gebhart/patrepeval huggingface dataset:
Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans (2012)

Coronaviruses are capable of infecting humans and many animal species. Most infections caused by human coronaviruses are relatively mild. However, the outbreak of severe acute respiratory syndrome (SARS) caused by SARS-CoV in 2002 to 2003 and the fatal infection of a human by HCoV-EMC/2012 in 2012 show that coronaviruses are able to cause severe, sometimes fatal disease in humans. We have determined the complete genome of HCoV-EMC/2012 using an unbiased virus discovery approach involving next-generation sequencing techniques, which enabled subsequent state-of-the-art bioinformatics, phylogenetics, and taxonomic analyses. By establishing its complete genome sequence, HCoV-EMC/2012 was characterized as a new genotype which is closely related to bat coronaviruses that are distant from SARS-CoV. We expect that this information will be vital to rapid advancement of both clinical and vital research on this emerging pathogen.
Time course of IL-6 expression in experimental CNS ischemia (1999)

Interleukin-6 (IL-6) appears to be an important modulator of the inflammatory response associated with CNS ischemia. Clinically, IL-6 values obtained in the first week post-stroke have been shown to correlate with infarct size and outcome. In this study we used a focal reversible stroke model to investigate the time course and relationship to outcome of IL-6 production in plasma, brain and CSF. Reversible middle cerebral artery occlusion or sham surgery was produced in 50 adult Swiss Webster mice by advancing an 8-0 filament into the internal carotid artery for 2 h (sham 1 min). At 3, 6, 12, 24, and 72 h (8 each ischemia; 2 each sham) groups of animals were evaluated on a 28 point clinical scale, blood and CSF obtained, and the brains were evaluated for infarct volume and IL-6 mRNA levels. Serum levels of IL-6 (ELISA mean +/- SD; undetectable in controls) overall sham group, 102 +/- 87; 3 h, 908 +/- 494* pg ml-1; 6 h, 1079 +/- 468* pg ml-1; 12 h, 980 +/- 221* pg ml-1; pg ml-1; 24 h, 320 +/- 314* pg ml-1; 72 h, 20 +/- 30* pg ml-1 (*p < or = 0.05 to sham). CSF levels (ELISA) overall sham group, 10 +/- 18; 3 h, 379 +/- 210* pg ml-1; 6 h, 157 +/- 61* pg ml-1; 12 h, 136 +/- 88* pg ml-1; 24 h, 127 +/- 99 pg ml-1; 72 h, 72 +/- 9* pg ml-1 (*p < or = 0.05 to sham). Brain IL-6 mRNA levels overall sham group, 20; 3 h, 480; 6 h, 599; 12 h, 7960; 24 h, 20267; 72 h, 0. There was an overall R2 of 0.20 between plasma and CSF IL-6. There was an overall R2 of 0.13 and 0.20 between infarct size and serum and CSF IL-6 level respectively, and an overall R2 of 0.10 and 0.17 between neurologic function and serum and CSF IL-6 level respectively. These findings confirm that IL-6 values increase following CNS ischemia with peak serum and CSF levels occurring before brain values. CSF IL-6 levels had a stronger correlation with neurologic function and infarct size than serum.
Efficient authentication schemes for routing in mobile ad hoc networks (2006)

