gebhart/patrepeval huggingface dataset:
Cytokines and Cell Adhesion Molecules in Cerebral Ischemia (1998)

The possibility of reopening an occluded cerebral artery by means of thrombolysis has renewed interest in a number of the several mechanisms that are active during acute cerebral ischemia. Over recent years, it has become apparent that leukocytes play a central role not only during the healing stage of brain infarction but also during the early phases of cerebral ischemia, when it is postulated that these cells produce harmful effects, particularly in the presence of reperfusion. This review is based on the critical analysis of more than 150 publications dealing with the role of leukocytes and some inflammatory mediators (cytokines, chemokines, and adhesion molecules) in cerebral ischemia. Animal studies indicate that leukocyte involvement is promoted by a variety of inflammatory molecules produced immediately after the onset of cerebral ischemia. Considerable experimental evidence suggests that these mediators play a key role in the progression from ischemia to irreversible injury (ie, cellular death and necrosis). However, the precise role of each molecule alone remains to be further elucidated as well as in relation to the complex network existing among different mediators. Progress in our understanding of the inflammatory mechanisms operating in cerebral ischemia has enabled the testing of new compounds with promising results in animals; in contrast, one recent controlled trial of an anti-leukocyte molecule in acute stroke patients showed negative results. This discrepancy may derive in part from our incomplete understanding of the complexity of the inflammatory mechanisms involved in cerebral ischemia. Our analysis suggests that until sufficient knowledge of the underlying disease mechanisms is acquired, more care should be taken when testing new and potentially efficacious drugs in stroke patients.
Presentation of autoantigen by human T cells (1991)

Activated human T cells express MHC class II and have been shown to present foreign Ag to autologous T cells. We now demonstrate that MHC class II+ T cell clones can present myelin basic protein (MBP) peptide autoantigen in the absence of traditional APC to autologous MBP reactive T cell clones. MBP peptide-pulsed T cell clones specifically stimulated autologous MBP-reactive T cell clones to flux calcium and proliferate. Activation responses were peptide epitope specific and blocked by mAb to MHC class II, indicating a TCR-mediated response. In addition, mAb to the adhesion molecules LFA-3, CD2, LFA-1, CD29, and to the tyrosine phosphatase CD45 also inhibited proliferation, indicating the involvement of T to T cell interactions. In contrast to peptide Ag, T cell clones did not respond to autologous T cells pulsed with HPLC-purified MBP, suggesting that T cells are unable to process whole MBP. However, batch-purified MBP Ag preparations containing lower m.w. breakdown products were presented by T cells, indicating that naturally occurring breakdown products of autoantigens could be presented by activated T cells in vivo. These results raise the possibility that T cell presentation of autoantigen at inflammatory sites may be important in regulation of immune responses to self Ag.
The Diagnostic Utility of Desmin: A Study of 584 Cases and Review of the Literature (1990)

The diagnostic utility of several antibodies against desmin and their optimal staining conditions have not been systematically evaluated. Sections of paraffin-embedded tissues from 584 cases were stained with a monoclonal antibody against desmin (Clone DER 11 from DAKO), using an avidin-biotin-peroxidase technique. The results were tabulated and compared with those from previous reports. The following observations were made: (1) When pronase digestion was performed before staining, desmin was equally demonstrable in tissues fixed in formalin, Zenker's, Bouin's, or B5 fixative; however, desmin staining was lost or significantly diminished in tissues fixed in absolute ethyl alcohol. In contrast, when pronase was not used, a positive staining was demonstrated only in tissue fixed in absolute ethyl alcohol. (2) Positive staining was found in normal muscle (92 of 92 cases), leiomyoma (12 of 13), rhabdomyoma (6 of 6), rhabdomyosarcoma (31 of 31), leiomyosarcoma (18 of 26). (3) Desmin was never found in epithelia, normal mesenchymal tissue other than muscle, tumors stimulating rhabdomyosarcoma, and epithelial tumors. (4) A positive staining was documented in 1 tumor (a fibrous histiocytoma) of 42 benign predominantly spindle cell tumors and in 8 of 89 predominantly spindle cell sarcomas. (5) Desmin was never documented in myoepithelial cells but stained myofibroblasts in 2 of 12 examples of granulation tissue and in 29 of 67 samples containing tumor-associated desmoplasia. The authors' data on the diagnostic sensitivity and specificity of the evaluated antibody should improve the use of desmin in diagnostic pathology.
Hybrid bilayer plasmonic metasurface efficiently manipulates visible light (2016)

