gebhart/patrepeval huggingface dataset:
In vitro establishment of AIDS-related lymphoma cell lines: phenotypic characterization, oncogene and tumor suppressor gene lesions, and heterogeneity in Epstein-Barr virus infection. (1993)

Lymphoma represents a major source of morbidity and mortality among AIDS patients. AIDS-associated non-Hodgkin lymphomas (AIDS-NHL) are almost invariably B-cell derived, are classified as high or intermediate grade lymphomas, and display three main histologic types: namely, small non-cleaved cell lymphoma (SNCCL), large cell immunoblastic plasmacytoid lymphoma (LC-IBPL), and large cell lymphoma (LCL). Here we report the in vitro establishment of three new AIDS-NHL cell lines (termed HBL-1, HBL-2, and HBL-3) derived from three AIDS-SNCCL patients differing in primary tumor sites and risk factors for HIV infection. The derivation of the cell lines from the original tumor clones was established by immunophenotypic and molecular genetic analysis. These cell lines display clonal immunoglobulin gene rearrangement, express surface immunoglobulin and B-cell restricted markers, and exhibit a phenotype consistent with SNCCL. Monoclonal Epstein-Barr virus infection was found in only one of the cell lines (HBL-1). Cytogenetic analysis demonstrated the presence of a chromosomal translocation involving the c-myc proto-oncogene and an immunoglobulin locus in all three cell lines. The pattern of genetic lesions detected in HBL-1, HBL-2, and HBL-3 reflects that found in primary AIDS-SNCCL and includes activation of the c-myc oncogene as well as inactivation of the p53 tumor suppressor gene. These cell lines should prove useful in studies of the biological, immunological, and viral factors involved in AIDS-associated lymphomagenesis.
A limiting dilution assay for quantifying Leishmania major in tissues of infected mice (1985)

A limiting dilution assay for the quantification of Leishmania major in infected mouse tissue was developed. The assay was found to be both sensitive and reliable, and, due to its design, could be scored either visually or following the incorporation of 3H-thymidine by the growing parasites. Results are presented in which the assay was employed to enumerate L. major in the tissues of susceptible (BALB/c) and resistant (CBA) mice at intervals after infection with L. major. It was found that parasites could be detected at the site of injection with L. major as early as 3 days after infection. By day 8, a substantial increase in the number of parasites at the lesion site had occurred in both strains of mice. Subsequently, whereas the number of parasites decreased in the lesions of CBA mice, their number steadily increased in the lesions of BALB/c mice. Parasites were detected in lymph nodes draining the lesion site in both BALB/c and CBA mice by 28 days after infection. Interestingly, a low number of L. major was found in the lymph nodes of CBA mice at 100 days after infection, a time when no parasites could be detected at the lesion site. Previous results from this laboratory have demonstrated that the adoptive transfer of L. major-specific L3T4-positive T-cell populations exacerbated cutaneous lesions induced by L. major in BALB/c mice. Experiments presented here indicate that the adoptive transfer of L. major-specific T-cells also exacerbated cutaneous leishmaniasis in CBA mice. Using the sensitive limiting dilution assay presently described, it was found that this unexpected exacerbative effect of L. major-specific T-cells on lesion development was accompanied by a substantial increase in the number of parasites in the lesions of the adoptively transferred mice.
Using Krylov Methods in the Solution of Large-Scale Differential-Algebraic Systems (1994)

In this paper, a new algorithm for the solution of large-scale systems of differential-algebraic equations is described. It is based on the integration methods in the solver DASSL, but instead of a direct method for the associated linear systems which arise at each time step, we apply the preconditioned GMRES iteration in combination with an Inexact Newton Method. The algorithm, along with those in DASSL, is implemented in a new solver called DASPK. We outline the algorithms and strategies used, and discuss the use of the solver. We develop and analyze some preconditioners for a certain class of DAE stems, and finally demonstrate the application of DASPK on two example problems.
Scalable Video Coding Extension for HEVC (2013)

