gebhart/patrepeval huggingface dataset:
Stool DNA and Occult Blood Testing for Screen Detection of Colorectal Neoplasia (2008)

Stool DNA test 1 provides no improvement over HemoccultSensa for detection of screen-relevant neoplasms. Stool DNA test 2 detects significantly more neoplasms than does Hemoccult or HemoccultSensa, but with more positive results in colonoscopically normal patients. Higher sensitivity of SDT-2 was particularly apparent for adenomas.
Grafted Poly(1→4-β-glucan) Strands on Silica: A Comparative Study of Surface Reactivity as a Function of Grafting Density (2011)

Grafted poly(β-glucan) (β-glu) strands on the surface of silica are synthesized with varying degrees of grafting density, and display an amorphous-like environment via (13)C CP/MAS NMR spectroscopy. Thermal gravimetric analysis of these materials under oxidative conditions shows increased β-glu thermal stability with higher degrees of grafting density. The range of temperature stability between the most and least hydrogen-bound grafted β-glu strands spans 321 to 260 °C. This range is bound by the combustion temperature previously measured for crystalline and amorphous cellulose, with the former having greater oxidative stability, and is likely controlled by the extent of hydrogen bonding of a grafted β-glu strand with the underlying silica surface. When using these materials as reactants for glycosidic bond hydrolysis, the total number of reducing ends formed during reaction is quantified using a BCA colorimetric assay. Results demonstrate that the material with greatest interaction with silica surface silanols undergoes hydrolysis at an initial rate that is 6-fold higher than the material with the lowest degree of such interaction. The role of the surface as a reactive interface that can endow oxidative stability and promote hydrolysis activity has broad implications for surface-catalyzed processes dealing with biomass-derived polymers.
Characterization of Carbohydrate-Binding Specificity of Concanavalin A by Competitive Binding of Pyridylamino Sugar Chains (1992)

Carbohydrate-binding specificity of Con A was characterized by competitive binding studies of pyridylamino (PA) sugar chains. PA-derivatives of 17 oligomannose-type sugar chains, Man1-9GlcNAc2-PA, and those of three complex-type sugar chains were used as ligands. The ratios of bound and free sugar concentrations, [LS]/[S], were determined by means of microequilibrium dialysis followed by high performance liquid chromatography as already reported [Mega, T. & Hase, S. (1991) J. Biochem. 109, 600-603]. The association constant, Ka, was calculated from [LS]/[S] of a sugar chain and that of a standard sugar chain by using the equation Ka = Ka0 x ([S0]/[LS0]) x ([LS]/[S]), where Ka0, [S0], and [LS0] are the association constant, and the free and bound ligand concentrations of the standard sugar chain, respectively. This calculation was effective for the determination of Ka of ligands with similar affinities to the standard sugar chain. The carbohydrate structures with highest affinity for Con A among those tested were found to be: [formula: see text]
Electrophilic Fatty Acids Regulate Matrix Metalloproteinase Activity and Expression (2011)

Nitro-fatty acids (NO(2)-FA) are electrophilic signaling mediators formed by reactions of nitric oxide and nitrite. NO(2)-FA exert anti-inflammatory signaling actions through post-translational protein modifications. We report that nitro-oleic acid (OA-NO(2)) stimulates proMMP-7 and proMMP-9 proteolytic activity via adduction of the conserved cysteine switch domain thiolate. Biotin-labeled OA-NO(2) showed this adduction occurs preferentially with latent forms of MMP, confirming a role for thiol alkylation by OA-NO(2) in MMP activation. In addition to regulating pro-MMP activation, MMP expression was modulated by OA-NO(2) via activation of peroxisome proliferator-activated receptor-γ. MMP-9 transcription was decreased in phorbol 12-myristate 13-acetate-stimulated THP-1 macrophages to an extent similar to that induced by the peroxisome proliferator-activated receptor-γ agonist Rosiglitazone. This was affirmed using a murine model of atherosclerosis, ApoE(-/-) mice, where in vivo OA-NO(2) administration suppressed MMP expression in atherosclerotic lesions. These findings reveal that electrophilic fatty acid derivatives can serve as effectors during inflammation, first by activating pro-MMP proteolytic activity via alkylation of the cysteine switch domain, and then by transcriptionally inhibiting MMP expression, thereby limiting the further progression of inflammatory processes.
CNT-Based MEMS/NEMS Gas Ionizers for Portable Mass Spectrometry Applications (2010)