Metasurfaces operating in the cross-polarization scheme have shown an interesting degree of control over the wavefront of transmitted light. Nevertheless, their inherently low efficiency in visible light raises certain concerns for practical applications. Without sacrificing the ultrathin flat design, we propose a bilayer plasmonic metasurface operating at visible frequencies, obtained by coupling a nanoantenna-based metasurface with its complementary Babinet-inverted copy. By breaking the radiation symmetry because of the finite, yet small, thickness of the proposed structure and benefitting from properly tailored intra- and interlayer couplings, such coupled bilayer metasurface experimentally yields a conversion efficiency of 17%, significantly larger than that of earlier single-layer designs, as well as an extinction ratio larger than 0 dB, meaning that anomalous refraction dominates the transmission response. Our finding shows that metallic metasurface can counterintuitively manipulate the visible light as efficiently as dielectric metasurface (~20% in conversion efficiency in Lin et al.'s study), although the metal's ohmic loss is much higher than dielectrics. Our hybrid bilayer design, still being ultrathin (~λ/6), is found to obey generalized Snell's law even in the presence of strong couplings. It is capable of efficiently manipulating visible light over a broad bandwidth and can be realized with a facile one-step nanofabrication process.
Image retrieval using scene graphs (2015)

This paper develops a novel framework for semantic image retrieval based on the notion of a scene graph. Our scene graphs represent objects (“man”, “boat”), attributes of objects (“boat is white”) and relationships between objects (“man standing on boat”). We use these scene graphs as queries to retrieve semantically related images. To this end, we design a conditional random field model that reasons about possible groundings of scene graphs to test images. The likelihoods of these groundings are used as ranking scores for retrieval. We introduce a novel dataset of 5,000 human-generated scene graphs grounded to images and use this dataset to evaluate our method for image retrieval. In particular, we evaluate retrieval using full scene graphs and small scene subgraphs, and show that our method outperforms retrieval methods that use only objects or low-level image features. In addition, we show that our full model can be used to improve object localization compared to baseline methods.
The Extra Domain A of Fibronectin Activates Toll-like Receptor 4 (2001)

Cellular fibronectin, which contains an alternatively spliced exon encoding type III repeat extra domain A (EDA), is produced in response to tissue injury. Fragments of fibronectin have been implicated in physiological and pathological processes, especially tissue remodeling associated with inflammation. Because EDA-containing fibronectin fragments produce cellular responses similar to those provoked by bacterial lipopolysaccharide (LPS), we examined the ability of recombinant EDA to activate Toll-like receptor 4 (TLR4), the signaling receptor stimulated by LPS. We found that recombinant EDA, but not other recombinant fibronectin domains, activates human TLR4 expressed in a cell type (HEK 293 cells) that normally lacks this Toll-like receptor. EDA stimulation of TLR4 was dependent upon co-expression of MD-2, a TLR4 accessory protein. Unlike LPS, the activity of EDA was heat-sensitive and persisted in the presence of the LPS-binding antibiotic polymyxin B and a potent LPS antagonist, E5564, which completely suppressed LPS activation of TLR4. These observations provided a mechanism by which EDA-containing fibronectin fragments promote expression of genes involved in the inflammatory response.
Simple Bayesian Algorithms for Best-Arm Identification (2020)

This paper considers the optimal adaptive allocation of measurement effort for identifying the best among a finite set of options or designs. An experimenter sequentially chooses designs to measure and observes noisy signals of their quality with the goal of confidently identifying the best design after a small number of measurements. Just as the multiarmed bandit problem crystallizes the tradeoff between exploration and exploitation, this “pure exploration” variant crystallizes the challenge of rapidly gathering information before committing to a final decision. The paper proposes several simple Bayesian algorithms for allocating measurement effort and, by characterizing fundamental asymptotic limits on the performance of any algorithm, formalizes a sense in which these seemingly naive algorithms are the best possible.
DNA vaccination: antigen presentation and the induction of immunity (2000)

DNA vaccination, or genetic immunization, is a novel vaccine technology that has great potential for reducing infectious disease and cancer-induced morbidity and mortality worldwide. Since their inception, DNA vaccines have been used to stimulate protective immunity against many infectious pathogens, malignancies, and autoimmune disorders in animal models. Plasmid DNA encoding a polypeptide protein antigen is introduced into a host where it enters host cells and serves as an epigenetic template for the high-efficiency translation of its antigen. An immune response, which is mediated by the cellular and/or humoral arms of the immune system and is specific for the plasmid-encoded antigen, ensues. It is thought that "professional" antigen-presenting cells play a dominant role in the induction of immunity by presenting vaccine peptides on MHC class I molecules, following direct transfection or "cross"-presentation, and MHC class II molecules after antigen capture and processing within the endocytic pathway. The correlates of immunity can be manipulated according to many immunization parameters, including the method of vaccine delivery, presence of genetic adjuvants, and vaccine regimen. DNA vaccines first advanced to the clinic five years ago, and the initial picture of their utility in humans is emerging. However, further analysis is required to determine their ultimate efficacy and safety in human beings. This technology has acquired a strong foothold in the field of experimental immunotherapy, and it is hoped that it will eventually represent the next generation of prophylactic and therapeutic vaccines.
Conductive Polymer Films as Ultrasensitive Chemical Sensors for Hydrazine and Monomethylhydrazine Vapor (1996)

