFR to Erk1/2 activation. We corroborated this by showing that Go6976, which is a PKCalpha-selective inhibitor in PC-3 cells, likewise abolished TPA-induced Erk1/2 activation and did not inhibit EGF/EGFR-induced Erk1/2 activation. Go6976 had similar effects in DU145 cells, providing evidence for a common PKCalpha-dependent Erk1/2 activation mechanism in androgen-independent human prostate cancer cells of distinct genetic origin. These results constitute a rational basis for selective PKCalpha inhibition as a modality of prostate cancer therapy.
Regulation of chloro- and methylphenol degradation in Comamonas testosteroni JH5 (1994)

Comamonas testosteroni JH5 was isolated from a mixed bacterial culture enriched on different chloro- and methylphenols. The strain completely mineralized a mixture consisting of 4-chlorophenol (4-CP) and 4-methylphenol (4-MP). During degradation of the mixture, 4-hydroxybenzyl alcohol, 4-hydroxybenzaldehyde, 4-hydroxybenzoic acid, and 4-chlorocatechol were detected as short-lived intermediates. Mineralization of 4-CP and that of 4-MP occurred successively and were accompanied by diauxic growth, whereas 4-CP and 2-methylphenol were mineralized simultaneously. It was ascertained that neither a reversible enzyme inhibition nor potential toxic intermediates caused the observed diauxie. Some facts support the hypothesis that the successive degradation of 4-CP and 4-MP is regulated on the level of transcription. C. testosteroni JH5 contained a meta-cleaving enzyme when pregrown on 4-CP and the isomeric monomethylphenols. Inactivation of this enzyme in the presence of 3-chlorocatechol was observed.
Bioorthogonal Chemistry for Site-Specific Labeling and Surface Immobilization of Proteins (2011)

Understanding protein structure and function is essential for uncovering the secrets of biology, but it remains extremely challenging because of the high complexity of protein networks and their wiring. The daunting task of elucidating these interconnections requires the concerted application of methods emerging from different disciplines. Chemical biology integrates chemistry, biology, and pharmacology and has provided novel techniques and approaches to the investigation of biological processes. Among these, site-specific protein labeling with functional groups such as fluorophors, spin probes, and affinity tags has greatly facilitated both in vitro and in vivo studies of protein structure and function. Bioorthogonal chemical reactions, which enable chemo- and regioselective attachment of small-molecule probes to proteins, are particularly attractive and relevant for site-specific protein labeling. The introduction of powerful labeling techniques also has inspired the development of novel strategies for surface immobilization of proteins to create protein biochips for in vitro characterization of biochemical activities or interactions between proteins. Because this process requires the efficient immobilization of proteins on surfaces while maintaining structure and activity, tailored methods for protein immobilization based on bioorthogonal chemical reactions are in high demand. In this Account, we summarize recent developments and applications of site-specific protein labeling and surface immobilization of proteins, with a special focus on our contributions to these fields. We begin with the Staudinger ligation, which involves the formation of a stable amide bond after the reaction of a preinstalled azide with a triaryl phosphine reagent. We then examine the Diels-Alder reaction, which requires the protein of interest to be functionalized with a diene, enabling conjugation to a variety of dienophiles under physiological conditions. In the oxime ligation, an oxyamine is condensed with either an aldehyde or a ketone to form an oxime; we successfully pursued the inverse of the standard technique by attaching the oxyamine, rather than the aldehyde, to the protein. The click sulfonamide reaction, which involves the Cu(I)-catalyzed reaction of sulfonylazides with terminal alkynes, is then discussed. Finally, we consider in detail the photochemical thiol-ene reaction, in which a thiol adds to an ene group after free radical initiation. Each of these methods has been successfully developed as a bioorthogonal transformation for oriented protein immobilization on chips and for site-specific protein labeling under physiological conditions. Despite the tremendous progress in developing such transformations over the past decade, however, the demand for new bioorthogonal methods with improved kinetics and selectivities remains high.
Multichannel Matrix Surround Decoders for Two-Eared Listeners (1996)

