gebhart/patrepeval huggingface dataset:
Rationale, progress and development of vaccines utilizing STING-activating cyclic dinucleotide adjuvants (2013)

A principal barrier to the development of effective vaccines is the availability of adjuvants and formulations that can elicit both effector and long-lived memory CD4 and CD8 T cells. Cellular immunity is the presumptive immune correlate of protection against intracellular pathogens: a group composed of bacteria, viruses and protozoans that is responsible for a staggering level of morbidity and mortality on a global scale. T-cell immunity is also correlated with clinical benefit in cancer, and the development of therapeutic strategies to harness the immune system to treat diverse malignancies is currently undergoing a renaissance. Cyclic dinucleotides (CDNs) are ubiquitous small molecule second messengers synthesized by bacteria that regulate diverse processes and are a relatively new class of adjuvants that have been shown to increase vaccine potency. CDNs activate innate immunity by directly binding the endoplasmic reticulum-resident receptor STING (stimulator of interferon genes), activating a signaling pathway that induces the expression of interferon-β (IFN-β) and also nuclear factor-κB (NF-κB) dependent inflammatory cytokines. The STING signaling pathway has emerged as a central Toll-like receptor (TLR) independent mediator of host innate defense in response to sensing cytosolic nucleic acids, either through direct binding of CDNs secreted by bacteria, or, as shown recently, through binding of a structurally distinct CDN produced by a host cell receptor in response to binding cytosolic double-stranded (ds)DNA. Although this relatively new class of adjuvants has to date only been evaluated in mice, newly available CDN-STING cocrystal structures will likely intensify efforts in this field towards further development and evaluation in human trials both in preventive vaccine and immunotherapy settings.
Click Chemistry as a Reliable Method for the High-Density Postsynthetic Functionalization of Alkyne-Modified DNA (2006)

[reaction: see text] We report the development of the Cu(I)-catalyzed Huisgen cycloaddition (click) reaction for the multiple postsynthetic labeling of alkyne-modified DNA. A series of alkyne-modified oligodeoxyribonucleotides (ODNs) of increasing alkyne density were prepared, and the click reaction using various azide labels was investigated. Complete high-density conversion was observed for ODNs containing up to six consecutive alkyne functions. Compatibility of the click conditions with long DNA strands was shown using a PCR product obtained with an alkyne-modified primer.
Prodrugs of L-cysteine as liver-protective agents. 2(R,S)-methylthiazolidine-4(R)-carboxylic acid (MTCA), a latent cysteine (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProdrugs of L-cysteine as liver-protective agents. 2(R,S)-methylthiazolidine-4(R)-carboxylic acid (MTCA), a latent cysteineHerbert T. Nagasawa, David J. D. Goon, Richard T. Zera, and Daniel L. YuzonCite this: J. Med. Chem. 1982, 25, 5, 489–491Publication Date (Print):May 1, 1982Publication History Published online1 May 2002Published inissue 1 May 1982https://pubs.acs.org/doi/10.1021/jm00347a001https://doi.org/10.1021/jm00347a001research-articleACS PublicationsRequest reuse permissionsArticle Views260Altmetric-Citations47LEARN 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
Noise analysis in isolation of iodine using three energies (1980)

The Poisson noise inherent in multispectral x-ray imaging systems is formulated to give the SNR under a limited exposure constraint. The SNR value is maximized with respect to the exposure partition among different x-ray energies. The study shows how to choose suitable spectra and the dose weights. The robustness of these dose weights is also demonstrated for systems of varying bone and tissue contents.
ROLE OF KUPFFER CELLS IN INTERLEUKIN-6 RELEASE FOLLOWING TRAUMA-HEMORRHAGE AND RESUSCITATION (1994)

