gebhart/patrepeval huggingface dataset:
Exosomes isolated from plasma of glioma patients enrolled in a vaccination trial reflect antitumor immune activity and might predict survival (2015)

Exosomes in plasma of glioma patients hold promise as biomarkers of prognosis. We aimed to determine whether changes in total exosomal protein and mRNA expression levels could serve as surrogate markers of immunological and clinical responses in glioma patients receiving antitumor vaccines. Exosomes were isolated from pre/post-vaccine plasma specimens in 20/22 patients enrolled in a phase I/II trial with the antitumor vaccine. Exosomal protein content was analyzed and mRNA expression levels for 24 genes were simultaneously assessed by qRT-PCR. Pre- to post-vaccination changes in exosomal protein and ΔCt values were correlated with immunological and clinical responses and survival using Spearman rank statistics and hazard ratios (HR). Exosomal protein levels positively correlated (<i>p</i> < 0.0043) with the WHO tumor grade at diagnosis. Protein levels were lower in post- vs. pre-vaccination exosome fractions. Post-therapy increases in tumor size were associated with elevations in exosome proteins in glioblastoma but not always in anaplastic astrocytoma (AA). Only exosomal ΔCt values for IL-8, TIMP-1, TGF-β and ZAP70 were significant (<i>p</i> < 0.04 to <i>p</i> < 0.001). The ΔCt for IL-8 and TGF-β mRNA positively correlated with post-vaccine immunologic responses to glioma antigens, while ΔCt for TIMP-1 mRNA was negatively correlated to ΔCt for IL-8 and TGF-β. Only ΔCt for IL-8 weakly correlated with OS and time to progression (TTP). In post-vaccine exosomes of the longest surviving patient with AA, mRNA for PD-1 was persistently elevated. Protein and mRNA expression levels for immune-related genes in plasma exosomes were useful in evaluating glioma patients' response to vaccination therapy.
Automatic, Dimensional and Continuous Emotion Recognition (2010)

Recognition and analysis of human emotions have attracted a lot of interest in the past two decades and have been researched extensively in neuroscience, psychology, cognitive sciences, and computer sciences. Most of the past research in machine analysis of human emotion has focused on recognition of prototypic expressions of six basic emotions based on data that has been posed on demand and acquired in laboratory settings. More recently, there has been a shift toward recognition of affective displays recorded in naturalistic settings as driven by real world applications. This shift in affective computing research is aimed toward subtle, continuous, and context-specific interpretations of affective displays recorded in real-world settings and toward combining multiple modalities for analysis and recognition of human emotion. Accordingly, this article explores recent advances in dimensional and continuous affect modeling, sensing, and automatic recognition from visual, audio, tactile, and brain-wave modalities.
Solvent effect on the protonation of some alkylamines (1980)

Thermodynamic data were obtained at 25 °C for the solution and protonation of six bases B: ammonia, three methylamines, and monoethyl and n-propylamines in dimethylsulfoxide (Me 2 SO) and propylene carbonate (PC). Vapour pressure, potentiometric, and calorimetric determinations were carried out. The solvent effect on the basicity order and protonation of the amines is analysed by using gas phase data and comparing the solution thermodynamics of gaseous B and BH + . The heat of solution of B in both solvents is close to its heat of condensation. The solution data for BH + are discussed in terms of two recent hydration data interpretations.
Analysis of RF-Pilot-Based Phase Noise Compensation for Coherent Optical OFDM Systems (2010)

In coherent optical long-haul transmission systems, orthogonal frequency-division multiplexing represents a promising modulation format. However, due to long symbol length, laser phase noise can be a major impairment. In this manuscript, the RF-pilot-based phase noise compensation scheme is analyzed and compared to conventional common-phase error compensation. It has been shown that the RF-pilot-based phase noise compensation scheme allows for a considerable increase in tolerable laser linewidth as compared to conventional common-phase error compensation at the cost of an increase in system complexity. For a 112-Gb/s transmission scheme, the tolerable linewidth is increased by a factor of ten as compared to common-phase error compensation.
Editor's Introduction (1977)