Although film matrix surround decoders are primarily four channel devices, with a single channel devoted to sound the sides and the rear, in practice there are almost always two or more surround speakers. These speakers are driven in parallel, with in some cases a delay modulation to “decorrelate ” the single surround channel. There is substantial interference between the various loudspeakers, resulting in a listener dependent comb filtering and a non-spacious surround. Although designs for decoders with more than one rear channel exist, these suffer from low separation between the rear channels when the decoder inputs are decorrelated- during music or effects like applause. Current decoders also suffer from various defects such as pumping of the music during dialog. This paper discusses a mathematical design for a matrix encoder and decoder with radically different properties- maximum lateral separation during music, accurate placement of directionally encoded material, and constant music level in the presence of any directionally encoded effect. Matrix equations for both a 5 channel and a 7 channel decoder are presented, along with an active and a passive encoder for 5 channel films. Comparitive listening tests show that the decoder reproduces standard films with substantially improved surround, and the combination of the encoder and the decoder reproduces 5 channel discrete films with little subjective loss.
vdFP - Video fingerprinting technologies for media and security applications - D1 : Report on existing technologies (2010)

Video fingerprinting is een bewezen en commercieel verkrijgbare techniek die ingezet kan worden om kopieÃ«n van of videomateriaal op te sporen. Video fingerprinting vergelijkt digitale videoâs met elkaar en moet typisch kunnen omgaan met zaken zoals verschillende video codecs, veranderde resolutie, het plaatsen van een logo, niet gelijke frame rates, etc. Ontwikkelingen in dit gebied zijn vooral gestimuleerd door de media wereld, die er belang bij heeft verspreiding van illegale kopieÃ«n van videomateriaal tegen te gaan. Er zijn echter meerdere toepassingen, ieder met eigen karakteristieken. In dit engelstalige rapport geven wij een overzicht van de bestaande video fingerprinting technieken. Naast video fingerprinting kijken wij ook naar een aantal gerelateerde technieken zoals audio fingerprinting en objectherkenning in videoâs. Voor elke technologie beschrijven wij de state-of-the-art en inventariseren wij bestaande, commerciÃ«le oplossingen.
Involvement of midbrain tectum neurokinin-mediated mechanisms in fear and anxiety (2012)

Electrical stimulation of midbrain tectum structures, particularly the dorsal periaqueductal gray (dPAG) and inferior colliculus (IC), produces defensive responses, such as freezing and escape behavior. Freezing also ensues after termination of dPAG stimulation (post-stimulation freezing). These defensive reaction responses are critically mediated by γ-aminobutyric acid and 5-hydroxytryptamine mechanisms in the midbrain tectum. Neurokinins (NKs) also play a role in the mediation of dPAG stimulation-evoked fear, but how NK receptors are involved in the global processing and expression of fear at the level of the midbrain tectum is yet unclear. The present study investigated the role of NK-1 receptors in unconditioned defensive behavior induced by electrical stimulation of the dPAG and IC of male Wistar rats. Spantide (100 pmol/0.2 μL), a selective NK-1 antagonist, injected into these midbrain structures had anti-aversive effects on defensive responses and distress ultrasonic vocalizations induced by stimulation of the dPAG but not of the IC. Moreover, intra-dPAG injections of spantide did not influence post-stimulation freezing or alter exploratory behavior in rats subjected to the elevated plus maze. These results suggest that NK-1 receptors are mainly involved in the mediation of defensive behavior organized in the dPAG. Dorsal periaqueductal gray-evoked post-stimulation freezing was not affected by intra-dPAG injections of spantide, suggesting that NK-1-mediated mechanisms are only involved in the output mechanisms of defensive behavior and not involved in the processing of ascending aversive information from the dPAG.
5‐Amino‐5‐deoxyribose derivatives. Synthesis and use in the preparation of “Reversed” Nucleosides (1966)