This paper describes a scalable video codec that was submitted as a response to the joint call for proposals issued by ISO/IEC MPEG and ITU-T VCEG on HEVC scalable extension. The proposed codec uses a multi-loop decoding structure. Several inter-layer texture prediction methods are employed to remove the inter-layer redundancy. Inter-layer prediction is also used when coding enhancement layer syntax elements such as motion parameter and intra prediction mode, to further reduce bit overhead. Additionally, alternative transforms as well as adaptive coefficients scanning are used to code the prediction residues more efficiently. Experimental results are presented to demonstrate the effectiveness of the proposed scheme. When compared to HEVC single-layer coding, the additional rate overhead for the proposed scalable extension is 1.2% to 6.4% to achieve two layers of SNR and spatial scalability.
Systematically perturbed folding patterns of amyotrophic lateral sclerosis (ALS)-associated SOD1 mutants (2005)

Amyotrophic lateral sclerosis is a neurodegenerative syndrome associated with 114 mutations in the gene encoding the cytosolic homodimeric enzyme Cu/Zn superoxide dismutase (SOD). In this article, we report that amyotrophic lateral sclerosis-associated SOD mutations with distinctly different disease progression can be rationalized in terms of their folding patterns. The mutations are found to perturb the protein in multiple ways; they destabilize the precursor monomers (class 1), weaken the dimer interface (class 2), or both at the same time (class 1 + 2). A shared feature of the mutational perturbations is a shift of the folding equilibrium toward poorly structured SOD monomers. We observed a link, coupled to the altered folding patterns, between protein stability, net charge, and survival time for the patients carrying the mutations.
Total synthesis of .beta.-lactam antibiotics. Epimerization of 6(7)-aminopenicillins and cephalosporins from .alpha. to .beta. (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of .beta.-lactam antibiotics. Epimerization of 6(7)-aminopenicillins and cephalosporins from .alpha. to .beta.Raymond A. Firestone, Natalie S. Maciejewicz, Ronald W. Ratcliffe, and B. G. ChristensenCite this: J. Org. Chem. 1974, 39, 4, 437–440Publication Date (Print):February 1, 1974Publication History Published online1 May 2002Published inissue 1 February 1974https://pubs.acs.org/doi/10.1021/jo00918a003https://doi.org/10.1021/jo00918a003research-articleACS PublicationsRequest reuse permissionsArticle Views539Altmetric-Citations56LEARN 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
AlphaB-crystallin selectively targets intermediate filament proteins during thermal stress. (1999)

In the lens the sHsp alphaB-crystallin may selectively target intermediate filaments for protection against unfolding during conditions of stress.
Long-Term Remissions of Severe Pemphigus After Rituximab Therapy Are Associated with Prolonged Failure of Desmoglein B Cell Response (2013)

Pemphigus is a severe blistering condition of the skin and mucosa caused by autoantibodies directed against desmogleins, which are a type of keratinocyte adhesion protein. B cell depletion by rituximab has short-term efficacy against pemphigus. We aimed to assess the long-term course of pemphigus patients after B cell depletion and to understand the immunological mechanisms that mediate long-lasting remissions. We evaluated the clinical course of 22 pemphigus patients treated with rituximab after a 79-month median follow-up and compared the anti-desmoglein B cell response and B and T lymphocyte subpopulations and repertoire between patients who achieved complete remission (CR) and those who had incomplete remission (IR). Thirteen patients (59%) experienced CR during the study, including 10 patients off treatment and 3 patients with prednisone doses <10 mg/day; 9 patients had IR. A marked increase was observed in the ratio of CD19(+)CD27(-) naïve B cells to CD19(+)CD27(+) memory B cells. Indeed, patients in CR had a fourfold higher number of transitional B cells and interleukin-10-secreting regulatory B cells than those in IR. Furthermore, CR was associated with modification of the initial B cell repertoire and the disappearance of desmoglein-specific circulating immunoglobulin G-positive (IgG(+)) B lymphocytes, whereas a skewed B cell repertoire was observed in patients in IR. Thus, a blockage of B cell maturation, a prolonged repopulation with naïve B cells, and a delayed reappearance of memory B cells, which resulted in the disappearance of circulating desmoglein-specific IgG(+) B lymphocytes, contribute to the long-lasting effectiveness of rituximab for treating pemphigus.
Fat Transport in Lipoproteins — An Integrated Approach to Mechanisms and Disorders (1967)