Mobile ad hoc network (MANET) has been generally regarded as an ideal network model for group communications. However, the security deployment for MANET routing operations is problematic. Firstly, existing secured routing protocols are deficient in achieving both authentication efficiency and full scale of security. In addition, the diversity of routing protocols presents difficulties in the generalisation of the security design. The most possible candidate solution, the digital signature, has far from been properly implemented from an ad hoc point of view. In this thesis, we are motivated to provide necessary security features to MANET routing operations in an efficient manner. Considering the feasibility of utilising digital signatures in MANET, we incorporate the notion of the online/offline signature scheme in our design, where the computational overhead is shifted to the offline phase. We also make use of the one-time signature scheme, which is efficient in computation, and the multisignature scheme, which is especially suitable for group authentication. Then, we observe the specialities of different routing protocols (AODV-ad hoc on-demand distance vector routing and DSR-dynamic source routing), as well as the similarities between above signature schemes. In our design, we exploit the effciency and the adaptability of signature schemes. As our contributions, we propose two authentication schemes to secure AODV and DSR protocol respectively. For AODV protocol, our ID-based online/offline signature schemes enhance the authentication performance by properly balancing the computational overhead, whereas the one-time signature scheme achieves the same objective by making trade-offs between computation power and memory storage. For DSR protocol, we provide a generic construction from ID-based online/offine signature schemes to ID-based multisignature schemes, so that the installation over AODV can be transformed to offer the same level of security for DSR. Our scheme is unique, in the sense that a single ID-based online/offline signature scheme can be applied to both AODV and DSR routing protocols.
Gene array analysis of osteoblast differentiation. (2001)

We have used gene array technology to chart changes in gene expression during differentiation of the mouse calvarial-derived MC3T3-E1 cell line to an osteoblast-like phenotype. Expression was analyzed on a mouse gene array panel of 588 cDNAs representing tightly regulated genes with key roles in various biological processes. When compared with NIH3T3 fibroblasts, MC3T3-E1 cells showed generally higher expression of cyclins and Bcl-2 family members, as well as specific expression of products such as the CD44 antigen, which is consistent with their calvarial origin. MC3T3-E1 cells also showed a surprisingly high level of p53. Differentiation in MC3T3-E1 cells involves withdrawal from the cell cycle by day 7, accompanied by matrix accumulation and, ultimately, mineralization. Gene expression patterns in induced MC3T3-E1 cells generally reflected these stages. Cyclins were sharply down-regulated, and expression of certain antiproliferative factors and tissue-restricted genes was induced. Many of the observed changes, such as the induction of follistatin, bone morphogenetic protein receptor 1A, transforming growth factor beta, and matrix remodeling factors, reflect expected patterns and support the physiological relevance of the results. Other observed changes were not anticipated and offer new insight into the osteoblast differentiation process. An example is the sharp induction of the Tob antiproliferative factor, which has previously been associated specifically with terminal differentiation in muscles. Another example is the induction of the DNA damage-associated proteins EI24 and Gadd45, apparently as a normal aspect of osteoblast differentiation. The oxidative stress-induced protein A170 and the transcription factor Nrf2, which regulates metabolic responses to oxidative stress, were also induced. This response may reflect the in vivo requirement for vascularization during bone growth and fracture repair. Other induced factors include tumor necrosis factor receptor-associated factor-1 (1-TRAF), which is a nuclear factor kappaB activator, cellular retinoic acid-binding protein II (CRABP-II), and the transcription factors S-II, SP2, and SEF2 (ITF2/E2:2). SEF2 is the first basic helix-loop-helix protein found to be up-regulated during osteoblast differentiation. Northern blots confirm the induction of SEF2.
Calcium Phosphate Transfection (1997)

This unit presents two methods of calcium phosphate-based eukaryotic cell transfection that can be used for both transient and stable transfections. In these protocols, plasmid DNA is introduced to monolayer cell cultures via a precipitate that adheres to the cell surface. A HEPES-buffered solution is used to form a calcium phosphate precipitate that is directly layered onto the cells. For some cells, shocking the cells with glycerol or DMSO improves transfection efficiency. In the alternate high-efficiency method, a BES-buffered system is used that allows the precipitate to form gradually in the medium and then drop onto the cells. While the alternate method is particularly efficient for stable transformation of cells with circular plasmid DNA, both protocols yield similar results for transformation with linear plasmid or genomic DNA, or for transient expression.
Diverse Hematological Malignancies Including Hodgkin-Like Lymphomas Develop in Chimeric MHC Class II Transgenic Mice (2009)

