gebhart/patrepeval huggingface dataset:
Development of HIV/AIDS Vaccine Using Chimeric gag-env Virus-Like Particles (1999)

We attempted to develop a candidate HIV/AIDS vaccine, by using unprocessed HIV-2 gag pr45 precursor protein. We found that a 45 kDa unprocessed HIV-2 gag precursor protein (pr45), with a deletion of a portion of the viral protease, assembles as virus-like particles (VLP). We mapped the functional domain of HIV-2 gag VLP formation in order to find the minimum length of gag protein to form VLP. A series of deletion mutants was constructed by sequentially removing the C-terminal region of HIV-2 gag precursor protein and expressed truncated genes in Spodoptera frugiperda (SF) cells by infecting recombinant baculoviruses. We found that deletion of up to 143 amino acids at the C-terminus of HIV-2 gag, leaving 376 amino acids at the N-terminus of the protein, did not affect VLP formation. There is a proline-rich region at the amino acid positions 373 to 377 of HIV-2 gag, and replacement of these proline residues by site-directed mutagenesis completely abolished VLP assembly. Our data demonstrate that the C-terminal p12 region of HIV-2 gag precursor protein, and zinc finger domains, are dispensable for gag VLP assembly, but the presence of at least one of the three prolines at amino acid positions 373, 375 or 377 of HIV-2NIH-Z is required for VLP formation. Animals immunized with these gag particles produced high titer antibodies and Western blot analyses showed that anti-gag pr45 rabbit sera react with p17, p24 and p55 gag proteins of HIV-1. We then constructed chimeric gag genes, which carry the hypervariable V3 region of HIV-1 gp120, because the V3 loop is known to interact with chemokine receptor as a coreceptor, and known to induce the major neutralizing antibodies and stimulate the cytoxic T lymphocyte responses in humans and mice. We expressed chimeric fusion protein of HIV-2 gag with 3 tandem copies of consensus V3 domain that were derived from 245 different isolates of HIV-1. In addition, we also constructed and expressed chimeric fusion protein that contains HIV-2 gag with V3 domains of HIV-1IIIB, HIV-1MN, HIV-1SF2 and HIV-1RF. The chimeric gag-env particles had a spherical morphology, and the size was slightly larger than that of a gag particle. Immunoprecipitation and Western blot analyses show that these chimeric proteins were recognized by HIV-1 positive human sera and antisera raised against V3 peptides, as well as by rabbit anti-gp120 serum. We obtained virus neutralizing antibodies in rabbits by immunizing these gag-env VLPs. In addition, we found that gag-env chimeric VLPs induce a strong CTL activity against V3 peptide-treated target cells. Our results indicate that V3 peptides from all major clades of HIV-1 carried by HIV-2 gag can be used as a potential HIV/AIDS vaccine.
Generating Text from Functional Brain Images (2011)

Recent work has shown that it is possible to take brain images acquired during viewing of a scene and reconstruct an approximation of the scene from those images. Here we show that it is also possible to generate text about the mental content reflected in brain images. We began with images collected as participants read names of concrete items (e.g., "Apartment'') while also seeing line drawings of the item named. We built a model of the mental semantic representation of concrete concepts from text data and learned to map aspects of such representation to patterns of activation in the corresponding brain image. In order to validate this mapping, without accessing information about the items viewed for left-out individual brain images, we were able to generate from each one a collection of semantically pertinent words (e.g., "door," "window" for "Apartment''). Furthermore, we show that the ability to generate such words allows us to perform a classification task and thus validate our method quantitatively.
Multiple Potential Risks for Stroke (2000)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Oximetry spectral analysis in the diagnosis of obstructive sleep apnoea (1999)

Using spectral analysis of oximetry data, we prospectively evaluated the validity of this methodology in patients clinically suspected of suffering from obstructive sleep apnoea (OSA). A total of 233 outpatients were studied. Nocturnal oximetry was performed simultaneously with conventional polysomnography for all participants. The power density of oxygen saturation was analysed using Fast-Fourier transformation of the oximetric signal. Nocturnal oximetry test results were considered as abnormal (suspicion of OSA) if a peak in the spectrum between the period boundaries 30 and 70 s was observed. A normal test result was defined as the absence of the 30-70 s peak from the spectrum. Single-blind evaluation was performed by three independent observers, and agreement of two or more of these was considered definitive. The peak amplitude and the ratio of the area enclosed in the 30-70 s peak to the total area of the spectrum (r(S)) were measured. The presence of a peak has a sensitivity of 78%, a specificity of 89%, a positive predictive value of 89% and a negative predictive value of 78%. Apnoea-hypopnoea indexes were correlated significantly with peak amplitude (r=0.74; P<0.001) and with r(S) (r=0.69; P<0.001). For a peak amplitude threshold of 0.7%(2), the sensitivity was 94% and the specificity was 65% for OSA diagnosis. Using a threshold for r(S) of 0.15, the sensitivity was 91% and the specificity was 67%. Thus the spectral analysis of nocturnal oximetry and identification of a peak at 30-70 s could be useful as a diagnostic technique for OSA subjects.
Correlation between particle size, in vivo particle persistence, and lung injury. (1994)

