gebhart/patrepeval huggingface dataset:
Macroporous Electrically Conducting Carbon Networks by Pyrolysis of Isocyanate-Cross-Linked Resorcinol-Formaldehyde Aerogels (2008)

Carbon (C) aerogels are made by pyrolysis of resorcinol-formaldehyde (RF) aerogels under Ar, and they combine electrical conductivity with a high open mesoporosity. However, because macropores are known to facilitate mass transfer, macroporous C-aerogels could be useful for application in separations or as fuel cell and battery electrodes. Macropores are typically incorporated in C-aerogels during gelation of the RF precursors by using either “hard” templating with silica or polystyrene beads, or “soft” templating with surfactants. Here, we report an alternative method, where open macroporosity is introduced by pyrolyzing RF aerogels whose skeletal nanoparticles have been cross-linked covalently with an isocyanate-derived polymer that coats conformally the entire RF framework. The structural, physical, and chemical evolution of the X-RF network was monitored at various stages during pyrolysis by DSC, TGA, SEM, N2 adsorption porosimetry, and 13C NMR. The accumulated evidence shows that the cross-linker first loses its chemical bonding with the skeletal nanoparticles and then melts, exerting surface tension forces on the RF framework, which cause a partial structural collapse that creates macropores. The xerogel-like internal texture of the macroporous walls is responsible for close contact of the carbon skeletal nanoparticles, resulting in an about 7× lower bulk electrical resistivity of the macroporous material relative to the corresponding mesoporous network, which is obtained by pyrolysis of native (i.e., non-cross-linked) RF aerogels. The new macroporous material was evaluated electrochemically for possible application as an electrode in batteries and fuel cells.
Sign-Agnostic Matrix Design for Spatial Artificial Reverberation with Feedback Delay Networks (2018)

Feedback delay networks (FDNs) are an efficient tool for creating artificial reverberation. Recently, various designs for spatially extending the FDN were proposed. A central topic in the design of spatial FDNs is the choice of the feedback matrix that governs the interaction between spatially distributed elements and therefore the spatial impression. In the design prototype, the feedback matrix is chosen to be unilossless such that the reverberation time is infinite. However, in physics-and aesthetics-driven design of spatial FDNs, the target feedback matrix is not necessarily unilossless. This contribution proposes an optimization method for finding a close unilossless feedback matrix and improves the accuracy by relaxing the specification of the target matrix phase component and focussing on the sign-agnostic component.
Hemopoietic origin of factor XIII A subunits in platelets, monocytes, and plasma. Evidence from bone marrow transplantation studies. (1989)

Factor XIII A subunit (FXIIIA) is found in plasma, platelets, and monocytes. The hemopoietic contributions to FXIIIA in these components were studied in patients transplanted with marrows from donors with different FXIIIA phenotypes. In three patients with successful engraftment (by DNA genotyping, red cell phenotyping, and cytogenetic studies) platelet and monocyte FXIIIA changed to donor phenotypes with hematologic recovery. Thus, FXIIIA in platelets and monocytes is synthesized de novo and/or from their progenitor cells. Plasma FXIIIA phenotype change after transplantation was more complex. Patient I changed from phenotype 1-1 (one electrophoretically fast band) to 1-2 (three bands) in 115 d; patients 2 and 3 did not change completely from phenotype 1-2 to 1-1 in up to 458 d, but did show enrichment of the fastest band. Thus, while there is a definite contribution of donor hemopoiesis to plasma FXIIIA, another source of recipient FXIIIA appears to be present to delay or prevent the phenotype change.
ChemInform Abstract: Triphenyl(5,5‐diethoxycarbonyl‐2,4‐pentadienylidene)phosphorane and Its Condensation Reactions. (1991)

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.
Efficient Presentation of Multiple Endogenous Epitopes to Both CD4 + and CD8 + Diabetogenic T Cells for Tolerance (2016)