A chimeric HLA-DR4-H2-E (DR4) homozygous transgenic mouse line spontaneously develops diverse hematological malignancies with high frequency (70%). The majority of malignancies were distributed equally between T and B cell neoplasms and included lymphoblastic T cell lymphoma (LTCL), lymphoblastic B cell lymphoma (LBCL), diffuse large B cell lymphoma (DLBCL), the histiocyte/T cell rich variant of DLBCL (DLBCL-HA/T cell rich DLBCL), splenic marginal zone lymphoma (SMZL), follicular B cell lymphoma (FBL) and plasmacytoma (PCT). Most of these neoplasms were highly similar to human diseases. Also, some non-lymphoid malignancies such as acute myeloid leukemia (AML) and histiocytic sarcoma were found. Interestingly, composite lymphomas, including Hodgkin-like lymphomas, were also detected that had CD30(+) Hodgkin/Reed-Sternberg (H/RS)-like cells, representing a tumor type not previously described in mice. Analysis of microdissected H/RS-like cells revealed their origin as germinal center B cells bearing somatic hypermutations and, in some instances, crippled mutations, as described for human Hodgkin lymphoma (HL). Transgene integration in an oncogene was excluded as an exclusive driving force of tumorigenesis and age-related lymphoma development suggests a multi-step process. Thus, this DR4 line is a useful model to investigate common molecular mechanisms that may contribute to important neoplastic diseases in man.
Evaluating the Effect of Treatment Persistence on the Economic Burden of Moderate to Severe Psoriasis and/or Psoriatic Arthritis Patients in the U.S. Department of Defense Population (2018)

This study was funded by Janssen Scientific Affairs. Lee is a paid employee of Janssen Scientific Affairs. Xie, Wang, Vaidya, and Baser are paid employees of STATinMED Research, which is a paid consultant to Janssen Scientific Affairs. This study was presented as an abstract at the Academy of Managed Care Pharmacy 2017 Annual Meeting, March 27-30, 2017, in Denver, CO.
Puzzlingly High Correlations in fMRI Studies of Emotion, Personality, and Social Cognition (2009)

Functional magnetic resonance imaging (fMRI) studiesofemotion, personality, and social cognition have drawn much attention in recent years, with high-profile studies frequently reporting extremely high (e.g., >.8) correlations between brain activation and personality measures. We show that these correlations are higher than should be expected given the (evidently limited) reliability of both fMRI and personality measures. The high correlations are all the more puzzling because method sections rarely contain much detail about how the correlations were obtained. We surveyed authors of 55 articles that reported findings of this kind to determine a few details on how these correlations were computed. More than half acknowledged using a strategy that computes separate correlations for individual voxels and reports means of only those voxels exceeding chosen thresholds. We show how this nonindependent analysis inflates correlations while yielding reassuring-looking scattergrams. This analysis technique was used to obtain the vast majority of the implausibly high correlations in our survey sample. In addition, we argue that, in some cases, other analysis problems likely created entirely spurious correlations. We outline how the data from these studies could be reanalyzed with unbiased methods to provide accurate estimates of the correlations in question and urge authors to perform such reanalyses. The underlying problems described here appear to be common in fMRI research of many kinds-not just in studies of emotion, personality, and social cognition.
Up‐ and down‐regulation of human lymphokine (IL‐2)‐activated killer cell induction by monocytes, depending on their functional state (1988)

Studies were made to determine whether freshly isolated monocytes from healthy donors could influence the induction of lymphokine (IL-2)-activated killer (LAK) activity. Highly purified lymphocytes (greater than 99%) and monocytes (greater than 90%) were isolated by counter-flow centrifugal elutriation from peripheral blood. Lymphocytes incubated for 4 days with IL-2 showed significant LAK activity against natural killer (NK) cell-resistant target (Daudi) cells, whereas monocytes treated for 4 days with IL-2 and/or IFN-gamma were not cytotoxic. Under the experimental conditions used, addition of monocytes to the lymphocyte cultures resulted in significant augmentation of the LAK activity, depending on the density of monocytes added. In contrast, monocytes stimulated by lipopolysaccharide (LPS) markedly suppressed LAK activity induced by IL-2, depending on the dose of LPS added. Similar up- and down-regulations of LAK cell induction by monocytes were observed with 4 lines of human lung cancer cells as targets for LAK activity. Although supernatants from untreated monocytes did not increase LAK induction, supernatants from LPS-stimulated monocytes suppressed LAK induction. The regulatory role of monocytes could not be replaced by the addition of exogenous interleukin I (IL-I) or tumor necrosis factor (TNF). Prostaglandin E did not seem to play a regulatory role, since addition of indomethacin did not affect the regulation of LAK cell induction by monocytes. These results clearly indicate that human monocytes may cause up- or down-regulation of the expression of IL-2-induced LAK activity, depending on their functional state.
Semi-supervised learning for automatic conceptual property extraction (2012)