Thin films of the electrically conductive polymer poly(3-hexylthiophene) were investigated as ultrasensitive chemical sensors for hydrazine and monomethylhydrazine vapor. The threshold limit value for these highly toxic species, which are used extensively as rocket fuels, has recently been lowered to 10 ppb for 8-h exposure, necessitating the development of instrumentation with improved sensitivity. The present study describes the fabrication, calibration, and testing of simple, rugged, polymer-based sensors for detection of hydrazines in both ambient and vacuum environments. For reasonable choices of film thickness, initial resistance, and integration time, it is demonstrated that concentrations in the 0.1-100 ppb range can be monitored with an accuracy of ±20%. The sensor can be utilized for both dosimetric and real-time detection. Reproducible fabrication was achieved using standard spin-coating techniques. The polymer sensors exhibit good specificity to hydrazines in the presence of NH(3), amines, and ambient H(2)O and have a shelf-life of several years when stored in cold, dry conditions.
Rational syntheses of core-shell Fex@Pt nanoparticles for the study of electrocatalytic oxygen reduction reaction (2013)

We report on the syntheses of core-shell Fex@Pt (x=0.4-1.2) nanoparticles (NPs) with Pt-shell thickness systematically controlled while the overall particle size is constant. The syntheses were achieved via one-pot ultrasound-assisted polyol synthesis (UPS) reactions. Fe1.2@Pt showed a record-breaking high core-element content (55 at%) of core-shell NPs. Based on observations from a series of control experiments, we propose a mechanism of the NPs' formation that enables control of shell thickness in UPS reactions. Fex@Pt NPs showed drastic enhancements in mass and specific activity for oxygen reduction reaction (ORR) and significantly enhanced durability compared to commercial Pt NPs. Fex@Pt with a 1 (monolayer) ML Pt shell showed the highest activity. The ab initio density functional theory calculations on the binding energies of oxygen species on the surfaces of Fex@Pt NPs showed that the 1 ML case is most favourable for the ORR, and in good agreement with the experimental results.
Human and bovine coronaviruses recognize sialic acid-containing receptors similar to those of influenza C viruses. (1988)

Human coronavirus OC43 and bovine coronavirus elute from agglutinated chicken erythrocytes when incubated at 37 degrees C, suggesting the presence of a receptor-destroying enzyme. Moreover, bovine coronavirus exhibits an acetylesterase activity in vitro using bovine submaxillary mucin as substrate similar to the enzymatic activity found in influenza C viruses. Furthermore, pretreatment of erythrocytes with either influenza C virus or bovine coronavirus eliminates subsequent binding and agglutination by either coronaviruses or influenza C virus, whereas binding of influenza A virus remains intact. In addition, hemagglutination by coronaviruses can be inhibited by pretreatment of erythrocytes with Arthrobacter ureafaciens or Clostridium perfringens neuraminidase or by addition of sialic acid-containing gangliosides. These results suggest that, like influenza C viruses, human coronavirus OC43 and bovine coronavirus recognize O-acetylated sialic acid or a similar derivative as cell receptor.
Synthesis of CMP-NeuAc from N-acetylglucosamine: generation of CTP from CMP using adenylate kinase (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of CMP-NeuAc from N-acetylglucosamine: generation of CTP from CMP using adenylate kinaseEthan S. Simon, Mark D. Bednarski, and George M. WhitesidesCite this: J. Am. Chem. Soc. 1988, 110, 21, 7159–7163Publication Date (Print):October 1, 1988Publication History Published online1 May 2002Published inissue 1 October 1988https://pubs.acs.org/doi/10.1021/ja00229a033https://doi.org/10.1021/ja00229a033research-articleACS PublicationsRequest reuse permissionsArticle Views940Altmetric-Citations119LEARN 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
Suppressive effects of cyclophosphamide and gemcitabine on regulatory T-cell induction in vitro. (2012)

Chemotherapy using CPA or GEM may have the potential to augment the antitumor effects of cancer immunotherapy by suppressing Treg induction.
Detection of Human Immunodeficiency Virus Type 1 Provirus in Mononuclear Cells by in Situ Polymerase Chain Reaction (1992)