Graduate study, as all facets of public life, is regulated by centralized authority in the Soviet Union. State control over the awarding of graduate degrees and academic ranks is vested in the Higher Certification Commission [Vysshaia attestatsionnaia komissiia] attached to the USSR Council of Ministers. Prior to October 1974, the commission was administered by the Ministry of Higher and Secondary Specialized Education. The commission's change of status, as well as the extensive reorganization of its administration that has resulted from this change, form the subject of this issue of Soviet Education.
Retarding the crystallization of PbI2for highly reproducible planar-structured perovskite solar cells via sequential deposition (2014)

A universally useful idea for preparing high quality perovskite films is proposed by retarding the crystallization of PbI<sub>2</sub>, which make possible highly reproducible planar structured perovskite solar cells.
Evaluation of the SmartCycler II System for Real-Time Detection of Viruses and Chlamydia From Ocular Specimens (2006)

The descriptive statistics of the SmartCycler II system obtained in a small laboratory were comparable to those of a central molecular laboratory for detecting viruses and Chlamydia species. Clinical Relevance Polymerase chain reaction has great potential in the routine diagnosis of ocular infections in any conventional laboratory.
Disruption of two novel genes by a translocation co-segregating with schizophrenia (2000)

A balanced (1;11)(q42.1;q14.3) translocation segregates with schizophrenia and related psychiatric disorders in a large Scottish family (maximum LOD = 6.0). We hypothesize that the translocation is the causative event and that it directly disrupts gene function. We previously reported a dearth of genes in the breakpoint region of chromosome 11 and it is therefore unlikely that the expression of any genes on this chromosome has been affected by the translocation. By contrast, the corresponding region on chromosome 1 is gene dense and, not one, but two novel genes are directly disrupted by the translocation. These genes have been provisionally named Disrupted-In-Schizophrenia 1 and 2 ( DISC1 and DISC2 ). DISC1 encodes a large protein with no significant sequence homology to other known proteins. It is predicted to consist of a globular N-terminal domain(s) and helical C-terminal domain which has the potential to form a coiled-coil by interaction with another, as yet, unidentified protein(s). Similar structures are thought to be present in a variety of unrelated proteins that are known to function in the nervous system. The putative structure of the protein encoded by DISC1 is therefore compatible with a role in the nervous system. DISC2 apparently specifies a non-coding RNA molecule that is antisense to DISC1, an arrangement that has been observed at other loci where it is thought that the antisense RNA is involved in regulating expression of the sense gene. Altogether, these observations indicate that DISC1 and DISC2 should be considered formal candidate genes for susceptibility to psychiatric illness.
Nitric oxide, oxidants, and protein tyrosine nitration (2004)

The occurrence of protein tyrosine nitration under disease conditions is now firmly established and represents a shift from the signal transducing physiological actions of (.)NO to oxidative and potentially pathogenic pathways. Tyrosine nitration is mediated by reactive nitrogen species such as peroxynitrite anion (ONOO(-)) and nitrogen dioxide ((.)NO2), formed as secondary products of (.)NO metabolism in the presence of oxidants including superoxide radicals (O2(.-)), hydrogen peroxide (H2O2), and transition metal centers. The precise interplay between (.)NO and oxidants and the identification of the proximal intermediate(s) responsible for nitration in vivo have been under controversy. Despite the capacity of peroxynitrite to mediate tyrosine nitration in vitro, its role on nitration in vivo has been questioned, and alternative pathways, including the nitrite/H2O2/hemeperoxidase and transition metal-dependent mechanisms, have been proposed. A balanced analysis of existing evidence indicates that (i) different nitration pathways can contribute to tyrosine nitration in vivo, and (ii) most, if not all, nitration pathways involve free radical biochemistry with carbonate radicals (CO3(.-)) and/or oxo-metal complexes oxidizing tyrosine to tyrosyl radical followed by the diffusion-controlled reaction with (.)NO2 to yield 3-nitrotyrosine. Although protein tyrosine nitration is a low-yield process in vivo, 3-nitrotyrosine has been revealed as a relevant biomarker of (.)NO-dependent oxidative stress; additionally, site-specific nitration focused on particular protein tyrosines may result in modification of function and promote a biological effect. Tissue distribution and quantitation of protein 3-nitrotyrosine, recognition of the predominant nitration pathways and individual identification of nitrated proteins in disease states open new avenues for the understanding and treatment of human pathologies.
Identification and Cloning of Genes Associated with the Guinea Pig Skin Delayed-Type Hypersensitivity Reaction (2001)