Antigen-specific immunotherapy of type 1 diabetes, typically via delivery of a single native β cell antigen, has had little clinical benefit to date. With increasing evidence that diabetogenic T cells react against multiple β cell antigens, including previously unappreciated neo-antigens that can be emulated by mimotopes, a shift from protein- to epitope-based therapy is warranted. To this end, we aimed to achieve efficient co-presentation of multiple major epitopes targeting both CD4<sup>+</sup> and CD8<sup>+</sup> diabetogenic T cells. We have compared native epitopes versus mimotopes as well as various targeting signals in an effort to optimize recognition by both types of T cells in vitro. Optimal engagement of all T cells was achieved with segregation of CD8 and CD4 epitopes, the latter containing mimotopes and driven by endosome-targeting signals, after delivery into either dendritic or stromal cells. The CD4<sup>+</sup> T cell responses elicited by the endogenously delivered epitopes were comparable with high concentrations of soluble peptide and included functional regulatory T cells. This work has important implications for the improvement of antigen-specific therapies using an epitope-based approach to restore tolerance in type 1 diabetes and in a variety of other diseases requiring concomitant targeting of CD4<sup>+</sup> and CD8<sup>+</sup> T cells.
Molecular biology and biotechnology: a comprehensive desk reference (1996)

Achilles cleavage actin and actin homologs AIDS AIDS HIV enzymes Alzheimer's disease amino acid synthesis annexins antibody molecules antisense oligonucleotides arabidopsis genome autoantibodies and autoimmunity automation in genome research bacterial growth and division bacterial pathogenesis bacteriorhodopsin biochemical genetics biodegradation of organic wastes bioelectronics bioenergetics of the cell bioinorganic chemistry biomaterials for organ regeneration biomolecular electronics and applications bioorganic chemistry bioprocess engineering bioreactor transport processes biosensors biotechnology breast cancer calcium biochemistry/cancer carbohydrate analysis carbohydrate antigens cardiovascular diseases cell-cell interactions cell death and ageing chaperones chemiluminescence and bioluminescence repressor-operator recognition restriction endonucleases and methyltransferases for the modification of DNA restriction landmark genomic scanning method retinoblastoma retinoids ribosome preparations and protein synthesis techniques ribozyme chemistry RNA scanning tunnelling microscopy in sequencing of DNA sequence alignment of proteins and nucleic acids sequence analysis sequence divergence estimation steroid hormones and receptors superantigens synthetic peptide libraries theoretical molecular biology transgenic animal patents transgenic fish/transgenic mammals translation of RNA protein transport proteins transposens in the human genome triple-helix forming oligonucleotides tumour suppressor genes ultraviolet radiation damage to DNA vaccine biotechnolog viral envelope assembly and budding viruses vitamins X-ray diffraction of biomolecules yeast artificial chromosomes techniques yeast genetics zinc finger DNA binding moti. (Part contents).
Shotgun Optical Maps of the Whole Escherichia coli O157:H7 Genome (2001)

We have constructed NheI and XhoI optical maps of Escherichia coli O157:H7 solely from genomic DNA molecules to provide a uniquely valuable scaffold for contig closure and sequence validation. E. coli O157:H7 is a common pathogen found in contaminated food and water. Our approach obviated the need for the analysis of clones, PCR products, and hybridizations, because maps were constructed from ensembles of single DNA molecules. Shotgun sequencing of bacterial genomes remains labor-intensive, despite advances in sequencing technology. This is partly due to manual intervention required during the last stages of finishing. The applicability of optical mapping to this problem was enhanced by advances in machine vision techniques that improved mapping throughput and created a path to full automation of mapping. Comparisons were made between maps and sequence data that characterized sequence gaps and guided nascent assemblies.
Immunogenicity and Reactogenicity of Influenza Subunit Vaccines Produced in MDCK Cells or Fertilized Chicken Eggs (1997)

