gebhart/patrepeval huggingface dataset:
Vaccination with prion peptide‐displaying papillomavirus‐like particles induces autoantibodies to normal prion protein that interfere with pathologic prion protein production in infected cells (2007)

Prion diseases are fatal neurodegenerative disorders caused by proteinaceous infectious pathogens termed prions (PrP(Sc)). To date, there is no prophylaxis or therapy available for these transmissible encephalopathies. Passive immunization with monclonal antibodies recognizing the normal host-encoded prion protein (PrP(C)) has been reported to abolish PrP(Sc) infectivity and to delay onset of disease. Because of established immunologic tolerance against the widely expressed PrP(C), active immunization appears to be difficult to achieve. To overcome this limitation, papillomavirus-like particles were generated that display a nine amino acid B-cell epitope, DWEDRYYRE, of the murine/rat prion protein in an immunogenic capsid surface loop, by insertion into the L1 major capsid protein of bovine papillomavirus type 1. The PrP peptide was selected on the basis of its previously suggested central role in prion pathogenesis. Immunization with PrP-virus-like particles induced high-titer antibodies to PrP in rabbit and in rat, without inducing overt adverse effects. As determined by peptide-specific ELISA, rabbit immune sera recognized the inserted murine/rat epitope and also cross-reacted with the homologous rabbit/human epitope differing in one amino acid residue. In contrast, rat immune sera recognized the murine/rat peptide only. Sera of both species reacted with PrP(C) in its native conformation in mouse brain and on rat pheochromocytoma cells, as determined by immunoprecipitation and fluorescence-activated cell sorting analysis. Importantly, rabbit anti-PrP serum contained high-affinity antibody that inhibited de novo synthesis of PrP(Sc) in prion-infected cells. If also effective in vivo, PrP-virus-like particle vaccination opens a unique possibility for immunologic prevention of currently fatal and incurable prion-mediated diseases.
CFD Modeling of Bayonet Type High Temperature Heat Exchanger and Chemical Decomposer With Different Packed Bed Designs (2007)

The present work is concerned with use of bayonet type high temperature heat exchanger as silicon carbide integrated decomposer (SID) which produces sulfuric acid decomposition product - sulfur dioxide. The product can be used within the sulfur iodine thermo-chemical cycle portion of the hydrogen production process. The chemical decomposition occurs in packed bed area of the decomposer. The engineering design of the packed bed is very much influenced by the structure of the packing matrix, which is governed by the shape, dimensions and the loading of the constituent particles. Optimum design of catalyst pellet in terms of shape configuration, packing method and available surface area can promote catalytic activity and the prevailing transport properties of the system. Knowledge of the underlying factors should enable designers to engineer the optimum design for a given system with prescribed conditions. The investigations of fluid flow and the arrangement of cylindrical and spherical pellets in packed bed are presented in the paper.
Transcriptomic heterogeneity in multifocal prostate cancer (2018)

Prostate Cancer Foundation, National Institutes of Health (U01 CA214170, R01 CA183857, University of Michigan Prostate Specialized Program of Research Excellence [S.P.O.R.E.] P50 CA186786-05, Weill Cornell Medicine S.P.O.R.E. P50 CA211024-01A1), Men of Michigan Prostate Cancer Research Fund, University of Michigan Comprehensive Cancer Center core grant (2-P30-CA-046592-24), A. Alfred Taubman Biomedical Research Institute, and Department of Defense.
Immunohistological localization of the myelinating cell‐specific receptor LPA1 (2002)