Although the cellular and molecular mechanisms underlying the delayed-type hypersensitivity (DTH) reaction have been investigated, the functions of infiltrating leukocytes and skin resident cells in the elicitation phase of the DTH reaction are not completely understood. To gain more insight into the role of these cells in the DTH reaction, we identified about 250 cDNA fragments showing elevated expression during the DNCB-induced guinea pig skin DTH reaction by differential display analysis. Characterization of 50 of them led to the identification of 28 genes whose expression was elevated in the DNCB-induced DTH reactive tissue. Sequencing of the 28 cDNA fragments and homology search analysis demonstrated that 10 of them represented known genes, some of which, in particular elafin (an elastase inhibitor) and ferritin, are considered to play roles in the DTH reaction. The other 18 fragments are probably derived from unknown genes. Cloning of the cDNAs of one of these genes indicated that it is that for guinea pig tryptophanyl-tRNA synthetase (WRS), a protein found to be induced by interferon-gamma and upregulated during the late stages of mononuclear phagocyte maturation in vitro. Strong induction of the WRS gene during the DTH reaction suggests its involvement in the in vivo immune response.
Indexing and retrieval of the MPEG compressed video (1998)

The <i>Journal of Electronic Imaging</i> (JEI), copublished bimonthly with the Society for Imaging Science and Technology, publishes peer-reviewed papers that cover research and applications in all areas of electronic imaging science and technology.
(α-Ethoxyvinyl)tributyltin; An Efficient Reagent for the Nucleophilic Acetylation of Organic Halides via Palladium Catalysis (1987)

Abstract (α-Ethoxyvinyl)tributyltin acts as a masked acetylating agent in the palladium catalyzed reaction with various organic halides, such as aryl bromides, vinyl bromides, benzyl chloride, and allyl chloride, giving, after hydrolysis of the resulting reaction mixture, good yields of the corresponding ketone product.
Combination of p53 Cancer Vaccine with Chemotherapy in Patients with Extensive Stage Small Cell Lung Cancer (2006)

This study provides clinical support for an emerging paradigm in cancer immunotherapy, wherein optimal use of vaccination might be more effective, not as a separate modality, but in direct combination with chemotherapy.
Design, Synthesis, and Biological Evaluation of Analogues of the Antitumor Agent, 2-{4-[(7-Chloro-2-quinoxalinyl)oxy]phenoxy}propionic Acid (XK469) (2001)

2-{4-[(7-Chloro-2-quinoxalinyl)oxy]phenoxy}propionic acid (XK469) is among the most highly and broadly active antitumor agents to have been evaluated in our laboratories and is currently scheduled to enter clinical trials in 2001. The mechanism or mechanisms of action of XK469 remain to be elaborated. Accordingly, an effort was initiated to establish a pharmacophore hypothesis to delineate the requirements of the active site, via a comprehensive program of synthesis of analogues of XK469 and evaluation of the effects of structural modification(s) on solid tumor activity. The strategy formulated chose to dissect the two-dimensional parent structure into three regionsI, ring A of quinoxaline; II, the hydroquinone connector linkage; and III, the lactic acid moietyto determine the resultant in vitro and in vivo effects of chemical alterations in each region. Neither the A-ring unsubstituted nor the B-ring 3-chloro-regioisomer of XK469 showed antitumor activity. The modulating antitumor effect(s) of substituents of differing electronegativities, located at the several sites comprising the A-ring of region I, were next ascertained. Thus, a halogen substituent, located at the 7-position of a 2-{4-[(2-quinoxalinyl)oxy]phenoxy}propionic acid, generated the most highly and broadly active antitumor agents. A methyl, methoxy, or an azido substituent at this site generated a much less active structure, whereas 5-, 6-, 8-chloro-, 6-, 7-nitro, and 7-amino derivatives all proved to be essentially inactive. When the connector linkage (region II) of 1 was changed from that of a hydroquinone to either a resorcinol or a catechol derivative, all antitumor activity was lost. Of the carboxylic acid derivatives of XK469 (region III), i.e., CONH2, CONHCH3, CON(CH3)2, CONHOH, CONHNH2, CN, or CN4H (tetrazole), only the monomethyl- and N,N-dimethylamides proved to be active.
A Framework for Self-Protecting Cryptographic Key Management (2008)