We report the fabrication and experimental characterization of a carbon nanotube (CNT)-based MEMS/NEMS electron impact gas ionizer with an integrated extractor gate for portable mass spectrometry. The ionizer achieves low-voltage ionization using sparse forests of plasma-enhanced chemical-vapor-deposited CNTs as field emitters and a proximal extractor grid with apertures aligned to the CNT forests to facilitate electron transmission. The extractor gate is integrated to the ionizer using a high-voltage MEMS packaging technology based on Si springs defined by deep reactive ion etching. The ionizer also includes a high-aspect-ratio silicon structure (¿foam) that facilitates sparse CNT growth and also enables uniform current emission. The devices were tested as field emitters in high vacuum (10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-8</sup> torr) and as electron impact ionizers using argon at pressures of up to 21 mtorr. The experimental data show that the MEMS extractor gate transmits up to 66% of the emitted current and that the ionizers are able to produce up to 0.139 mA of ion current with up to 19% ionization efficiency while consuming 0.39 W.
Femtosecond pulse generation in a Ti:Al_2O_3 laser by using second- and third-order intracavity dispersion (1992)

We investigate the effects of third-order dispersion on pulse width by using a femtosecond Ti:A1(2)O(3) laser with independently adjustable second- and third-order intracavity dispersion compensation. A novel technique for compensating third-order dispersion is demonstrated using Gires-Tournois interferometers that are fabricated monolithically by using multilayer dielectric films. With the addition of intracavity third-order compensation, pulse-width reduction from 45 to 28 fs is achieved. The dispersion compensation effect produced by the Gires-Tournois interferometers is measured in situ using frequency-domain dispersion measurement techniques.
Nickel- or palladium-catalyzed cross coupling. 31. Palladium- or nickel-catalyzed reactions of alkenylmetals with unsaturated organic halides as a selective route to arylated alkenes and conjugated dienes: scope, limitations, and mechanism (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNickel- or palladium-catalyzed cross coupling. 31. Palladium- or nickel-catalyzed reactions of alkenylmetals with unsaturated organic halides as a selective route to arylated alkenes and conjugated dienes: scope, limitations, and mechanismEiichi Negishi, Tamotsu Takahashi, Shigeru Baba, David E. Van Horn, and Nobuhisa OkukadoCite this: J. Am. Chem. Soc. 1987, 109, 8, 2393–2401Publication Date (Print):April 1, 1987Publication History Published online1 May 2002Published inissue 1 April 1987https://doi.org/10.1021/ja00242a024RIGHTS & PERMISSIONSArticle Views2995Altmetric-Citations273LEARN 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 InReddit PDF (1 MB) Get e-Alertsclose Get e-Alerts
Neural crest migration is driven by a few trailblazer cells with a unique molecular signature narrowly confined to the invasive front (2015)

Neural crest (NC) cell migration is crucial to the formation of peripheral tissues during vertebrate development. However, how NC cells respond to different microenvironments to maintain persistence of direction and cohesion in multicellular streams remains unclear. To address this, we profiled eight subregions of a typical cranial NC cell migratory stream. Hierarchical clustering showed significant differences in the expression profiles of the lead three subregions compared with newly emerged cells. Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells. Computational modeling predicted that a small fraction of lead cells that detect directional information is optimal for successful stream migration. Single-cell profiling then revealed a unique molecular signature that is consistent and stable over time in a subset of lead cells within the most advanced portion of the migratory front, which we term trailblazers. Model simulations that forced a lead cell behavior in the trailing subpopulation predicted cell bunching near the migratory domain entrance. Misexpression of the trailblazer molecular signature by perturbation of two upstream transcription factors agreed with the in silico prediction and showed alterations to NC cell migration distance and stream shape. These data are the first to characterize the molecular diversity within an NC cell migratory stream and offer insights into how molecular patterns are transduced into cell behaviors.
Exosome Encased Spherical Nucleic Acid Gold Nanoparticle Conjugates as Potent MicroRNA Regulation Agents (2013)

Exosomes are a class of naturally occurring nanomaterials that play crucial roles in the protection and transport of endogenous macromolecules, such as microRNA and mRNA, over long distances. Intense effort is underway to exploit the use of exosomes to deliver synthetic therapeutics. Herein, transmission electron microscopy is used to show that when spherical nucleic acid (SNA) constructs are endocytosed into PC-3 prostate cancer cells, a small fraction of them (<1%) can be naturally sorted into exosomes. The exosome-encased SNAs are secreted into the extracellular environment from which they can be isolated and selectively re-introduced into the cell type from which they were derived. In the context of anti-miR21 experiments, the exosome-encased SNAs knockdown miR-21 target by approximately 50%. Similar knockdown of miR-21 by free SNAs requires a ≈3000-fold higher concentration.
Query Processing, Approximation, and Resource Management in a Data Stream Management System. (2003)

This paper describes our ongoing work developing the Stanford Stream Data Manager (STREAM), a system for executing continuous queries over multiple continuous data streams. The STREAM system supports a declarative query language, and it copes with high data rates and query workloads by providing approximate answers when resources are limited. This paper describes specific contributions made so far and enumerates our next steps in developing a general-purpose Data Stream Management System.
Immunosuppressive effects of glycosylation inhibiting factor on the IgE and IgG antibody response. (1986)