Although interleukin-6 (IL-6) plays an important role in the pathophysiology of trauma-hemorrhage and resuscitation, the cellular origin of this inflammatory cytokine remains unknown. This study was undertaken to determine whether Kupffer cells (KC) are a major source of IL-6 release following trauma-hemorrhage and resuscitation. KC numbers were significantly (p < .05) reduced in vivo with gadolinium chloride (GdCl3; 10 mg/kg IV). KC-reduced (KC(-)) and KC-normal (saline-treated; KC(+)) rats underwent laparotomy (i.e., trauma-induced), followed by either sham operation or hemorrhage. Hemorrhaged rats were bled to and maintained at a mean arterial pressure of 40 mmHg until 40% of the shed blood volume was returned as Ringer's lactate, and then resuscitated with Ringer's lactate (four times shed blood volume over 1 h). Results indicate that KC reduction per se had no effect on any measured parameter at any time. At 0.5 and 2.0 h postresuscitation, mean arterial pressure, heart rate, cardiac output, stroke volume, and hematocrit were reduced to a similar extent in both the KC(+) and KC(-) hemorrhage groups. KC reduction did, however, significantly reduce plasma IL-6 concentration (means +/- S.E.; U/ml) at both 0.5 h (KC(+) = 709 +/- 391 vs. KC(-) = 159 +/- 5) and at 2.0 h (KC(+) = 527 +/- 394 vs. KC(-) = 83 +/- 20) postresuscitation. In conclusion, this study demonstrates that KC are a major source of in vivo IL-6 release following trauma-hemorrhage and resuscitation.
Heterodimerization among thyroid hormone receptor, retinoic acid receptor, retinoid X receptor, chicken ovalbumin upstream promoter transcription factor, and an endogenous liver protein. (1992)

Thyroid hormone receptor (TR) binds to DNA as a monomer, homodimer, and heterodimer with nuclear proteins. We have confirmed that the TR can heterodimerize with retinoid X receptors (RXRs)-alpha and -beta, and have found that another member of the nuclear receptor superfamily, chicken ovalbumin upstream promoter transcription factor (COUP-TF), also formed heterodimers with the TR in the context of binding to a palindromic thyroid hormone-responsive element (TREp). The interaction between COUP-TF and the TR was confirmed using specific antibodies which supershifted the COUP-TF/TR DNA complexes. The complex between the TR and the major TR heterodimerization partner in liver was unaffected by antibodies to COUP-TF and RXR beta, but was supershifted by an anti-RXR alpha antibody, indicating that the liver protein is highly related to RXR alpha. Indeed, the TR/RXR and TR/liver protein heterodimers contact the same guanidine residues in TREp. The retinoic acid receptor (RAR) also heterodimerized with COUP-TF as well as with RXR alpha, RXR beta, and the TR heterodimerization partner in liver. In contrast to its ability to heterodimerize with the TR and RAR, we did not detect heterodimers between COUP-TF and either RXR alpha, RXR beta, or the liver nuclear protein in the context of binding to the TREp. These results show that the major TR heterodimerization partner in liver is highly related to RXR alpha, but that other nuclear receptors such as COUP-TF can heterodimerize with the TR and RAR, suggesting that selective protein-protein interactions may be involved in the tissue and target gene specificities of hormone action.
Polymer-based flexible capacitive sensor for three-axial force measurements (2012)

We have developed a flexible-substrate-based three-axial force sensor, composed of finger-shaped electrode capacitors, whose operation is based on the measurement of a capacitance change induced upon applying a three-axial load. The electrode design supports high sensitivity to shear forces. An overall flexibility of the sensor and elasticity of the capacitor's dielectric is obtained by integrating three polymers in the sensor's technology process, namely polyimide, parylene-C, and polydimethylsiloxane, combined with standard metallization processes. We have theoretically modeled the sensor's capacitance and its three-axial force sensitivity. The unit capacitors have static capacitances in the range of 20 pF. The electro-mechanical characterization of the capacitors reveals in the normal direction a sensitivity Sz = 0.024 kPaâ1 for pressures &lt;10 kPa, whereas for higher pressures the measured sensitivity Sz = 6.6 Ã 10â4 kPaâ1. Typical measured shear force sensitivity Sx = 2.8 Ã 10â4 kPaâ1. These values give our transducer high potential for use in skin-like sensing applications.
Nitric oxide synthase inhibition does not alter the reactive hyperemic response in the cutaneous circulation (2003)