LP(A1) (also termed Edg-2 or VZG-1) is a G-protein-coupled receptor for lysophosphatidic acid and its gene transcripts have been found selectively expressed by mature myelin-producing cells. We have raised in rabbit a polyclonal antibody against a sequence unique to LP(A1) and common to rat, mouse, and human orthologues. In Western blots, LP(A1) immunoreactivity appeared as 44-53 kDa bands in extracts from recombinant RH7777 cells expressing LP(A1), mouse purified oligodendrocytes, or human white matter, but not from wild-type RH7777 cells or purified astrocytes. In glial cultures, LP(A1) immunoreactivity was restricted to oligodendrocytes, appeared at cell membrane and processes, colocalized with myelin basic protein, and appeared before myelin/oligodendrocyte glycoprotein. In slices of rat and human brains, LP(A1) immunoreactivity was found in myelinated tracts, as well as in oligodendrocyte somata and their myelinating fibers. Immunoreactivities of LP(A1) and myelin basic protein colocalized in the brain, but oligodendrocyte soma showed stronger signals for LP(A1) than myelinated fibers, whereas the reverse was true for myelin basic protein. These results strengthen the view that LP(A1) is involved in myelin formation or maintenance.
Consideration of the Control Method Using EGR for the HCCI Engine Running on DME (2005)

A Homgeneous Charge Compression Ignition (HCCI) engine is supposed to achieve high thermal effciency and low NOx PM emissions at the same time. Though it is expected to come into practical use, it has some serious problems such as ignition timing control, knocking at high load and securing of high combustion effciency. In this study, a four-stroke HCCI engine running on Di-Methyl Ether (DME) is developed to make it practicable as a generator engine. A new HCCI combustion control method, controlling the gas fraction of internal EGR gas at high temperature, external EGR gas at low temperature and premixture at stoichiometric ratio, is proposed. And effects of the gas fraction on HCCI combustion are researched by numerical calculation with elementally reactions and experiment. To conclude, HCCI combustion can be optimized with controlling the fraction of internal EGR gas, external EGR gas and premixture.
Efficacy of Prednisolone for Bell Palsy in Children (2022)

This study provides Class I evidence that for children with Bell palsy, prednisolone does not significantly change recovery of complete facial function at 1 month. However, this study lacked the precision to exclude an important harm or benefit from prednisolone.
Bayesian learning for sparse signal reconstruction (2004)

Sparse Bayesian learning and specifically relevance vector machines have received much attention as a means of achieving parsimonious representations of signals in the context of regression and classification. We provide a simplified derivation of this paradigm from a Bayesian evidence perspective and apply it to the problem of basis selection from overcomplete dictionaries. Furthermore, we prove that the stable fixed points of the resulting algorithm are necessarily sparse, providing a solid theoretical justification for adapting the methodology to basis selection tasks. We then include simulation studies comparing sparse Bayesian learning with basis pursuit and the more recent FOCUSS class of basis selection algorithms, empirically demonstrating superior performance in terms of average sparsity and success rate of recovering generative bases.
ChemInform Abstract: New Synthesis of 2,3‐Disubstituted and 2,2,3‐Trisubstituted 2H‐1‐ Benzothiopyran Derivatives. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Interaction of Sodium Dodecyl Sulfate with Methacrylate−PEG Comb Copolymers (2005)

A series of sodium methacrylate and poly(ethylene glycol) (PEG) comb copolymers (MAA/PEG) with approximate PEG chain lengths of 7, 11, and 22 ethylene oxide units were synthesized by free radical polymerization. Their weight-average molecular mass was found to be approximately 66 000. A commercial sample of a PEG comb polymer with an acrylic backbone was also used in the studies (Sokalan HP 80). The interaction of the MAA/PEG comb polymers and pure sodium methacrylate (SPMA) with sodium dodecyl sulfate (SDS) was studied by ESR spectroscopy using 5-doxyl stearic acid (5-DSA) spin probe and by conductivity measurements. Surfactant aggregation in water occurred at SDS concentrations lower than the surfactant critical micelle concentration (cmc) and depended on the polymer concentration. The observations have been attributed to changes in the effective ionic strength of the systems due to the polymer itself, and it has been concluded that there is no interaction between the MAA/PEG comb copolymers or SPMA and SDS. This has been confirmed by the fact that the decrease in surfactant aggregation concentration is similar in magnitude to the decrease observed on adding NaCl when counterion ion condensation effects are taken into account. It is apparent that the electrostatic repulsions between the surfactant molecules and the methacrylate backbone of the MAA/PEG comb copolymers inhibit association of SDS with the PEG side chains.
1720: Compare the Urethral Contractility After Muscle Derived Cells or Fibroblastic Cells Injeciton into Dennervated RAT Urethral Sphincter (2004)