Abstract Glycosylation inhibiting factor (GIF) was purified from culture filtrates of a T cell hybridoma, 23A4, by affinity chromatography on anti-lipomodulin Sepharose. The factor exhibited phospholipase inhibitory activity upon dephosphorylation. Immunization of BDF1 mice with aluminum hydroxide gel (alum)-absorbed dinitrophenyl derivatives of ovalbumin (DNP-OA) resulted in persistent IgE and IgG antibody formation. However, repeated injections of the affinity-purified GIF into the DNP-OA-primed mice beginning on the day of priming prevented the primary anti-hapten antibody responses of both the IgE and the IgG1 isotypes. Treatment with GIF also diminished on-going IgE antibody formation in the DNP-OA-primed mice. The treatment changed the nature of IgE-binding factors formed by BDF1 spleen cells. Incubation of spleen cells from OA + alum-primed mice with OA resulted in the formation of IgE-potentiating factor, whereas spleen cells of OA-primed, GIF-treated mice formed IgE-suppressive factor upon antigenic stimulation. It was also found that Lyt-2+ T cells in the OA-primed, GIF-treated mouse spleen cells released GIF, which had affinity for OA and bore I-Jb determinant(s). Transfer of a Lyt-1+ cell-depleted fraction of the OA-primed, GIF-treated mouse spleen cells into naive syngeneic animals resulted in suppression of the primary anti-DNP IgE antibody response of the recipients to alum-absorbed DNP-OA, but failed to affect the anti-DNP antibody response to DNP-keyhole limpet hemocyanin. The results indicate that GIF treatment during the primary response to OA facilitated the generation of antigen-specific suppressor T cells.
RNA TRANSPORT AND LOCAL CONTROL OF TRANSLATION (2005)

In eukaryotes, the entwined pathways of RNA transport and local translational regulation are key determinants in the spatio-temporal articulation of gene expression. One of the main advantages of this mechanism over transcriptional control in the nucleus lies in the fact that it endows local sites with independent decision-making authority, a consideration that is of particular relevance in cells with complex cellular architecture such as neurons. Localized RNAs typically contain codes, expressed within cis-acting elements, that specify subcellular targeting. Such codes are recognized by trans-acting factors, adaptors that mediate translocation along cytoskeletal elements by molecular motors. Most transported mRNAs are assumed translationally dormant while en route. In some cell types, especially in neurons, it is considered crucial that translation remains repressed after arrival at the destination site (e.g., a postsynaptic microdomain) until an appropriate activation signal is received. Several candidate mechanisms have been suggested to participate in the local implementation of translational repression and activation, and such mechanisms may target translation at the level of initiation and/or elongation. Recent data indicate that untranslated RNAs may play important roles in the local control of translation.
The order and orientation of mouse lambda-genes explain lambda-rearrangement patterns. (1988)

Mouse lambda-genes are rearranged in specific V lambda-JC lambda associations: V lambda 1 has only been found to rearrange with JC lambda 3 or JC lambda 1, whereas V lambda 2 mainly rearranges with JC lambda 2 and very rarely with JC lambda 1,3. In order to determine the physical basis for these associations we have cloned the respective lambda-genes and large portions of their flanking regions by chromosomal walking in a total of 141 kb of phage and cosmid clones. With the use of unique probes obtained from such clones, the order and orientation of the mouse lambda-gene segments were determined by analyzing patterns of DNA deletion associated with lambda-gene rearrangements in various cell lines. All V and C gene segments were found to be in the same transcriptional orientation, and V2 and V1 were found not to be next to each other, thus supporting the gene order V2-C2-C4-V1-C3-C1.
Toso controls encephalitogenic immune responses by dendritic cells and regulatory T cells (2014)

The ability to mount a strong immune response against pathogens is crucial for mammalian survival. However, excessive and uncontrolled immune reactions can lead to autoimmunity. Unraveling how the reactive versus tolerogenic state is controlled might point toward novel therapeutic strategies to treat autoimmune diseases. The surface receptor Toso/Faim3 has been linked to apoptosis, IgM binding, and innate immune responses. In this study, we used Toso-deficient mice to investigate the importance of Toso in tolerance and autoimmunity. We found that Toso(-/-) mice do not develop severe experimental autoimmune encephalomyelitis (EAE), a mouse model for the human disease multiple sclerosis. Toso(-/-) dendritic cells were less sensitive to Toll-like receptor stimulation and induced significantly lower levels of disease-associated inflammatory T-cell responses. Consistent with this observation, the transfer of Toso(-/-) dendritic cells did not induce autoimmune diabetes, indicating their tolerogenic potential. In Toso(-/-) mice subjected to EAE induction, we found increased numbers of regulatory T cells and decreased encephalitogenic cellular infiltrates in the brain. Finally, inhibition of Toso activity in vivo at either an early or late stage of EAE induction prevented further disease progression. Taken together, our data identify Toso as a unique regulator of inflammatory autoimmune responses and an attractive target for therapeutic intervention.
Mice with human immune system components as in vivo models for infections with human pathogens (2011)