Abstract Methyl 5‐amino‐5‐deoxy‐2,3‐ O ‐isopropylidene‐β‐D‐ribofuranoside (III) has been synthesized and used as an intermediate in the preparation of the kinetin analog, methyl 5‐deoxy‐5‐(purin‐6‐yl)amino‐β‐D‐ribofuranoside (X). The related 1‐substituted adenine, methyl 5‐ (6‐aminopurin‐1‐yl)‐5‐deoxy‐2,3‐ O ‐isopropylidene‐β‐D‐ribofuranoside (XIII), was prepared by cyclization of 1‐benzyl‐5‐cyano‐4‐ethoxymethyleneaminoimidazole (XI) with III and subsequent debenzylation with sodium in liquid ammonia. The structures and stereochemistry of these compounds were established by a combination of ultraviolet and nuclear magnetic resonance spectroscopy.
Fabrication of biological microarrays using microcantilevers (2003)

Arrays of silicon-based microcantilevers with properly designed passivated aluminum electrodes have been used to generate microarrays by depositing microspots of biological samples using a direct contact deposition technique. The approach proposed here can be compared to the dip-pen technique but with the noticeable difference that electrostatic fields are generated onto the cantilevers to increase the height of liquid rise on the cantilever surface when dipping them into the liquid to be deposited. Both electrowetting through the reduction of the contact angle and dielectrophoresis through electrostatic forces can be used to favor the loading efficiency. These phenomena are particularly pronounced on the microscale due to the fact that physical scaling laws favor electrostatic forces. Moreover, at this scale, conductive heat dissipation is enhanced and therefore joule heating can be minimized. Using this approach, with a single loading, arrays of more than a hundred spots, from the femtoliter to the picoliter range, containing fluorescent-labeled oligonucleotides and proteins were directly patterned on a glass slide.
A MicroRNA Feedback Circuit in Midbrain Dopamine Neurons (2007)

MicroRNAs (miRNAs) are evolutionarily conserved, 18- to 25-nucleotide, non-protein coding transcripts that posttranscriptionally regulate gene expression during development. miRNAs also occur in postmitotic cells, such as neurons in the mammalian central nervous system, but their function is less well characterized. We investigated the role of miRNAs in mammalian midbrain dopaminergic neurons (DNs). We identified a miRNA, miR-133b, that is specifically expressed in midbrain DNs and is deficient in midbrain tissue from patients with Parkinson's disease. miR-133b regulates the maturation and function of midbrain DNs within a negative feedback circuit that includes the paired-like homeodomain transcription factor Pitx3. We propose a role for this feedback circuit in the fine-tuning of dopaminergic behaviors such as locomotion.
The THAP–zinc finger protein THAP1 regulates endothelial cell proliferation through modulation of pRB/E2F cell-cycle target genes (2006)

Abstract We recently cloned a novel human nuclear factor (designated THAP1) from postcapillary venule endothelial cells (ECs) that contains a DNA-binding THAP domain, shared with zebrafish E2F6 and several Caenorhabditis elegans proteins interacting genetically with retinoblastoma gene product (pRB). Here, we show that THAP1 is a physiologic regulator of EC proliferation and cell-cycle progression, 2 essential processes for angiogenesis. Retroviral-mediated gene transfer of THAP1 into primary human ECs inhibited proliferation, and large-scale expression profiling with microarrays revealed that THAP1-mediated growth inhibition is due to coordinated repression of pRB/E2F cell-cycle target genes. Silencing of endogenous THAP1 through RNA interference similarly inhibited EC proliferation and G1/S cell-cycle progression, and resulted in down-regulation of several pRB/E2F cell-cycle target genes, including RRM1, a gene required for S-phase DNA synthesis. Chromatin immunoprecipitation assays in proliferating ECs showed that endogenous THAP1 associates in vivo with a consensus THAP1-binding site found in the RRM1 promoter, indicating that RRM1 is a direct transcriptional target of THAP1. The similar phenotypes observed after THAP1 overexpression and silencing suggest that an optimal range of THAP1 expression is essential for EC proliferation. Together, these data provide the first links in mammals among THAP proteins, cell proliferation, and pRB/E2F cell-cycle pathways.
Structural evidence that endothelial cell growth factor beta is the precursor of both endothelial cell growth factor alpha and acidic fibroblast growth factor. (1986)