Demands to match security with performance in Web applications where access to shared data needs to be controlled dynamically make self-protecting security schemes attractive. Yet, standard schemes focus primarily on correctness as opposed to adaptability and so need to be extended to handle these new scenarios. One of the approaches to enforcing cryptographically controlled access to shared data is to encrypt it with a single secret key that is then distributed to the users requiring access. Data security is ensured by replacing the group key and re-encrypting the affected data whenever group membership changes. Thus, key management (KM) is expensive when changes in group membership occur frequently and involve large amounts of data. This paper presents a framework, based on the autonomic computing paradigm, that allows a KM scheme to continually monitor the rate at which changes in group membership occur and generate keys as well as encrypted replicas to anticipate future changes. Since the keys and encrypted data are generated by anticipation rather than on demand, the long-term cost of KM is minimized. A prototype implementation and experiments showing performance improvements demonstrate the effectiveness of the proposed framework.
Detection of Gene Expression (1989)

The detection of gene expression can be accomplished in several ways. “Classical” methods (still important, of course) relied on the observation of biochemical or phenotypic changes in cells or organisms in order to determine the expression of a specific gene. Later, advances in macromolecular separation technology made feasible the identification and isolation of a particular gene product or protein molecule. With the advent of recombinant DNA techniques, it is now possible to detect and analyze the transcriptional product of any gene. There are several methods now in widespread use for studying specific RNA molecules. These methods include in situ hybridization,1 Northern gels,2 dot-or slot-blots,2,3 S-1 nuclease assays,4 and RNase protection studies.5 In this chapter, we describe a new and powerful method to detect gene expression at the RNA level. Protocols will be outlined and discussed in detail and some applications will be briefly described. No attempt has been made to exhaustively review the literature in this fast moving area, so we wish to apologize beforehand to the numerous authors whose work may have not been cited in this chapter.
Idiotype‐pulsed antigen presenting cells following autologous transplantation for multiple myeloma may be associated with prolonged survival (2009)

Vaccines are attractive as consolidation therapy after autologous stem cell transplantation (ASCT) for multiple myeloma (MM). We report the results of a phase II trial of the immunotherapeutic, APC8020 (Mylovenge), given after ASCT for MM. We compared the results with that of other patients with MM who underwent ASCT at Mayo Clinic during the same time period. Twenty-seven patients were enrolled on the trial between July, 1998 and June, 2001, and the outcomes were compared to that of 124 consecutive patients transplanted during the same period, but not enrolled on the trial. The median (range) follow-up for patients still alive from the vaccine trial is 6.5 (2.9-8 years), and 7.1 (6-8 years) in the control group. The median age was 57.4 range (36.1-71.3) in the DB group and 56.4 (range, 30-69) in the trial group. Known prognostic factors including PCLI, B2M, and CRP were comparable between the groups. The median overall survival for the trial patients was 5.3 years (95% CI: 4.0 years-N/A) compared to 3.4 years (95% CI: 2.7-4.6 years) for the DB group (P = 0.02). The median time to progression and progression-free survival for the trial group was similar to the DB group. Although not a controlled trial, the vaccines given after ASCT appear to be associated with improved overall survival compared to historical controls. This approach warrants further investigation to confirm this and define the role of vaccine therapy in myeloma.
Upgrading SONET rings with WDM instead of TDM: an economic analysis (2003)

We compare a time-division multiplexed (TDM) upgrade of a legacy SONET ring to a single higher speed ring, versus a wavelength-division multiplexed (WDM) upgrade path, in which it is possible to retain the legacy ring and add additional "virtual rings" at different wavelengths and lower speeds. The paper makes the case that the WDM option can be economically compelling.
Dynamics of Surfactant-Suspended Single-Walled Carbon Nanotubes in a Centrifugal Field (2008)