You have accessJournal of UrologyDiscussed Poster,Wednesday, May 12, 2004,8:00 am - 12:00 pm1 Apr 20041720: Compare the Urethral Contractility After Muscle Derived Cells or Fibroblastic Cells Injeciton into Dennervated RAT Urethral Sphincter Dong Deuk Kwon, Yong Tae Kim, Jang H. Kim, Kristin A. Erickson, Ryan Pruchnic, Ronald Jankowski, Johnny Huard, Fernando D. Miguel, Naoki Yoshimura, William C. De Groat, and Michael B. Chancellor Dong Deuk KwonDong Deuk Kwon More articles by this author , Yong Tae KimYong Tae Kim More articles by this author , Jang H. KimJang H. Kim More articles by this author , Kristin A. EricksonKristin A. Erickson More articles by this author , Ryan PruchnicRyan Pruchnic More articles by this author , Ronald JankowskiRonald Jankowski More articles by this author , Johnny HuardJohnny Huard More articles by this author , Fernando D. MiguelFernando D. Miguel More articles by this author , Naoki YoshimuraNaoki Yoshimura More articles by this author , William C. De GroatWilliam C. De Groat More articles by this author , and Michael B. ChancellorMichael B. Chancellor More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)38912-2AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1720: Compare the Urethral Contractility After Muscle Derived Cells or Fibroblastic Cells Injeciton into Dennervated RAT Urethral Sphincter." The Journal of Urology, 171(4S), p. 455 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 171Issue 4SApril 2004Page: 455 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Dong Deuk Kwon More articles by this author Yong Tae Kim More articles by this author Jang H. Kim More articles by this author Kristin A. Erickson More articles by this author Ryan Pruchnic More articles by this author Ronald Jankowski More articles by this author Johnny Huard More articles by this author Fernando D. Miguel More articles by this author Naoki Yoshimura More articles by this author William C. De Groat More articles by this author Michael B. Chancellor More articles by this author Expand All Advertisement PDF DownloadLoading ...
Phenobarbital selectively modulates the glucagon-stimulated activity of adenylate cyclase by depressing the lipid phase separation occurring in the outer half of the bilayer of liver plasma membranes (1981)

The glucagon-stimulated (coupled) activity of rat liver plasma-membrane adenylate cyclase could be selectively modulated by the anionic drug phenobarbital, whereas the fluoride-stimulated (uncoupled) activity remained unaffected. It is suggested that the cationic drug phenobarbital preferentially interacts with the external half of the bilayer, as the negatively charged phospholipids are found at the cytosol-facing side. This results in a selective fluidization of the external half of the bilayer, leading to a depression in the high-temperature onset of the lipid phase transition (from 28 degree to 16 degree C) occurring there. This was detected both by e.s.r. analysis, using a fatty acid spin probe, and also by Arrhenius plots of glucagon-stimulated activity, where the enzyme forms a transmembrane complex with the receptor and is sensitive to the lipid environment of both halves of the bilayer. However, in the absence of hormone, adenylate cyclase only senses the lipid environment of the inner (cytosol) half of the bilayer. Thus its fluoride stimulated activity and Arrhenius plots of this activity remained unaffected by the presence of phenobarbital (less than 12 mM) in the assay. These results support the view that independent modulation of the fluidity or chemical constituents of each half of the bilayer can selectively affect the receptor-coupled and uncoupled activities of adenylate cyclase.
The expression of Dishevelled-3 and glutamine metabolism in malignant pleural mesothelioma (2012)

Malignant pleural mesothelioma (MPM) is a highly aggressive tumour.1 Biomarker information for MPM is lacking and could prove useful for understanding MPM metastasis and proliferation, and for providing potential targets for therapy. The Dishevelled (Dvl) family of proteins are membrane-proximal signalling intermediates in the Wnt pathway.2 Moreover, we previously found that the Wnt pathway is activated in mesothelioma through Dvl3 overexpression.3 Excitatory amino acid transporters (EAATs) are known to function as glutamate carriers.4 ,5 Among the EAATs, EAAT1 is a ubiquitous subtype. Glutamine synthetase (GS) is another important enzyme that plays a role in the metabolic pathway of glutamate.6 In this study, we evaluated the possible association among expression levels of Dvl3, EAAT1 and GS in MPM to determine possible biomarkers and therapeutic targets.