A tissue culture method using MDCK cells grown under serum-free conditions was developed to produce an inactivated influenza subunit vaccine. The first clinical data suggest it to be equal to the conventional egg-derived influenza subunit vaccine. In a double-blind controlled trial, 2 groups (n = 57 each) of adult volunteers were immunized with experimental bivalent influenza subunit vaccine derived from either MDCK cells or hens' eggs. Each vaccine contained 15 microg of hemagglutinin of influenza A/Taiwan/1/186 (H1N1) and 15 microg of hemagglutinin of B/Panama/45/90. No clinically relevant adverse reactions were observed in either vaccine group, and the incidence of systemic and local vaccine reactions was comparable in both groups. Standard hemagglutination inhibition antibody titers were determined using both MDCK- and egg-derived test antigens. The data reveal that both vaccines are safe and well-tolerated and meet the criteria for immunogenicity as stated in the European Community's "Harmonisation of Requirements for Influenza Vaccines."
Reversal of Spontaneous Autoimmune Insulitis in Nonobese Diabetic Mice by Soluble Lymphotoxin Receptor (2001)

One striking feature of spontaneous autoimmune diabetes is the prototypic formation of lymphoid follicular structures within the pancreas. Lymphotoxin (LT) has been shown to play an important role in the formation of lymphoid follicles in the spleen. To explore the potential role of LT-mediated microenvironment in the pathogenesis of insulin-dependent diabetes mellitus (IDDM), an LTbeta receptor-immunoglobulin fusion protein (LTbetaR-Ig) was administered to nonobese diabetic mice. Early treatment with LTbetaR-Ig prevented insulitis and IDDM, suggesting that LT plays a critical role in the insulitis development. LTbetaR-Ig treatment at a late stage of the disease also dramatically reversed insulitis and prevented diabetes. Moreover, LTbetaR-Ig treatment prevented the development of IDDM by diabetogenic T cells in an adoptive transfer model. Thus, LTbetaR-Ig can disassemble the well established lymphoid microenvironment in the islets, which is required for the development and progression of IDDM.
Interferon-γ inhibits replication of subgenomic and genomic hepatitis C virus RNAs (2002)

Persistent infection with hepatitis C virus (HCV) is a major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. All treatments known so far rely on the antiviral activity of interferon alfa (IFN-alpha) that is given alone or in combination with ribavirin. Unfortunately, only a fraction of the patients clear the virus during therapy and for those who do not respond there is currently no alternative treatment. Selectable subgenomic HCV RNAs (replicons) have been recently used to investigate the effect of IFN-alpha on HCV replication. However, it has not yet been analyzed whether other cytokines also play a role in the innate immune response against HCV. Here we show that IFN-gamma inhibits protein synthesis and RNA replication of subgenomic and genomic HCV replicons. We further show that the inhibitory action of IFN-gamma does not rely on the production of nitric oxide or the depletion of tryptophan. In conclusion, our results suggest that cytotoxic T cells and natural killer cells may contribute to HCV clearance not only by cell killing but also by producing IFN-gamma, thereby enhancing the intracellular inhibition of viral replication.
Design, synthesis, characterization, and use of all-organic, nonionic photogenerators of acid (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDesign, synthesis, characterization, and use of all-organic, nonionic photogenerators of acidF. M. Houlihan, T. X. Neenan, E. Reichmanis, J. M. Kometani, and T. ChinCite this: Chem. Mater. 1991, 3, 3, 462–471Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/cm00015a020https://doi.org/10.1021/cm00015a020research-articleACS PublicationsRequest reuse permissionsArticle Views269Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Building a Kinetic Framework for Group II Intron Ribozyme Activity: Quantitation of Interdomain Binding and Reaction Rate (1994)