Two endothelial cell growth factors (ECGF) have been purified from bovine brain and termed alpha- and beta-ECGF [Burgess, W. H., Mehlman, T., Friesel, R., Johnson, W. V. & Maciag, T. (1985) J. Biol. Chem. 260, 11389-11392]. Amino acid sequence analysis indicates that beta-ECGF represents a 20 amino acid amino-terminal extension of alpha-ECGF and a 14 amino acid amino-terminal extension of acidic fibroblast growth factor. These data indicate that both alpha-ECGF and acidic fibroblast growth factor may be derived from beta-ECGF by posttranslational processing. Analysis of the amino-terminal 14 residues of beta-ECGF by fast-atom-bombardment mass spectrometry established the amino acid sequence of this region and the identity of the blocking group at the amino terminus (acetyl).
Extracellular ATP Stimulates Interleukin-Dependent Cultured Mast Cells and Eosinophils through Calcium Mobilization (1991)

We examined the effect of ATP and related nucleotides on the changes in intracellular calcium ([Ca2+]i) in murine bone marrow-derived mast cells (BMMC) and human cord blood-derived eosinophils (EO) cultured in the presence of interleukins. ATP, ADP and AMP released a substantial amount of histamine and leukotriene C4 from BMMC, and EO showed locomotive activity in response to ATP, ADP and GTP. These reactions were accompanied with an increase in [Ca2+]i in BMMC and in EO. The rise in [Ca2+]i in BMMC induced by ATP or antigen at optimal concentrations was inclined to be persisting. On the other hand, these nucleotides induced a rapid and transient rise in [Ca2+]i in EO. Purified human peripheral EO also exhibited locomotive activity and an increase in [Ca2+]i in response to ATP. These results indicate that extracellular ATP activates interleukin-dependent cultured mast cells and EO through Ca2+ mobilization, and suggest that ATP, which is known to be released from activated platelets or autonomic nerves, may stimulate in vivo counterparts of these cultured inflammatory cells.
The TRPM6/EGF Pathway Is Downregulated in a Rat Model of Cisplatin Nephrotoxicity (2013)

Cisplatin-induced hypomagnesemia is described in humans and rats, but the underlying mechanisms are still unclear. Recent studies have shown that epidermal growth factor (EGF) stimulates Mg(2+) re-absorption in the distal convoluted tubule via the Mg(2+) channel TRPM6. This study investigates the role of TRPM Mg(2+) channels, claudines, and EGF in the Mg(2+) homeostasis in a rat model of cisplatin-induced nephrotoxicity. Wistar rats were given 2.5 mg/kg cisplatin per week for 3 weeks and were euthanized 4 or 9 weeks after the first administration. The cisplatin treatment significantly increased the fractional excretion of Mg(2+). Real-time RT-PCR and/or Western blots were performed to assess the renal expression TRPM6, TRPM7, claudin-16, claudin-19, EGF, EGF receptor (EGFR) and EGFR-pathway components. The renal mRNA expression of TRPM6 and EGF showed a significant decrease after cisplatin treatment, while the TRPM7, claudin-16 and EGFR expressions remained stable. The claudin-19 mRNA expression was significantly upregulated after cisplatin treatment. Western blotting confirmed the mRNA expression data for the claudins, but an showed upregulation of EGFR only at week 9. The role of the EGFR pathway, involving Pi3-AKT-Rac1, in cisplatin-induced nephropathy, could not be substantiated in further detail. This study shows that cisplatin treatment results in EGF and TRPM6 downregulation in the rat kidney, causing renal Mg(2+) loss. Our results are in line with the hypothesis that EGF influences the renal expression or activation of TRPM6 and plays a significant role in Mg(2+) loss in medication-induced nephropathy.