Many pathogens relevant to human disease do not infect other animal species. Therefore, animal models that reconstitute or harbor human tissues are explored as hosts for these. In this review, we will summarize recent advances to utilize mice with human immune system components, reconstituted from hematopoietic progenitor cells in vivo. Such mice can be used to study human pathogens that replicate in leukocytes. In addition to studying the replication of these pathogens, the reconstituted human immune system components can also be analyzed for initiating immune responses and control against these infections. Moreover, these new animal models of human infectious disease should replicate the reactivity of the human immune system to vaccine candidates and, especially, the adjuvants contained in them, more faithfully.
Comparison of a polymerase chain reaction assay and a conventional microbiologic method for detection of methicillin-resistant Staphylococcus aureus (1992)

The presence or absence of a methicillin resistance gene in 58 clinical isolates of Staphylococcus aureus was examined by the polymerase chain reaction (PCR) and Southern blot analyses. The results were analyzed in relation to those of the MIC assay of methicillin and oxacillin. PCR assay results were identical to those of Southern blot analysis of genomic DNA digested with HindIII (positive, 28 strains; negative, 30 strains). Among the 28 PCR-positive strains, 6 strains showed methicillin susceptibility by the conventional susceptibility test (MICs, less than or equal to 8 micrograms/ml). Culturing of the six strains with ceftizoxime led to an increase in the phenotypic level of resistance to methicillin and oxacillin, indicating that these strains should be classified as methicillin-resistant S. aureus (MRSA). The PCR assay was found to be a sensitive and reliable procedure for the rapid diagnosis of MRSA infection, even in cases in which the conventional MIC assay failed to detect MRSA.
Platelet Preservation (1969)

Standard refrigerated storage (at 4°C) resulted in a marked shortening of the life-span of platelets labeled with 51Cr and reinfused into the original donor. Storage at ambient, room temperature (22°C) preserved a normal platelet life-span. Platelets stored at this higher temperature should be adequate for transfusion purposes for as long as 96 hours. The use of cold temperatures should be abandoned in the preparation and storage of platelets for transfusion purposes.
Melatonin: A Coordinating Signal for Mammalian Reproduction? (1985)

There is a daily rhythm in the production of the pineal hormone melatonin in all mammalian species. Production is stimulated by darkness and inhibited by light. This provides a signal reflecting the changing environmental lighting cycle. In seasonally breeding mammals that use changes in the photoperiod to time their reproductive cycles, temporal signals to the reproductive system are controlled by the daily rhythm in melatonin production.
The Carboxyl-terminal Domain of Receptor-associated Protein Facilitates Proper Folding and Trafficking of the Very Low Density Lipoprotein Receptor by Interaction with the Three Amino-terminal Ligand-binding Repeats of the Receptor (1999)

The 39-kDa receptor-associated protein (RAP) is a specialized antagonist that inhibits all known ligand interactions with receptors that belong to the low density lipoprotein (LDL) receptor gene family. Recent studies have demonstrated a role for RAP as a molecular chaperone for the LDL receptor-related protein during receptor folding and trafficking within the early secretory pathway. In the present study, we investigated a potential role for RAP as a chaperone for the very low density lipoprotein (VLDL) receptor, another member of the LDL receptor gene family. Using intracellular cross-linking techniques, we found that RAP is associated with newly synthesized VLDL receptor. In the absence of RAP co-expression, newly synthesized VLDL receptor exhibited slower trafficking along the early secretory pathway, most likely due to misfolding of the receptor. The role of RAP in the folding of the VLDL receptor was further studied using an anchor-free, soluble VLDL receptor. Metabolic pulse-chase labeling experiments showed that while only 3% of the soluble VLDL receptor was folded and secreted in the absence of RAP co-expression, over 50% of the soluble receptor was secreted in the presence of RAP co-expression. The functions of RAP in VLDL receptor folding and trafficking were mediated by its carboxyl-terminal repeat but not by the amino-terminal and central repeats. Using truncated VLDL receptor constructs, we identified the RAP-binding site within the first three ligand-binding repeats of the VLDL receptor. Thus, our present study demonstrates that RAP serves as a folding and trafficking chaperone for the VLDL receptor via interactions of its carboxyl-terminal repeat with the three amino-terminal ligand-binding repeats of the VLDL receptor.