Clinical data were obtained from 39 patients with primary MPM between 1997 and 2009. The diagnosis of malignant mesothelioma was confirmed by a review of the pathology reports in all cases. We also used human mesothelioma cell lines H28, 211H, H2052, MS-1, H290, H513 and human normal mesothelial cell line LP9 in this research.

Thirty-eight mesothelioma samples (seven that included adjacent normal pleural tissues to serve as controls) were obtained from the patients who were mentioned above. Samples for one patient were not available for EAAT1 staining, …
New Models of the Tracheal Airway Define the Glandular Contribution to Airway Surface Fluid and Electrolyte Composition (2001)

Antibacterial defenses in the airway are dependent on multifactorial influences that determine the composition of both fluid and/or electrolytes at the surface of the airway and the secretory products that aid in bacterial killing and clearance. In cystic fibrosis (CF), these mechanisms of airway protection may be defective, leading to increased colonization with Pseudomonas aeruginosa. Submucosal glands, a predominant site of cystic fibrosis transmembrane conductance regulator (CFTR) protein expression in the airway, have been hypothesized to play an important role in protection of the airway. Furthermore, recent studies have suggested that the salt concentration at the airway surface may be a key factor in regulating the activity of antibacterial substances in the airway. To explore these issues, we have used a new model of the ferret tracheal airway to evaluate the contribution of submucosal glands in regulating airway surface fluid and electrolyte composition. Using tracheal xenograft models with and without submucosal glands, we have characterized several aspects of airway physiology that may be important in defining antibacterial properties. These endpoints included the contribution of submucosal glands in defining bioelectric properties of the surface airway epithelium, airway surface fluid (ASF) chloride composition, ASF volumes, and secretion of the antibacterial factor lysozyme. Findings from these studies demonstrate a significantly elevated secreted fluid volume (Vs) and chloride concentration ([Cl](s)) in ASF from airways with submucosal glands (Vs = 47 +/- 4 microl; [Cl](s) = 128 +/- 5 mM), as compared with xenograft airways without glands (Vs = 36 +/- 2 microl; [Cl](s) = 103 +/- 6 mM). Furthermore, a temperature labile factor secreted by submucosal glands appears to alter the baseline activation of 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid and/or diphenylamine-2-carboxylic acid-sensitive chloride channels in the surface airway epithelium. Lastly, the lysozyme content of tracheal airways with submucosal glands was 8.5-fold higher than were airways without glands. These studies demonstrate that submucosal glands affect both the ionic composition and bioelectric properties of the airway and suggest that models evaluating antibacterial properties of the airway in CF should take into account the contribution of glands in airway physiology.
Notice of Removal: The directivity of piezoelectric matrix transducer elements mounted on an ASIC (2017)

Removed.
Pico-second pulse shaping by use of planar integrated optics (2001)

Planar-integrated substrate-mode optics for ps-pulse shaping is proposed. A 12ps 1550nm optical pulse is shaped to a pulse train by modulating its spectral distribution at the Fourier focal plane. Experimental results with 0 and π phase masks are presented.
Primary and Secondary Aminophosphines as Novel P‐Stereogenic Building Blocks for Ligand Synthesis (2010)

Set the N free! The reactivity of the amino group of P-stereogenic aminophosphines allows the further elaboration of the aminophosphine unit whilst preserving the original chirality of the phosphorus atom (see picture; Rh green). P-stereogenic aminodiphosphine ligands can easily be prepared in optically pure forms, feature distinct structural and electronic characteristics, and can be used in asymmetric hydrogenation reactions.
CD74 is a novel transcription regulator (2016)

