gebhart/patrepeval huggingface dataset:
Immunity to influenza in ferrets. XIV: Comparative immunity following infection or immunization with live or inactivated vaccine. (1981)

Immunization by live influenza virus induced a greater protective effect against subsequent challenge by the homologous virus than by the corresponding killed virus vaccine. Furthermore, tracheas excised from 11-day and 28-day influenza-virus-infected ferrets were more resistant to reinfection than tracheas excised from ferrets immunized by killed influenza vaccine, despite equivalent serum antibody titres at these times. Histological examination of trachea sections taken from vaccinated and virus-infected animals showed an increased cellular inflammatory infiltrate in the latter at Days 11 and 28 after immunization. The amount of IgG detected in these sections, measured by a fluorescent antibody technique, correlated with the extent of cellular infiltration, the fluorescence being both intra- and extracellular for sections from virus-infected animals, but only extracellular in sections from Day-28 vaccinated animals. In contrast there was little or no cellular infiltration into lung tissues, the levels of IgG detected being comparable to those in sections taken from control animals. These results provide further evidence that live influenza vaccines induce local antibody in the upper respiratory tract of ferrets, in contrast to killed influenza vaccines, and that this local induction may play a significant role in the greater protective efficacy of live influenza vaccines.
Assessing the Laryngeal Cough Reflex and the Risk of Developing Pneumonia After Stroke (1999)

A normal RCT after an acute stroke indicates a neurologically intact laryngeal cough reflex, a protected airway, and a low risk for developing aspiration pneumonia with oral feeding. An abnormal RCT indicates risk of an unprotected airway and an increased incidence of aspiration pneumonia. Alternate feeding strategies and preventive measures are necessary with an abnormal RCT. Clinical treatment algorithm and prescription of food, fluids, and medications are discussed on the basis of RCT results.
Expression of PiT1 and PiT2 retroviral receptors and transduction efficiency of tumor cells. (2002)

Recombinant retroviral vectors are still the most common gene delivery vehicles for gene therapy purposes, especially for construction of genetically modified tumor vaccines (GMTV). However, these vehicles are characterized by relatively low titre and in the case of many tumor cell lines, low transduction efficiency. We constructed bicistronic retroviral vector pseudotypes of amphotropic murine leukemia virus (A-MuLV) and gibbon ape leukemia virus (GaLV), encoding enhanced green fluorescent protein (EGFP) as a rapid and easily detectable reporter gene. Transduction of five different human melanoma and four renal carcinoma cell lines by these two virus pseudotypes revealed differences in transduction efficiency, which wase markedly lower for the renal carcinoma cell lines. Stimulation of retroviral receptor expression (PiT1 and PiT2) by phosphate depletion induced a limited increase of receptor mRNA levels, but did not improve the gene transfer efficiency. In contrast, simultaneous transduction with both vector pseudotypes markedly increased the transduction efficiency, compared to GaLV or A-MuLV alone. The same effect could be achieved by several repeated exposures of target cells to fresh vector preparation. Overexpression of GaLV receptor (PiT1) in target cells significantly increased the transduction rate and enabled retrovirus mediated gene transfer into the cells which normally are not transducible by GaLV pseudotypes. We demonstrated that, using different transduction strategies, the relatively inefficient, widely used retroviral vector systems could be significantly improved.
Roles of IL-4 and IFN-gamma in stabilizing the T helper cell type 1 and 2 phenotype (1997)

It has previously been reported that Th1 CD4 T cell populations can be converted to IL-4 producers, whereas Th2 populations are refractory to IL-12-mediated IFN-gamma production. We have recently shown that CD30 is a marker for the IL-4 response and have therefore used CD30 here to study Th1 and Th2 commitment. We show that Th2 cell populations normally show a stable phenotype and fail to respond to IL-12 because of endogenous IL-4 production. IFN-gamma abrogates this antagonistic effect of IL-4 and permits the conversion of Th2 populations to IFN-gamma producers by IL-12. In the complete absence of IL-4, however, IFN-gamma is not required for this transformation, and Th1 cells generated by IL-12 become committed to the Th1 pathway and lose the ability to respond to IL-4. Thus, the balance between local IL-4 and IFN-gamma in an immune response is a key factor in determining the outcome of the CD4 effector T cell response.
A subjective method for the measurement of monochromatic* aberrations of the eye (1977)