Ribozyme kinetics and binding studies of a two-piece group II intron were used to mechanistically characterize a reaction analogous to the first step of RNA splicing. Domain 5 RNA (D5) catalyzes specific hydrolysis of an RNA substrate (exD123) composed of sequences surrounding the 5' exon/intron boundary. Both single- and multiple-turnover kinetic analyses produced similar values of kcat (0.04 and 0.1 min-1, respectively) and Km (270 and 190 nM, respectively) for 5' splice site hydrolysis catalyzed by D5. Base pairing is not believed to stabilize the binding of D5 to exD123, so the low Km values suggest that unusual tertiary interactions provide considerable energetic stabilization to this complex. The strength of D5-exD123 binding was confirmed using a new direct binding assay based on gel filtration chromatography. In this initial application of the assay, which systematically underestimates binding by approximately 3-fold, Kd values were obtained in relative agreement with Km. This agreement, together with agreement between kinetically determined variables, suggests that the reaction is described by a straightforward Michaelis-Menten mechanism and that kcat is the rate of the chemical step. This is supported by the log/linear pH/rate profile for kcat which has a slope = 1 up to pH 6.2, consistent with a form of general base catalysis within this linear range. The shape of the plot suggests that the active site responsible for 5' splice site hydrolysis has a pKa of > or = 7.0.
Human tumor-associated antigens defined by monoclonal antibodies. (1984)

Melanoma-associated antigens extracted from cultured human melanoma cells or isolated from their spent culture medium react specifically with monoclonal antibody and are represented by glycoproteins with molecular weights of 260,000 (260K), 250,000 (250K), and 100,000 (100K). The 260 and 250K antigens are present only in spent culture medium or detergent extracts of melanoma cells, respectively. The 100K antigen is an oncofetal marker present on tumor cells of different histological type. Indirect immunofluorescence data indicate that the 250K antigen is present on the surface of melanoma cells from excised melanoma tissues when the 100K antigen appears to be present in the cytosol. Subunit structure determination indicates that the 100K antigen is a single polypeptide chain whereas the 250K antigen extracted from melanoma cells is associated with a proteoglycan fragment which is important for its cell surface expression.
Short Interfering RNA (siRNA)—Mediated RNA Interference (RNAi) in Human Cells (2003)

Transient gene silencing in mammalian cells can be mediated by double stranded RNA (dsRNAs) molecules of approximately 20-25 nucleotides termed short interfering (siRNAs). Naturally occurring siRNAs in lower eukaryotes have characteristic structural elements; however, little is known about what features are critical for an exogenous siRNA to mediate RNAi in mammals. We have recently determined some of the critical parameters that influence the efficiency of siRNA-mediated RNAi in mammalian cells and have been considering the use of RNAi as a functional genomics tool, particularly for high throughput analysis, and the potential use of RNAi as a therapeutic tool.
The Thymus as an Inductive Site for T Lymphopoiesis (2007)

Like all hematopoietic cells, T lymphocytes are derived from bone-marrow-resident stem cells. However, whereas most blood lineages are generated within the marrow, the majority of T cell development occurs in a specialized organ, the thymus. This distinction underscores the unique capacity of the thymic microenvironment to support T lineage restriction and differentiation. Although the identity of many of the contributing thymus-derived signals is well established and rooted in highly conserved pathways involving Notch, morphogenetic, and protein tyrosine kinase signals, the manner in which the ensuing cascades are integrated to orchestrate the underlying processes of T cell development remains under investigation. This review focuses on the current definition of the early stages of T cell lymphopoiesis, with an emphasis on the nature of thymus-derived signals delivered to T cell progenitors that support the commitment and differentiation of T cells toward the alphabeta and gammadelta T cell lineages.
Haptic Virtual Fixture for Robotic Cardiac Catheter Navigation (2011)