CD74 is a cell-surface receptor for the cytokine macrophage migration inhibitory factor. Macrophage migration inhibitory factor binding to CD74 induces its intramembrane cleavage and the release of its cytosolic intracellular domain (CD74-ICD), which regulates cell survival. In the present study, we characterized the transcriptional activity of CD74-ICD in chronic lymphocytic B cells. We show that following CD74 activation, CD74-ICD interacts with the transcription factors RUNX (Runt related transcription factor) and NF-κB and binds to proximal and distal regulatory sites enriched for genes involved in apoptosis, immune response, and cell migration. This process leads to regulation of expression of these genes. Our results suggest that identifying targets of CD74 will help in understanding of essential pathways regulating B-cell survival in health and disease.
Error-based or target-based? A unifying framework for learning in recurrent spiking networks (2021)

Learning in biological or artificial networks means changing the laws governing the network dynamics in order to better behave in a specific situation. In the field of supervised learning, two complementary approaches stand out: error-based and target-based learning. However, there exists no consensus on which is better suited for which task, and what is the most biologically plausible. Here we propose a comprehensive theoretical framework that includes these two frameworks as special cases. This novel theoretical formulation offers major insights into the differences between the two approaches. In particular, we show how target-based naturally emerges from error-based when the number of constraints on the target dynamics, and as a consequence on the internal network dynamics, is comparable to the degrees of freedom of the network. Moreover, given the experimental evidences on the relevance that spikes have in biological networks, we investigate the role of coding with specific patterns of spikes by introducing a parameter that defines the tolerance to precise spike timing during learning. Our approach naturally lends itself to Imitation Learning (and Behavioral Cloning in particular) and we apply it to solve relevant closed-loop tasks such as the button-and-food task, and the 2D Bipedal Walker. We show that a high dimensionality feedback structure is extremely important when it is necessary to solve a task that requires retaining memory for a long time (button-and-food). On the other hand, we find that coding with specific patterns of spikes enables optimal performances in a motor task (the 2D Bipedal Walker). Finally, we show that our theoretical formulation suggests protocols to deduce the structure of learning feedback in biological networks.
Harvesting Low Molecular Weight Biomarkers Using Gold Nanoparticles (2015)

We developed and characterized a platform based on gold (Au) nanoparticles (NPs) coated with poly(acrylic acid) (PAA) for harvesting positively charged, low molecular weight (LMW) proteins. The particles are synthesized using a layer by layer (LbL) procedure: first the gold NPs are coated with positively charged polyethylenimine (PEI) and subsequently with PAA. This simple procedure produces stable PAA-PEI-Au (PPAu) NPs with high selectivity and specificity. PPAu NPs successfully harvested, separated, and detected various LMW proteins and peptides from serum containing a complex mixture of abundant high molecular weight (HMW) proteins, including bovine serum albumin (BSA) and Immunoglobulin G (IgG). In addition, PPAu NPs selectively harvested and separated LMW proteins from serum in the presence of another positively charged competing protein. Furthermore, PPAu NPs successfully harvested a LMW biomarker in a mock diseased state. This system can be applied in various biomedical applications where selective harvesting and identifying of LMW proteins is required. A particularly useful application for this system can be found in early cancer diagnosis as described hereinafter.
Supplementary Figure S5 from RhoB Determines Tumor Aggressiveness in a Murine EGFR<sup>L858R</sup>-Induced Adenocarcinoma Model and Is a Potential Prognostic Biomarker for Lepidic Lung Cancer (2023)

&lt;p&gt;Supplementary Figure S5. Western blot of phospho-ERK1/2 and phospho-Akt from protein lysate of healthy lungs and lung tumors from EGFR/rhob mice, with corresponding quantifications&lt;/p&gt;
Phase stability and sodium-vacancy orderings in a NaSICON electrode (2021)

We elucidate the complex thermodynamics of sodium (Na) intercalation into the sodium super-ionic conductor (NaSICON)-type electrode, Na x V 2 (PO 4 ) 3 , for promising Na-ion batteries with high-power density.