We have designed an aberroscope that differs from Tscherning's classical instrument in that it makes use of an artificial astigmatism rather than an artificial myopia to defocus the image of a point source of light. A subject views the source through a ±5 D crossed cylinder lens with axes at 45° to the principal axes of an intercalated grid and sees a shadow image of the grid. The distortions of this grid image are quantitatively related to the wave aberration of the eye. Using this device we have obtained drawings for more than 50 subjects. These drawings of the grid pattern have been analyzed by means of a two-dimensional polynomial curve Fitting technique that computes Taylor polynomial terms to the fourth order. From the Taylor coefficients it is possible to reconstruct the wave aberration surface. Examination of the Taylor terms so obtained shows that the monochromatic aberrations of the eye are dominated by third-order Taylor terms within the range of physiological pupil sizes, and that spherical aberration frequently appears predominantly about one axis only, a condition that we have termed "cylindrical" aberration. We have computed the optical MTF of our subjects' eyes and find that the role of aberrations in degrading the MTF may be greater than generally believed.
A new atisane diterpene: ent-16α-hydroxyatis-13-en-3-one from Androstachys johnsonii prain (1985)

The title diterpene, a rare example of the naturally occurring ent-atis-13-ene type, has been isolated as the 2-benzylidene derivative from the heartwood hexane extract of Androstachys johnsonii Prain. Its structure was determined by n.m.r. and X-ray crystallography. It is suggested that the title compound is biogenetically produced from an ent-12-oxybeyer-15-ene precursor. An interesting reaction reported here was found to convert a vicinal diol into a monoketone using the diethyl azodicarboxylate–triphenylphosphine–benzoic acid system.
Matplotlib: A 2D Graphics Environment (2007)

Matplotlib is a 2D graphics package used for Python for application development, interactive scripting,and publication-quality image generation across user interfaces and operating systems
A New Mechanism for Anaerobic Unsaturated Fatty Acid Formation inStreptococcus pneumoniae (2002)

The anaerobic pathway for unsaturated fatty acid synthesis was established in the 1960s in Escherichia coli. The double bond is introduced into the growing acyl chain by FabA, an enzyme capable of both the dehydration of beta-hydroxydecanoyl-acyl carrier protein (ACP) to trans-2-decenoyl-ACP, and the isomerization of trans-2 to cis-3-decenoyl-ACP. However, there are a number of anaerobic bacteria whose genomes do not contain a fabA homolog, although these organisms nonetheless produce unsaturated fatty acids. We cloned and biochemically characterized a new enzyme in type II fatty acid synthesis from Streptococcus pneumoniae that carries out the isomerization of trans-2-decenoyl-ACP to cis-3-decenoyl-ACP, but is not capable of catalyzing the dehydration of beta-hydroxy intermediates. This tetrameric enzyme, designated FabM, has no similarity to FabA, but rather is a member of the hydratase/isomerase superfamily. Thus, the branch point in the biosynthesis of unsaturated fatty acids in S. pneumoniae occurs following the formation of trans-2-decenoyl-ACP, in contrast to E. coli where the branch point takes place after the formation of beta-hydroxydecanoyl-ACP.
Structure and binding properties of water-soluble cavitands and capsules (2006)

Synthetic receptors are modern tools for investigations into the forces involved in recognition. A widely exploited class of receptors are the resorcin[4]arene-based cavitands and capsules. This critical review (71 references) describes the evolution of water-soluble versions of these structures, along with insights the resulting host-ndash complexes have provided with regard to complexation driving forces in water. An emphasis has been placed on the influence of host structure on guest affinity and dynamics.
Evidence that T cell activation is required for HIV-1 entry in CD4+ lymphocytes. (1989)