Reactive hyperemia is the sudden rise in blood flow after release of an arterial occlusion. Currently, the mechanisms mediating this response in the cutaneous circulation are poorly understood. The purpose of this study was to 1). characterize the reactive hyperemic response in the cutaneous circulation and 2). determine the contribution of nitric oxide (NO) to reactive hyperemia. Using laser-Doppler flowmetry, we characterized reactive hyperemia after 3-, 5-, 10-, and 15-min arterial occlusions in 10 subjects. The total hyperemic response was calculated by taking the area under the curve (AUC) of the hyperemic response minus baseline skin blood flow (SkBF) [i.e., total hyperemic response = AUC - [baseline SkBF as %maximal cutaneous vascular conductance (CVC(max) x duration of hyperemic response in s]]. For the characterization protocol, the total hyperemic response significantly increased as the period of ischemia increased from 5 to 15 min (P < 0.05). However, the 3-min response was not significantly different from the 5-min response. In the NO contribution protocol, two microdialysis fibers were placed in the forearm skin of eight subjects. One site served as a control and was continuously perfused with Ringer solution. The second site was continuously perfused with 10 mM NG-nitro-l-arginine methyl ester (l-NAME) to inhibit NO synthase. CVC was calculated as flux/mean arterial pressure and normalized to maximal blood flow (28 mM sodium nitroprusside). The total hyperemic response in control sites was not significantly different from l-NAME sites after a 5-min occlusion (3261 +/- 890 vs. 2907 +/- 531% CVC(max. s). Similarly, total hyperemic responses in control sites were not different from l-NAME sites (9155 +/- 1121 vs. 9126 +/- 1088% CVC(max. s) after a 15-min arterial occlusion. These data suggest that NO does not directly mediate reactive hyperemia and that NO is not produced in response to an increase in shear stress in the cutaneous circulation.
T Cells Expressing Activated LFA-1 Are More Susceptible to Infection with Human Immunodeficiency Virus Type 1 Particles Bearing Host-Encoded ICAM-1 (1998)

The incorporation of host-derived proteins in nascent human immunodeficiency virus type 1 (HIV-1) particles is a well-established phenomenon. We recently demonstrated that the physical presence of host-encoded ICAM-1 glycoproteins on HIV-1 leads to a significant increase in virus infectivity in an ICAM-1/LFA-1-dependent fashion (J.-F. Fortin, R. Cantin, G. Lamontagne, and M. Tremblay, J. Virol. 71:3588-3596, 1997). We show here that conversion of LFA-1 to high affinity for ICAM-1 with the use of anti-LFA-1 antibodies (clones NKI-L16 and MEM83) markedly enhances the susceptibility of different target T-lymphoid cell lines, as well as of primary peripheral blood mononuclear cells, to infection by ICAM-1-bearing HIV-1 particles (6- to 95-fold). It is known that T-cell receptor (TCR) cross-linking induces a transient increase in LFA-1 affinity for ICAM-1. Treatment of peripheral blood mononuclear cells with anti-TCR antibodies (clone OKT3) resulted in a transient increase in susceptibility to infection by ICAM-1-positive virions that parallels the previously reported kinetics of the LFA-1/ICAM-1 adhesion mechanism. Our results led us to postulate that the strong interaction taking place between virally incorporated ICAM-1 and cell surface-activated LFA-1 markedly enhances the efficiency of virus binding and entry, thus favoring greater infection by ICAM-1-bearing HIV-1 particles. In view of the knowledge that primary HIV-1 isolates harbor host-derived ICAM-1 on their surfaces, these results provide new information about the role of host-derived ICAM-1 in the life cycle of HIV-1 and how it could positively modulate the dynamics of the viral infection, mainly in cellular compartments, such as the lymphoid tissues, where the level of cellular activation is high and where the probability of encountering a T cell expressing the activated LFA-1 form is also elevated.
Chondrocyte Transplantation Using a Collagen Bilayer Matric for Cartilage Repair (1997)