For a given concrete noun concept, humans are usually able to cite properties (e.g., elephant is animal, car has wheels) of that concept; cognitive psychologists have theorised that such properties are fundamental to understanding the abstract mental representation of concepts in the brain. Consequently, the ability to automatically extract such properties would be of enormous benefit to the field of experimental psychology. This paper investigates the use of semi-supervised learning and support vector machines to automatically extract concept-relation-feature triples from two large corpora (Wikipedia and UKWAC) for concrete noun concepts. Previous approaches have relied on manually-generated rules and hand-crafted resources such as WordNet; our method requires neither yet achieves better performance than these prior approaches, measured both by comparison with a property norm-derived gold standard as well as direct human evaluation. Our technique performs particularly well on extracting features relevant to a given concept, and suggests a number of promising areas for future focus.
Reactions of Carbodiimides. III. The Reactions of Carbodiimides with Peptide Acids1,2 (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of Carbodiimides. III. The Reactions of Carbodiimides with Peptide Acids1,2DeLos F. DeTar, Richard Silverstein, and Fulton F. Rogers Jr.Cite this: J. Am. Chem. Soc. 1966, 88, 5, 1024–1030Publication Date (Print):March 1, 1966Publication History Published online1 May 2002Published inissue 1 March 1966https://pubs.acs.org/doi/10.1021/ja00957a029https://doi.org/10.1021/ja00957a029research-articleACS PublicationsRequest reuse permissionsArticle Views648Altmetric-Citations70LEARN 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
Mice deficient in cystathionine beta-synthase: animal models for mild and severe homocyst(e)inemia. (1995)

Studies by various investigators have indicated that elevated levels of plasma homocyst(e)ine are strongly associated with the occurrence of occlusive vascular diseases. With the eventual aim of determining whether or not elevated plasma homocyst(e)ine concentrations are directly causative of cardiovascular diseases, we have generated mice that are moderately and severely homocyst(e)inemic. Homologous recombination in mouse embryonic stem cells was used to inactivate the cystathionine beta-synthase [L-serine hydrolyase (adding homocysteine), EC 4.2.1.22] gene. Homozygous mutants completely lacking cystathionine beta-synthase were born at the expected frequency from matings of heterozygotes, but they suffered from severe growth retardation and a majority of them died within 5 weeks after birth. Histological examination showed that the hepatocytes of homozygotes were enlarged, multinucleated, and filled with microvesicular lipid droplets. Plasma homocyst(e)ine levels of the homozygotes were approximately 40 times normal. These mice, therefore, represent a model for severe homocyst(e)inemia resulting from the complete lack of cystathionine beta-synthase. Heterozygous mutants have approximately 50% reduction in cystathionine beta-synthase mRNA and enzyme activity in the liver and have twice normal plasma homocyst(e)ine levels. Thus, the heterozygous mutants are promising for studying the in vivo role of elevated levels of homocyst(e)ine in the etiology of cardiovascular diseases.
Surface emitting second harmonic generation in vertical resonator (1991)

The efficiency of surface emitting second harmonic generators can be significantly increased by resonating the second harmonic field in a vertical cavity structure. These resonant devices can be several orders of magnitude more efficient than similar nonresonant devices. Milliwatt visible outputs can be expected for tens of milliwatts of infra-red input in a doubly resonant structure for reasonable device parameters.
Integral-Transform Formulation of Diffraction Theory* (1967)