A hydrodynamic model is used to describe the motion of surfactant-suspended single-walled carbon nanotubes in a density gradient, while being subjected to a centrifugal field. The number of surfactant molecules adsorbed on each nanotube determines its effective density and, hence, its position in the gradient after centrifugation has been completed. Analysis of the spatial concentration distributions of CoMoCAT nanotubes suspended with 2 w/v% sodium cholate yielded 2.09, 2.14, and 2.08 surfactant molecules adsorbed per nanometer along the length of the (6,5), (7,5), and (8,7) nanotubes, respectively. The estimates are commensurate with experimental values reported in the literature and can be used to predict the fate of sodium cholate-suspended nanotubes in the separation process. Since the density of the surfactant-nanotube assembly is highly sensitive to the number of adsorbed molecules, a perturbation would cause it to be enriched at a different location in the gradient. The level of sensitivity is also reflected in the 95% confidence levels that are reported in this work.
Cholesterol Crystals Induce Complement-Dependent Inflammasome Activation and Cytokine Release (2014)

Inflammation is associated with development of atherosclerosis, and cholesterol crystals (CC) have long been recognized as a hallmark of atherosclerotic lesions. CC appear early in the atheroma development and trigger inflammation by NLRP3 inflammasome activation. In this study we hypothesized whether CC employ the complement system to activate inflammasome/caspase-1, leading to release of mature IL-1β, and whether complement activation regulates CC-induced cytokine production. In this study we describe that CC activated both the classical and alternative complement pathways, and C1q was found to be crucial for the activation. CC employed C5a in the release of a number of cytokines in whole blood, including IL-1β and TNF. CC induced minimal amounts of cytokines in C5-deficient whole blood, until reconstituted with C5. Furthermore, C5a and TNF in combination acted as a potent primer for CC-induced IL-1β release by increasing IL-1β transcripts. CC-induced complement activation resulted in upregulation of complement receptor 3 (CD11b/CD18), leading to phagocytosis of CC. Also, CC mounted a complement-dependent production of reactive oxygen species and active caspase-1. We conclude that CC employ the complement system to induce cytokines and activate the inflammasome/caspase-1 by regulating several cellular responses in human monocytes. In light of this, complement inhibition might be an interesting therapeutic approach for treatment of atherosclerosis.
Observations on Pasture Management and Grazing (1997)

Selection of the notes was based on an interest in pasture management, improving grazing systems, and grazing animal behavior as it might apply to Utah. This interest was stimulated as a result of research on pasture use and development and as a participant on the USU Pasture Committee.
Inhibition by all-trans-retinoic acid of tumor necrosis factor and nitric oxide production by peritoneal macrophages (1994)

Besides their growth-inhibiting and differentiation-inducing properties, retinoids have been shown to exert immunomodulatory and anti-inflammatory functions by mechanisms that are not well understood. Tumor necrosis factor-alpha (TNF), a cytokine produced by mononuclear phagocytes, has been shown to be an important mediator of endotoxin-induced septic shock, cachexia, bone resorption, and inflammation. Nitric oxide may also have a role in septic shock, hypotension, and vasodilatation. In this study, we examined the effects of retinoids on the production of TNF and nitric oxide by murine peritoneal macrophages. Of the various retinoids studied, all-trans-retinoic acid (RA) was most potent; it almost completely inhibited the production of TNF by macrophages activated with endotoxin and interferon-gamma. The inhibitory effect was dependent on the dose and duration of RA exposure to macrophages. RA also blocked phorbol ester-induced TNF production in a macrophage cell line (RAW 264.7). Besides TNF, the retinoid suppressed the production of nitric oxide from activated peritoneal macrophages. The importance of these results in relation to controlling various harmful effects of cytokines released by activated macrophages is discussed.
Diffusion Dynamics of Glycine Receptors Revealed by Single-Quantum Dot Tracking (2003)

Semiconductor quantum dots (QDs) are nanometer-sized fluorescent probes suitable for advanced biological imaging. We used QDs to track individual glycine receptors (GlyRs) and analyze their lateral dynamics in the neuronal membrane of living cells for periods ranging from milliseconds to minutes. We characterized multiple diffusion domains in relation to the synaptic, perisynaptic, or extrasynaptic GlyR localization. The entry of GlyRs into the synapse by diffusion was observed and further confirmed by electron microscopy imaging of QD-tagged receptors.
Velocardiofacial Syndrome (2000)

Velocardiofacial syndrome is associated with an increased incidence of immune cytopenias and, thus, warrants evaluation in any child with the clinical diagnosis of VCFS. This immune deficit may be transient and depends on the age of the evaluation of the child.