We have developed a novel, two-layered, collagen matrix seeded with chondrocytes for repair of articular cartilage. It consists of a dense collagen layer which is in contact with bone and a porous matrix to support the seeded chondrocytes. The matrices were implanted in rabbit femoral trochleas for up to 24 weeks. The control groups received either a matrix without cells or no implant. The best histological repair was seen with cell-seeded implants. The permeability and glycosaminoglycan content of both implant groups were nearly normal, but were significantly less in tissue from empty defects. The type-II collagen content of the seeded implants was normal. For unseeded implants it was 74.3% of the normal and for empty defects only 20%. The current treatments for articular injury often result in a fibrous repair which deteriorates with time. This bilayer implant allowed sustained hyaline-like repair of articular defects during the entire six-month period of observation.
Improving Fault Tolerance in High-Precision Clock Synchronization (2010)

The very popular Precision Time Protocol (PTP or IEEE 1588) is widely used to synchronize distributed systems with high precision. The underlying principle is a master/slave concept based on the regular exchange of synchronization messages. This paper investigates an approach to enhance PTP with fault tolerance and to overcome the transient deterioration of synchronization accuracy during a recovery from a master failure. To this end, a concept is proposed where a group of masters negotiates a fault-tolerant agreement on the system-wide time and transparently synchronizes the associated IEEE 1588 slaves. Experimental verification on the basis of an Ethernet implementation shows that the approach is feasible and indeed improves the overall synchronization accuracy in terms of fault tolerance.
Favourable response to therapy with the anti‐CD20 monoclonal antibody rituximab in primary chronic cold agglutinin disease (2001)

The 'primary' form of chronic cold agglutinin disease is a clonal B-cell lymphoproliferative disorder that is notoriously difficult to treat with drugs, including corticosteroids, alkylating agents, alpha-interferon and purine analogues. We performed a small, open, uncontrolled, prospective study to evaluate the effect of therapy with the monoclonal anti-CD20 antibody rituximab. Six patients with clonal CD20(+)kappa(+) B-cell proliferation received seven courses of rituximab 375 mg/m(2), d 1, 8, 15, and 22. One patient achieved a complete response. Four partial responses were observed, including a response to re-treatment in one patient. Two patients were categorized as non-responders. Haemoglobin levels increased by a median of 4.1 g/dl in the total group and 4.7 g/dl in the responders, who also experienced a substantial improvement of clinical symptoms. The treatment was well tolerated. We discuss the effect of rituximab therapy compared with other treatment options, and try to explain why two individual patients did not respond. Despite the small numbers, the results are very encouraging. Further studies of rituximab therapy for chronic cold agglutinin disease are warranted.
Sequestration of the δ Opioid Receptor (1996)

The primary structure of the opioid receptors have revealed that many of the structural features that are conserved in other G protein-coupled receptors are also conserved in the opioid receptors. Upon exposure to agonists, some G protein-coupled receptors internalize rapidly, whereas other structurally homologous G protein-coupled receptors do not. It is not known whether opioid receptors are regulated by rapid endocytosis. In transfected Chinese hamster ovary cells expressing the epitope-tagged wild type delta opioid receptor, exposure to 100 nM [D-Ala2,D-Leu5]enkephalin causes internalization of the receptor within 30 min as determined by confocal microscopy. The rate of internalization of the wild type receptor is rapid with a half-maximal reduction by about 10 min, as determined by the reduction in mean surface receptor fluorescence intensity measured using flow cytometry. In contrast, the cells expressing receptors lacking the C-terminal 15 or 37 amino acids exhibit a substantially slower rate of internalization. Furthermore, the cells expressing receptors with point mutations of any of the Ser/Thr between Ser344 and Ser363 in the C-terminal tail exhibit a significant reduction in the rate of receptor internalization. These results suggest that a portion of the C-terminal tail is involved in receptor internalization. Agents that block the formation of clathrin-coated pits considerably reduce the extent of agonist-mediated internalization of the wild type receptor. Taken together, these results suggest that the wild type opioid receptor undergoes rapid agonist-mediated internalization via a classic endocytic pathway and that a portion of the C-terminal tail plays an important role in this internalization process.
A low resistivity n++-InGaN/p++-GaN polarization-induced tunnel junction (2016)