HyperlipoproteinemiaDefinitionsUp to this point we have concentrated on laying the support for 2 generalizations. The first is that, with the exception of free fatty acid concentrations, which have no lipoprotein equivalents, all abnormalities in plasma lipid concentrations or dyslipidemia can be translated into dyslipoproteinemia. The second is that the shift of emphasis to lipoproteins offers distinct advantages in the recognition and management of such disorders. We have already discussed the relatively few cases in which hypolipoproteinemia is a clinical problem, and the remainder of the review will be devoted to hyperlipoproteinemia.Hyperlipoproteinemia (hyperlipidemia) falls into 2 . . .
How to display data by color schemes compatible with red-green color perception deficiencies (2013)

Visualization of data concerns most scientists. The use of color is required in order to display multidimensional information. In addition, color encoding a univariate image can improve the interpretation significantly. However up to 10% of the adult male population are affected by a red-green color perception deficiency which hampers the correct interpretation and appreciation of color encoded information. This work attempts to give guidelines on how to display a given dataset in a balanced manner. Three novel color maps are proposed providing readers with normal color perception a maximum of color contrast while being a good compromise for readers with color perception deficiencies.
MONAS: Multi-Objective Neural Architecture Search using Reinforcement Learning (2018)

Recent studies on neural architecture search have shown that automatically designed neural networks perform as good as expert-crafted architectures. While most existing works aim at finding architectures that optimize the prediction accuracy, these architectures may have complexity and is therefore not suitable being deployed on certain computing environment (e.g., with limited power budgets). We propose MONAS, a framework for Multi-Objective Neural Architectural Search that employs reward functions considering both prediction accuracy and other important objectives (e.g., power consumption) when searching for neural network architectures. Experimental results showed that, compared to the state-ofthe-arts, models found by MONAS achieve comparable or better classification accuracy on computer vision applications, while satisfying the additional objectives such as peak power.
Bax mRNA therapy using cationic liposomes for human malignant melanoma (2008)

Bax mRNA therapy using liposomes has stronger anti-tumor effects than Bax gene therapy using a plasmid, and the results suggest that Bax mRNA lipofection may be a viable treatment for malignant melanoma.
Observations by Light and Electron Microscopy on Wool Cuticle Fractions Obtained by Ultrasonics (1963)

The “cuticle material” produced by the action of ultrasonic vibrations on wool fibers has been examined by microscopic techniques. It was found that despite prior laboratory cleaning of virgin wool with solvents the contamination of the wool fiber surface by dust particles, keratinized flakes derived from the skin epidermis, and bacteria was extremely high. Ultrasonic treatments in aqueous solution remove most of these contaminants but are insufficient for releasing much cuticle material. The study has indicated that stringent measures must be taken to remove contaminating particles from the fiber surface prior to ultrasonic release of cuticle material for chemical study. Although an anionic detergent was tested and found to remove most contaminants, a cleaning procedure has not been devised which could be regarded as completely effective.
Feline aminopeptidase N serves as a receptor for feline, canine, porcine, and human coronaviruses in serogroup I (1996)