An exact integral-transform formulation of the theory of the diffraction of monochromatic scalar waves from an infinite plane boundary with known boundary values is developed from first principles. The formulation is analogous to the Fourier-transform formulation of Fraunhofer diffraction, except that it is exact and is valid for both Fresnel and Fraunhofer diffraction. The known wavefunction on the boundary is expanded into a linear superposition of point-convergence patterns. The point-convergence pattern is defined as the pattern of the wavefunction that must exist on the boundary in order to produce a Dirac delta-function distribution of the wavefunction on a plane of observation that is parallel to the boundary. This pattern is described by a point-convergence function h determined by the position of the delta-function singularity on the plane of observation and the distance of that plane from the boundary. The point-convergence function is orthogonal to a function g called the point-divergence function. Together, g and h serve as kernels for a new integral transform called the diffraction transform. The pattern of the wavefunction on the plane of observation is the diffraction transform of the wavefunction on the boundary. We show that g represents the field of a dipole while h cannot be expressed by an ordinary function and must be defined as a functional. Successive diffraction transformations are discussed, and the transform formulation of Fraunhofer diffraction is obtained as a special case from the diffraction-transform theory.
Sphingosine Kinase Expression Increases Intracellular Sphingosine-1-Phosphate and Promotes Cell Growth and Survival (1999)

Sphingosine-1-phosphate (SPP) is a bioactive lipid that has recently been identified as the ligand for the EDG family of G protein-coupled cell surface receptors. However, the mitogenic and survival effects of exogenous SPP may not correlate with binding to cell-surface receptors (Van Brocklyn, J.R., M.J. Lee, R. Menzeleev, A. Olivera, L. Edsall, O. Cuvillier, D.M. Thomas, P.J.P. Coopman, S. Thangada, T. Hla, and S. Spiegel. 1998. J. Cell Biol. 142:229-240). The recent cloning of sphingosine kinase, a unique lipid kinase responsible for the formation of SPP, has provided a new tool to investigate the role of intracellular SPP. Expression of sphingosine kinase markedly increased SPP levels in NIH 3T3 fibroblasts and HEK293 cells, but no detectable secretion of SPP into the medium was observed. The increased sphingosine kinase activity in NIH 3T3 fibroblasts was sufficient to promote growth in low- serum media, expedite the G(1)/S transition, and increase DNA synthesis and the proportion of cells in the S phase of the cell cycle with a concomitant increase in cell numbers. Transient or stable overexpression of sphingosine kinase in NIH 3T3 fibroblasts or HEK293 cells protected against apoptosis induced by serum deprivation or ceramide elevation. N,N-Dimethylsphingosine, a competitive inhibitor of sphingosine kinase, blocked the effects of sphingosine kinase overexpression on cell proliferation and suppression of apoptosis. In contrast, pertussis toxin did not abrogate these biological responses. In Jurkat T cells, overexpression of sphingosine kinase also suppressed serum deprivation- and ceramide-induced apoptosis and, to a lesser extent, Fas-induced apoptosis, which correlated with inhibition of DEVDase activity, as well as inhibition of the executionary caspase-3. Taken together with ample evidence showing that growth and survival factors activate sphingosine kinase, our results indicate that SPP functions as a second messenger important for growth and survival of cells. Hence, SPP belongs to a novel class of lipid mediators that can function inside and outside cells.
Skin replacements. (1998)

There is much progress to be made to optimize the development of laboratory-grown temporary and permanent skin replacements. Replacement of both epidermal and dermal layers is important for achieving optimal take of cultured grafts and for optimizing the quality of wound healing. Although the use of retained cadaver allodermis on the wound bed may improve the performance of cultured epithelium, the development of successful, complete dermal-epidermal skin replacements (composite grafts) would greatly simplify burn management. In the future, handling and stability of the cultured grafts should be improved, and clinical outcomes should be expected to be superior. Unfortunately, funding for this type of applied research has not achieved high priority from the federal government granting agencies, despite the great clinical need for improved technology. Future progress depends largely upon commercial support.