Abstract A low resistivity n ++ -InGaN/p ++ -GaN tunnel junction is illustrated. The tunneling current density of tunnel junction with 30 percent In content in InGaN layer turns out to be extraordinary high (10 kA cm −2 ) even at a relatively low bias voltage (0.1 V) compared with traditional n ++ -GaN/p ++ -GaN. And we optimize the InGaN layer including the thickness, indium component and the doping concentration to increase the tunneling probability with the 1D Schrödinger Poisson self-consistent method and WKB (Wentzel-Kramers-Brillouin) approximation. It is shown that the peak value of electric field in tunnel junction caused by spontaneous polarization and piezoelectric effect reaches 7.1 MV cm −1 with the 2D hole gas concentration of 2 × 10 20 cm −3 at the interface between InGaN and GaN. That indicates n ++ -InGaN/p ++ -GaN tunnel junction has a potential application in GaN-based optoelectronic device.
Crystal Structure of a Laccase from the FungusTrametes versicolor at 1.90-Å Resolution Containing a Full Complement of Coppers (2002)

Laccase is a polyphenol oxidase, which belongs to the family of blue multicopper oxidases. These enzymes catalyze the one-electron oxidation of four reducing-substrate molecules concomitant with the four-electron reduction of molecular oxygen to water. Laccases oxidize a broad range of substrates, preferably phenolic compounds. In the presence of mediators, fungal laccases exhibit an enlarged substrate range and are then able to oxidize compounds with a redox potential exceeding their own. Until now, only one crystal structure of a laccase in an inactive, type-2 copper-depleted form has been reported. We present here the first crystal structure of an active laccase containing a full complement of coppers, the complete polypeptide chain together with seven carbohydrate moieties. Despite the presence of all coppers in the new structure, the folds of the two laccases are quite similar. The coordination of the type-3 coppers, however, is distinctly different. The geometry of the trinuclear copper cluster in the Trametes versicolor laccase is similar to that found in the ascorbate oxidase and that of mammalian ceruloplasmin structures, suggesting a common reaction mechanism for the copper oxidation and the O(2) reduction. In contrast to most blue copper proteins, the type-1 copper in the T. versicolor laccase has no axial ligand and is only 3-fold coordinated. Previously, a modest elevation of the redox potential was attributed to the lack of an axial ligand. Based on the present structural data and sequence comparisons, a mechanism is presented to explain how laccases could tune their redox potential by as much as 200 mV.
New tools and methods for direct programmatic access to the dbSNP relational database (2010)

Genome-wide association studies often incorporate information from public biological databases in order to provide a biological reference for interpreting the results. The dbSNP database is an extensive source of information on single nucleotide polymorphisms (SNPs) for many different organisms, including humans. We have developed free software that will download and install a local MySQL implementation of the dbSNP relational database for a specified organism. We have also designed a system for classifying dbSNP tables in terms of common tasks we wish to accomplish using the database. For each task we have designed a small set of custom tables that facilitate task-related queries and provide entity-relationship diagrams for each task composed from the relevant dbSNP tables. In order to expose these concepts and methods to a wider audience we have developed web tools for querying the database and browsing documentation on the tables and columns to clarify the relevant relational structure. All web tools and software are freely available to the public at http://cgsmd.isi.edu/dbsnpq. Resources such as these for programmatically querying biological databases are essential for viably integrating biological information into genetic association experiments on a genome-wide scale.
Anterior-Posterior Ground Reaction Forces as a Measure of Paretic Leg Contribution in Hemiparetic Walking (2006)

PP was found to provide a quantitative measure of the coordinated output of the paretic leg. Further research on this measure of forward propulsion may lead to the provision of an effective tool for distinguishing functional compensation from physiological restitution.