The relationship of T cell activation to HIV entry and generation of viral DNA intermediates was studied in freshly isolated CD4+ T lymphocytes. Unstimulated cells exposed to infectious virus for up to 48 h did not synthesize any detectable unintegrated HIV DNA duplex forms or integrated genomic provirus. However, activation of these cells with either PHA or OKT3 (anti-CD3) mAb before viral exposure resulted in the generation of unintegrated HIV DNA after 6 h and integrated copies after 24 h. Cell-to-cell fusion studies showed significantly attenuated fusion between freshly isolated resting T cells and T cells constitutively expressing high levels of HIV envelope glycoprotein (HXB/gpt) compared with T cells first stimulated with either PHA or OKT3 mAb. The baseline fusion observed with resting T cells is believed to be a consequence of allogeneic stimulation by the HXB/gpt cell line. These results provide evidence that HIV entry and HIV envelope-dependent cell-to-cell fusion require T cell activation.
Aspergillus nidulans verA is required for production of the mycotoxin sterigmatocystin (1994)

Aspergillus nidulans produces the carcinogenic mycotoxin sterigmatocystin (ST), the next-to-last precursor in the aflatoxin (AF) biosynthetic pathway found in the closely related fungi Aspergillus flavus and Aspergillus parasiticus. We identified and characterized an A. nidulans gene, verA, that is required for converting the AF precursor versicolorin A to ST. verA is closely related to several polyketide biosynthetic genes involved in polyketide production in Streptomyces spp. and exhibits extended sequence similarity to A. parasiticus ver-1, a gene proposed to encode an enzyme involved in converting versicolorin A to ST. By performing a sequence analysis of the region 3' to verA, we identified two additional open reading frames, designated ORF1 and ORF2. ORF2 is closely related to a number of cytochrome P-450 monooxygenases, while ORF1 shares identity with the gamma subunit of translation elongation factor 1. Given that several steps in the ST-AF pathway may require monooxygenase activity and that AF biosynthetic genes are clustered in A. flavus and A. parasiticus, we suggest that verA may be part of a cluster of genes required for ST biosynthesis. We disrupted the verA coding region by inserting the A. nidulans argB gene into the center of the coding region and transformed an A. nidulans argB2 mutant to arginine prototrophy. Seven transformants that produced DNA patterns indicative of a verA disruption event were grown under ST-inducing conditions, and all of the transformants produced versicolorin A but negligible amounts of ST (200-fold to almost 1,000-fold less than the wild type), confirming the hypothesis that verA encodes an enzyme necessary for converting versicolorin A to ST.
Direct drive: Simulations and results from the National Ignition Facility (2016)

Direct-drive implosion physics is being investigated at the National Ignition Facility. The primary goal of the experiments is twofold: to validate modeling related to implosion velocity and to estimate the magnitude of hot-electron preheat. Implosion experiments indicate that the energetics is well-modeled when cross-beam energy transfer (CBET) is included in the simulation and an overall multiplier to the CBET gain factor is employed; time-resolved scattered light and scattered-light spectra display the correct trends. Trajectories from backlit images are well modeled, although those from measured self-emission images indicate increased shell thickness and reduced shell density relative to simulations. Sensitivity analyses indicate that the most likely cause for the density reduction is nonuniformity growth seeded by laser imprint and not laser-energy coupling. Hot-electron preheat is at tolerable levels in the ongoing experiments, although it is expected to increase after the mitigation of CBET. Future work will include continued model validation, imprint measurements, and mitigation of CBET and hot-electron preheat.
Allergen-specific modulation of cytokine synthesis patterns and IgE responses in vivo with chemically modified allergen (1993)