In manual or robot-assisted catheter intervention, excessive manipulation force may cause tissue perforation. Using images acquired by an imaging device routinely used for catheter interventions such as X-ray fluoroscopy, the structure and size of blood vessels and the relative position of the catheter tip inside the vessel can be obtained. To prevent collision of the catheter tip and the vessel wall, vision-assisted control methods using forbidden-region virtual fixture (FRVF) technique can be utilized and an experimental implementation has been performed in this study. A master-slave configured robotic platform for cardiac catheter was used for this study. The robotic master handle can provide haptic rendering to the user. A vessel phantom model mimicking human vasculature for the inner radii was fabricated for simulated intervention experiments. A digital optical camera was used for image acquisition. After the vessel phantom and the catheter tip were segmented, distance between the vessel centerline and the catheter tip was calculated and the forbidden region that the catheter tip should keep away from was set for the safe catheter manipulation. Virtual force generation algorithm was implemented for feeding the signal indicating the catheter tip penetrating into the forbidden region back to the user in the robotic master handle. To validate the suggested method, in vitro experiments were conducted. Through a chain of image filtering procedures including edge detection, the catheter tip and the vessel wall were able to be well segmented. The virtual force generator worked appropriately. The developed FRVF technique could provide helpful auxiliary information to clinicians for safer manipulation of catheters in cardiac catheterization procedures.
Optical pulse generation by electrooptic-modulation method and its application to integrated ultrashort pulse generators (2000)

We have developed ultrashort pulse generation by the electrooptic modulation method, where continuous-wave laser light of any wavelength can be converted to trains of ultrashort optical pulses with a variable and high repetition frequency by means of an electrooptic phase modulator for the generation of deeply chirped light, and an optical group-delay-dispersion circuit or an optical synthesizer for the compression of the chirped light. Adopting the technologies of domain inversion and guided-wave optics to this electrooptic modulation method, it will be possible to realize integrated ultrashort optical pulse generators.
Colorimetric Bio-Barcode Amplification Assay for Cytokines (2005)

The bio-barcode amplification assay has become a powerful tool in detecting tens to hundreds of biological targets such as proteins and nucleic acids in the entire sample. However, current bio-barcode detection schemes still require many experimental steps including microarrayer-based immobilization of oligonucleotides on a glass chip, silver enhancement of immobilized gold nanoparticles on a chip, and light-scattering measurement. Here, we report a colorimetric bio-barcode method that minimizes the above requirements while detecting 30 aM concentrations of cytokines (approximately 3 orders of magnitude more sensitive than conventional nonenzymatic cytokine detection assays). The assay is based on porous microparticles, which enable loading of a large number of barcode DNA per particle, and gold nanoparticle-based colorimetric barcode detection method.
Dendritic cell-tumor cell hybrids enhance the induction of cytotoxic T lymphocytes against murine colon cancer: A comparative analysis of antigen loading methods for the vaccination of immunotherapeutic dendritic cells (2006)

Dendritic cells (DCs) have been used successfully for inducing effective anti-tumor immune responses in advanced cancer patients undergoing tumor-specific immunotherapy. Appropriate antigen pulsing is a crucial parameter for optimizing the efficacy of immunotherapy as well as anti-tumor protection therapy. Using a murine colon cancer model, we evaluated the anti-tumor efficacy of four different preparations of DC vaccines that contained either a whole tumor or its derivatives, including i) DCs pulsed with tumor lysate, ii) DCs pulsed with necrotic tumor cells, iii) DCs pulsed with apoptotic tumor cells, and iv) DC-tumor cell fusion hybrids. Our data show that DC-tumor cell fusion hybrids and DCs pulsed with irradiated apoptotic tumor cells were more potent than DCs with freeze-thawed necrotic tumor cells for the induction of protective anti-tumor responses. The vaccination of DCs pulsed with tumor lysate failed to elicit any anti-tumor effect. In animals administered with higher doses of a tumor-cell challenge, DC-tumor cell fusion hybrids elicited the most effective anti-tumor response. Among the preparations tested, mice immunized with DC-tumor cell fusion hybrids resulted in the greatest induction of cytotoxicity as measured by the cytotoxic T lymphocyte activity of both the splenocytes and the Thy1.2-positive T lymphocytes. Furthermore, the in vitro production of IFN-gamma polarized to the Th1 cytokine responses was highest in the splenocytes derived from mice vaccinated with DC-tumor cell fusion hybrids. Our results suggest that DC-tumor cell fusion hybrids are more potent inducers of protection against solid tumors, such as colon cancer, than other antigen-loading strategies using whole tumor cell materials.