Two members of coronavirus serogroup I, human respiratory coronavirus HCV-229E and porcine transmissible gastroenteritis virus (TGEV), use aminopeptidase N (APN) as their cellular receptors. These viruses show marked species specificity in receptor utilization, as HCV-229E can utilize human but not porcine APN, while TGEV can utilize porcine but not human APN. To determine whether feline APN could serve as a receptor for two feline coronaviruses in serogroup I, feline infectious peritonitis virus (FIPV) and feline enteric coronavirus (FeCV), we cloned the cDNA encoding feline APN (fAPN) by PCR from cDNA isolated from a feline cell line and stably expressed it in FIPV- and FeCV-resistant mouse and hamster cells. The predicted amino acid sequence of fAPN shows 78 and 77% identity with human and porcine APN, respectively. When inoculated with either of two biologically different strains of FIPV or with FeCV, fAPN-transfected mouse and hamster cells became infected and viral antigens developed in the cytoplasm. Infectious FIPV was released from hamster cells stably transfected with fAPN. The fAPN-transfected mouse and hamster cells were challenged with other coronaviruses in serogroup I including canine coronavirus, porcine coronavirus TGEV, and human coronavirus HCV-229E. In addition to serving as a receptor for the feline coronaviruses, fAPN also served as a functional receptor for each of these serogroup I coronaviruses as shown by development of viral antigens in the cytoplasm of infected mouse or hamster cells stably transfected with fAPN. In contrast, fAPN did not serve as a functional receptor for mouse hepatitis virus (MHV-A59), which is in serogroup II and utilizes mouse biliary glycoprotein receptors unrelated to APN. Thus, fAPN serves as a receptor for a much broader range of group I coronaviruses than human and porcine APNs. The human, porcine, and canine coronaviruses in serogroup I that are able to use fAPN as a receptor have previously been shown to infect cats without causing disease. Therefore, host factors in addition to receptor specificity apparently affect the virulence and transmissibility of nonfeline serogroup I coronaviruses in the cat.
Rhabdomyosarcoma Lysis by T Cells Expressing a Human Autoantibody-Based Chimeric Receptor Targeting the Fetal Acetylcholine Receptor (2006)

Rhabdomyosarcomas are the most frequent malignant soft tissue tumors of childhood; however, because current multimodality treatments fail to improve the poor survival rate of children with metastatic rhabdomyosarcoma, new treatments are required. We previously identified the gamma-subunit of the fetal acetylcholine receptor (fAChR) as a specific cell surface target in rhabdomyosarcoma. Here, we engineered human T lymphocytes to express chimeric receptors composed of the antigen-binding domain of a human anti-fAChR antibody joined to the signaling domain of the human T-cell receptor zeta-chain. The interaction of fAChRzeta-transduced T cells with fAChR-positive rhabdomyosarcoma cell lines, but not with fAChR-negative control cells, induced T-cell activation characterized by strong secretion of IFN-gamma and delayed lysis of tumor cells. Importantly, we found that in six of six rhabdomyosarcoma patients, chemotherapy increased fAChR expression on residual tumor cells in vivo. Our observations suggest that these fully human chimeric fAChRzeta-transduced T cells, which should be well tolerated by the patient, have potential use in vivo both as a primary treatment for rhabdomyosarcoma and as a complementary approach to eradicate residual tumor cells after chemotherapy.
Total Synthesis of 34‐Hydroxyasimicin and Its Photoactive Derivative for Affinity Labeling of the Mitochondrial Complex I (2004)

The asymmetric total synthesis of the 34-hydroxyasimicin and its 3-(4-benzoylphenyl)propionate ester was achieved by means of a convergent synthetic strategy. This ester, which contains eight asymmetric centers, represents the first photoaffinity-labeling agent that is derived from an Annonaceous acetogenin. The key transformations in the synthesis include the Sharpless asymmetric dihydroxylation reaction, the Wittig olefination reaction, an oxidative cyclization reaction with rhenium(vii) oxide, the Williamson etherification reaction, and a palladium-catalyzed cross-coupling reaction. Use of the target molecule for photoaffinity-labeling studies of bovine mitochondrial NADH-ubiquinone oxidoreductase (Complex I) may shed light on the structure/function of this intricate enzyme and on the origin of the high antitumor activity exhibited by the Annonaceous acetogenins.
Economic forecasting at high‐frequency intervals (1993)