Hypersensitivity and IgE synthesis are highly dependent on the balance in which production of IL-4 and IFN-gamma is induced. An immunologic approach that alters the dominant pattern of cytokine synthesis and antibody production that is elicited after exposure to native allergen is described. High M(r), glutaraldehyde-polymerized OVA administered (i.p.) before or after immunization with unmodified OVA induces > or = 95% inhibition of specific IgE synthesis concomitant with 300- to 800-fold increases in IgG2a production in C57BL/6 mice. These changes result from a genetically controlled shift in the pattern of cytokine production within the allergen-specific T cell repertoire as demonstrated by i) susceptibility of the changes induced upon administration of modified allergen to in vivo treatment with anti-IFN-gamma mAb and ii) a 5- to 7-fold increase in the ratio of IFN-gamma:IL-4 synthesis after overnight culture directly ex vivo. This system should prove useful in identification of the factors which are influential in the commitment of T cells to Th1- or Th2-like patterns of cytokine synthesis. Moreover, as defective induction of IFN-gamma by allergen-specific T cells appears to play a role in elevated IgE synthesis and human allergy, this approach may have therapeutic potential.
Genomics and Perinatal Care (2012)

A mong both prospective parents and providers of medical care, genetic and social concerns peak during the perinatal period. Advances in genomics and assisted reproductive technology have created new opportunities to detect genetic disorders and susceptibilities at multiple times during perinatal care and thus are relevant to these concerns. Emerging therapies for single-gene disorders may reshape these discussions.
Concise Review: Induced Pluripotent Stem Cells Versus Embryonic Stem Cells: Close Enough or Yet Too Far Apart? (2011)

The state of a cell is defined by the genes it transcribes and the epigenetic landscape that regulates their expression. Pluripotent cells have markedly different epigenetic signatures when compared with differentiated cells. Permissive chromatin, high occurrence of bivalent domains, and low levels of heterochromatin allow pluripotent cells to react to distinctive stimuli and undergo changes of cell state by differentiating into various tissues. Differentiated cells can be reprogrammed by a set of transcription factors to induced pluripotent stem cells (iPSC) that convert their transcriptional and epigenetic state to pluripotency and thus closely resemble embryonic stem cells (ESC). However, questions remain on whether the epigenetic reprogramming is complete or if there are some recurring iPSC specific aberrations that impede their full pluripotency potential. For this reason, iPSC need to be closely compared with ESC, which is used as a golden standard for in vitro pluripotency. Transcribed genes, epigenetic landscape, differentiation potential, and mutational load show small but distinctive dissimilarities between these two cell types.
Protease-activated receptors start a family. (1994)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Growth of enterobacteria on fructo‐oligosaccharides (1997)

Fructo-oligosaccharides (FOS) can be fermented by most species of enterobacteria present in the human intestine. Fermentation was confirmed by increased growth rates, low final pH and degradation patterns using high performance anion exchange chromatography (HPAEC). Growth rates were increased when FOS was added to the growth medium. Growth rates on all substrates differed widely between strains within the same species. HPAEC analysis showed that each strain degraded the oligosaccharides differently, but a preference for the smaller oligosaccharides was observed. No differences were observed between the two commercial preparations, the inulo-oligosaccharides and neosugars. Fermentation was rapid as could be determined by acidification tests using cell suspensions. It can be concluded that enterobacteria may play a role in overall fermentation of FOS in the colon and, in addition, due to competitive exclusion, may prevent survival of ingested pathogenic enterobacteria.
Prediction of sequential antigenic regions in proteins (1985)

Prediction of antigenic regions in a protein will be helpful for a rational approach to the synthesis of peptides which may elicit antibodies reactive with the intact protein. Earlier methods are based on the assumption that antigenic regions are primarily hydrophilic regions at the surface of the protein molecule. The method presented here is based on the amino acid composition of known antigenic regions in 20 proteins which is compared with that of 314 proteins [(1978) Atlas of Protein Sequence and Structure, vol. 5, suppl. 3, 363-373]. Antigenicity values were derived from the differences between the two data sets. The method was applied to bovine ribonuclease, the B-subunit of cholera toxin and herpes simplex virus type 1 glycoprotein D. There was a good correlation between the predicted regions and previously determined antigenic regions.
Incorporation of D-amino acids into peptides via enzymic condensation in organic solvents (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIncorporation of D-amino acids into peptides via enzymic condensation in organic solventsAlexey L. Margolin, Dar Fu Tai, and Alexander M. KlibanovCite this: J. Am. Chem. Soc. 1987, 109, 25, 7885–7887Publication Date (Print):December 1, 1987Publication History Published online1 May 2002Published inissue 1 December 1987https://pubs.acs.org/doi/10.1021/ja00259a049https://doi.org/10.1021/ja00259a049research-articleACS PublicationsRequest reuse permissionsArticle Views346Altmetric-Citations136LEARN 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
Interleukin-1 Receptor Antagonist Expression in Sarcoidosis (1993)