In HIV-1 infection, the proportion of PBMC that are infected appears to be at least 10 times higher than previously described. It is likely that most infected cells contain HIV-1 provirus in a latent or defective form that was not detected in some earlier studies.
Register promotion in C programs (1997)

The combination of pointers and pointer arithmetic in C makes the task of improving C programs somewhat more difficult than improving programs written in simpler languages like Fortran. While much work has been published that focuses on the analysis of pointers, little has appeared that uses the results of such analysis to improve the code compiled for C. This paper examines the problem of register promotion in C and presents experimental results showing that it can have dramatic effects on memory traffic.
Conformation and interaction of dinucleoside mono- and diphosphates. 3. L-adenylyl-(3'-5')-L-adenosine and L-adenylyl-(2'-5')-L-adenosine (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConformation and interaction of dinucleoside mono- and diphosphates. 3. L-adenylyl-(3'-5')-L-adenosine and L-adenylyl-(2'-5')-L-adenosineIchiro Tazawa, Setsuko Tazawa, Lloyd M. Stempel, and Paul O. P. Ts'oCite this: Biochemistry 1970, 9, 18, 3499–3514Publication Date (Print):September 1, 1970Publication History Published online1 May 2002Published inissue 1 September 1970https://pubs.acs.org/doi/10.1021/bi00820a003https://doi.org/10.1021/bi00820a003research-articleACS PublicationsRequest reuse permissionsArticle Views111Altmetric-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
Finding Good Configurations in High-Dimensional Spaces: Doing More with Less (2008)

Manually tuning tens to hundreds of configuration parameters in a complex software system like a database or an application server is an arduous task. Recent work has looked into automated approaches for recommending good configuration settings that adaptively search the full space of possible configurations. These approaches are based on conducting experiments where each experiment runs the system with a selected configuration to observe the resulting performance. Experiments can be time-consuming and expensive, so only a limited number of experiments can be done even in systems with hundreds of configuration parameters. In this paper, we consider the problem of finding good configurations under the two constraints of high dimensionality (i.e., many parameters) and few experiments. We show how certain design decisions made in previous algorithms for finding good configurations make them perform poorly in this setting. We propose a new algorithm called MOWILE (MOre WIth LEss) that addresses these limitations, and outperforms previous algorithms by large margins as the number of parameters increase. Our empirical evaluation gives interesting insights that will benefit system administrators who apply experiment-driven approaches for configuration tuning.
Mapping the T cell epitopes of the Babesia bovis antigen 12D3: implications for vaccine design (1998)

The Babesia bovis antigen 12D3 was analysed to identify potential T-cell epitopes. Two predictive algorithms identified 13 possible sites but there was minimal agreement between the different predictive methods. Experimental determination of the T-cell epitopes recognized by nine cattle was achieved using a panel of overlapping peptides which identified seven different epitopes, five of which were clustered together around residues 210-320 of the molecule. No T cell epitopes were located within the tightly disulphide bonded core of 12D3. Using a series of truncated peptides, the location of two of the epitopes was mapped to residues 35-43 and 266-275. The sequences of these two epitopes was compared with a database of previously described binding motifs for MHC II alleles and each epitope was found to contain three sequence motifs recognized by HLA-DR alleles. The BoLA-DRB3 alleles occurring in these cattle were determined by a sequence specific oligonucleotide hybridization assay. Within those cattle whose T cells proliferated in response to 12D3, there was a consistent pattern of epitope recognition and presence of particular DRB3 alleles. The implications for effective vaccine design are discussed.
cDNA cloning, expression and characterization of human prostaglandin F synthase1 (1999)

A cDNA clone of prostaglandin F synthase (PGFS) was isolated from human lung by using cDNA of bovine lung-type PGFS as a probe and its protein expressed in Escherichia coli was purified to apparent homogeneity. The human PGFS catalyzed the reduction of prostaglandin (PG) D2, PGH2 and phenanthrenequinone (PQ), and the oxidation of 9alpha,11beta-PGF2 to PGD2. The kcat/Km values for PGD2 and 9alpha,11beta-PGF2 were 21000 and 1800 min(-1) mM(-1), respectively, indicating that the catalytic efficiency for PGD2 and 9alpha,11beta-PGF2 was the highest among the various substrates, except for PQ. The PGFS activity in the cytosol of human lung was completely absorbed with antihuman PGFS antiserum. Moreover, mRNA of PGFS was expressed in peripheral blood lymphocytes and the expression in lymphocytes was markedly suppressed by the T cell mitogen concanavalin A. These results support the notion that human PGFS plays an important role in the pathogenesis of allergic diseases such as asthma.