Abstract Forecasting on the basis of the daily flow of monthly or more frequent statistical reports on the economy can enhance the predictive accuracy of quarterly structural models. The high degree of serial correlation in economic data can be used advantageously in quarterly forecasting for a horizon as long as 6 months—perhaps somewhat longer. The model used for high‐frequency (weekly) forecasting of the US economy has a national accounting structure and tries to follow the choice of indicators that are used in preparing early estimates of national income and product accounts (NIPA). Estimates are separately generated for the income side and the product side of NIPA. At the level of GDP and closely related aggregates a third prediction is also generated from estimates of the principal components of major monthly indicators. A simple average of three estimates of GDP, together with detail on NIPA components and scores of monthly indicators has been produced every weekend, summarizing the business week's flow of information. This procedure is followed not only for producing a steady stream of high‐frequency forecasts but also for providing adjustment factors that can be used for model recalibration, without judgemental input. The tracking of the US economy is illustrated for the period starting before the invasion of Kuwait until the end of the Gulf War.
Detailed Comparative Analysis of the Catalytic Mechanisms of β-N-Acetylglucosaminidases from Families 3 and 20 of Glycoside Hydrolases (2005)

Beta-N-acetylglucosaminidases are commonly occurring enzymes involved in the degradation of polysaccharides and glycoconjugates containing N-acetylglucosamine residues. Such enzymes have been classified into glycoside hydrolase families 3 and 20 and are believed to follow distinct chemical mechanisms. Family 3 enzymes are thought to follow a standard retaining mechanism involving a covalent glycosyl enzyme intermediate while family 20 enzymes carry out a substrate-assisted mechanism involving the transient formation of an enzyme-sequestered oxazoline or oxazolinium ion intermediate. Detailed mechanistic analysis of representatives of these two families provides support for these mechanisms as well as detailed insights into transition state structure. Alpha-secondary deuterium kinetic isotope effects of kH/kD = 1.07 and 1.10 for Streptomyces plicatus beta-hexosaminidase (SpHex) and Vibrio furnisii beta-N-acetylglucosaminidase (ExoII) respectively indicate transition states with oxocarbenium ion character in each case. Brønsted plots for hydrolysis of a series of aryl hexosaminides are quite different in the two cases. For SpHex a large degree of proton donation is suggested by the relatively low value of beta(lg) (-0.29) on kcat/Km, compared with a beta(lg) of -0.79 for ExoII. Most significantly the Taft plots derived from kinetic parameters for a series of p-nitrophenyl N-acyl glucosaminides bearing differing levels of fluorine substitution in the N-acyl group are completely different. A very strong dependence (slope = -1.29) is seen for SpHex, indicating direct nucleophilic participation by the acetamide, while essentially no dependence (0.07) is seen for ExoII, suggesting that the acetamide plays purely a binding role. Taken together these data provide unprecedented insight into enzymatic glycosyl transfer mechanisms wherein the structures of both the nucleophile and the leaving group are systematically varied.
Epigene conversion: a proposal with implications for gene mapping in humans. (1992)

Epigenetic modification of DNA is now recognized as a potentially important factor in the inheritance and expression of some mutations; its ability to complicate human genetic analysis is concurrently becoming apparent. One unusual form of epigenetic modification, dominant position-effect variegation (PEV), has been used as a model for Huntington disease. In dominant PEV, a fully dominant mutant phenotype results from stable epigenetic inactivation of an allele adjacent to the structural alteration (cis-inactivation) combined with a complementary inactivation of the homologous normal allele (trans-inactivation). We now propose that trans-inactivation of the normal allele may occasionally persist through meiosis. Such "epigene conversion" occurring at the Huntington disease locus in a few percent of meioses would largely account for the published anomalies in that region's genetic map. This concept could also explain anomalous linkage map data for other disease-causing alleles in humans.