Sarcoidosis is a systemic granulomatous disease with a marked propensity for involvement of the pulmonary parenchyma and thoracic lymphatic system. This granulomatous process is characterized by aggregations of mononuclear cells, multinucleated giant cells, and variable degrees of fibrosis. The agent(s) responsible for the initiation of the inflammatory granulomatous process remain unknown. Interleukin-1 beta (IL-1) is a cytokine that has been shown to possess potent proinflammatory properties and is likely to play a role in mediating many of the immunopathologic events observed in sarcoidosis. Despite the degree of granulomatous inflammation, both the pulmonary and systemic pathogenic changes associated with sarcoidosis have a remarkable propensity for spontaneous resolution. The interleukin-1 receptor antagonist (IRAP), an endogenous inhibitor of IL-1 bioactivity, may have a critical role as an in vivo immunomodulator of IL-1-dependent granulomatous inflammation of sarcoidosis. In this study we demonstrate constitutive expression of IRAP mRNA and antigen from bronchoalveolar lavage fluid cells and cell-free fluid, respectively, obtained from both normal subjects and patients with sarcoidosis. However, immunolocalization of IRAP was found to be significantly localized to the sarcoid granuloma as compared with the uninvolved lung interstitium. Our findings indicate that IRAP expression is compartmentalized (granuloma) within the interstitium of patients with sarcoidosis. Thus, IRAP may function as an important in vivo immunomodulator of granulomatous inflammation.
V600E BRAF is associated with disabled feedback inhibition of RAF–MEK signaling and elevated transcriptional output of the pathway (2009)

Tumors with mutant BRAF and those with receptor tyrosine kinase (RTK) activation have similar levels of phosphorylated ERK, but only the former depend on ERK signaling for proliferation. The mitogen-activated protein kinase, extracellular signal-regulated kinase kinase (MEK)/ERK-dependent transcriptional output was defined as the genes whose expression changes significantly 8 h after MEK inhibition. In (V600E)BRAF cells, this output is comprised of 52 genes, including transcription factors that regulate transformation and members of the dual specificity phosphatase and Sprouty gene families, feedback inhibitors of ERK signaling. No such genes were identified in RTK tumor cells, suggesting that ERK pathway signaling output is selectively activated in BRAF mutant tumors. We find that RAF signaling is feedback down-regulated in RTK cells, but is insensitive to this feedback in BRAF mutant tumors. Physiologic feedback inhibition of RAF/MEK signaling down-regulates ERK output in RTK cells; evasion of this feedback in mutant BRAF cells is associated with increased transcriptional output and MEK/ERK-dependent transformation.
NF2 deficiency promotes tumorigenesis and metastasis by destabilizing adherens junctions (2003)

Mutation of the Neurofibromatosis 2 (NF2) tumor suppressor gene leads to cancer development in humans and mice. Recent studies suggest that Nf2 loss also contributes to tumor metastasis. The Nf2-encoded protein, merlin, is related to the ERM (ezrin, radixin, and moesin) family of membrane:cytoskeleton-associated proteins. However, the cellular mechanism whereby merlin controls cell proliferation from this location is not known. Here we show that the major cellular consequence of Nf2 deficiency in primary cells is an inability to undergo contact-dependent growth arrest and to form stable cadherin-containing cell:cell junctions. Merlin colocalizes and interacts with adherens junction (AJ) components in confluent wild-type cells, suggesting that the lack of AJs and contact-dependent growth arrest in Nf2(-/-) cells directly results from the absence of merlin at sites of cell:cell contact. Our studies indicate that merlin functions as a tumor and metastasis suppressor by controlling cadherin-mediated cell:cell contact.