Dosimetry parameters such as deposition, clearance, retention, and translocation and dissolution of inhaled particles in and to different lung compartments may be important for the persistence of particles in the lung and may correlate with adverse pulmonary effects. We investigated such correlations using a model involving TiO2 particles of two particle sizes (20 nm diameter, ultrafine; 250 nm diameter, fine) of the same crystalline structure (anatase). A 12-week inhalation experiment in rats resulted in a similar mass deposition of the two particle types in the lower respiratory tract. The ultrafine particles elicited a persistently high inflammatory reaction in the lungs of the animals compared to the larger-sized particles. In the postexposure period (up to 1 year) retention in the alveolar space per se was not different between fine and ultrafine TiO2. However, the following differences between the particle types were noted: a significantly different total pulmonary retention, both quantitatively (significantly prolonged retention of the ultrafine TiO2) and qualitatively (increased translocation to the pulmonary interstitium and persistence there of the ultrafine TiO2); greater epithelial effects (Type II cell proliferation; occlusion of pores of Kohn) and the beginning of interstitial fibrotic foci with ultrafine TiO2; significant sustained impairment of alveolar macrophage function after ultrafine TiO2 exposure as measured by the clearance of test particles. A correlation between particle surface area and effects was observed. A comparison of the adverse reactions with dosimetric parameters of TiO2 in different lung compartments in the postexposure period showed a correlation of the persistence of effects in both the alveolar and interstitial space with the persistence of particles in the respective compartment.
The Effect of Storage on the Accumulation of Oxidative Biomarkers in Donated Packed Red Blood Cells (2009)

The presence of an oxidative environment in transfused PRBC increases with storage time. This could partially explain the increased risk of developing TRALI related to the transfusion of older blood products.
Enantiomerically pure dimethyl (2S)-N-(9-phenylfluoren-9-yl)-3,4-didehydroglutamate as chiral educt. Chirospecific synthesis of (+)-5-O-carbamoylpolyoxamic acid and 3-alkylglutamates (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnantiomerically pure dimethyl (2S)-N-(9-phenylfluoren-9-yl)-3,4-didehydroglutamate as chiral educt. Chirospecific synthesis of (+)-5-O-carbamoylpolyoxamic acid and 3-alkylglutamatesManuel M. Paz and F. Javier SardinaCite this: J. Org. Chem. 1993, 58, 25, 6990–6995Publication Date (Print):December 1, 1993Publication History Published online1 May 2002Published inissue 1 December 1993https://pubs.acs.org/doi/10.1021/jo00077a015https://doi.org/10.1021/jo00077a015research-articleACS PublicationsRequest reuse permissionsArticle Views401Altmetric-Citations32LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Mast cells as orchestrators of the allergic reaction: the IgE-IgE receptor mast cell network (2001)

Correspondence to Ruby Pawankar, M.D., Ph.D, Dept. of Otolaryngology, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo 113-8603, Japan. Fax: +81 48 597 2861; e-mail: Pawankar_Ruby/[email protected]
Direct Magnesiation of Polyfunctionalized Arenes and Heteroarenes Using (tmp)2Mg⋅2 LiCl (2007)

Outstripping lithium bases: A wide range of polyfunctional aryl and heteroaryl magnesium reagents were efficiently prepared in THF by direct magnesiation with (tmp)2Mg⋅2 LiCl, an exceptionally active base. These compounds can serve as intermediates in natural product synthesis. In the example shown a palladium-catalyzed cross-coupling reaction is used to prepare a derivative of salicylic acid. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z701487_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Evaluation of an enzyme‐linked immunosorbent assay for detection and quantification of hepatitis B virus PreS1 envelope antigen in serum samples: comparison with two commercial assays for monitoring hepatitis B virus DNA (2000)

An in-house sensitive and easy-to-use solid-phase enzyme-linked immunoassay (ELISA) was adapted for the detection and quantification of hepatitis B virus (HBV) PreS1 envelope antigen in serum, and compared with the HBV DNA Hybrid Capturetrade mark system from Murex and the polymerase chain reaction (PCR) Amplicortrade mark HBV Monitor assay from Roche. Twenty-five patients with chronic hepatitis B after liver transplantation were included in this study. The sensitivity of our ELISA was found to be 50 pg of HBsAg/PreS1Ag ml-1. The linearity was between 0.1 and 100 ng ml-1. Intra-assay reproducibility was obtained with a standard deviation of <1%. No correlation between the presence of serum PreS1 antigen and viral DNA detected by direct hybridization (Murex) was observed. In contrast, there was a significant 96% correspondence in the presence of PreS1 antigen and viral DNA detected and quantified by the PCR assay (Roche). In conclusion, the most important and reliable markers for monitoring residual HBV replication in serum were HBV DNA by the PCR assay, and virus envelope PreS1Ag by our in-house ELISA. Thus, PreS1Ag disappearance in serum could be used for evaluating the efficacy of antiviral therapies.
Occurrence of a Rare 49·66 Structural Topology, Chirality, and Weak Ferromagnetism in the [NH4][MII(HCOO)3] (M = Mn, Co, Ni) Frameworks (2006)

We report the synthesis, crystal structures, thermal, IR, UV-vis, and magnetic properties of a series of divalent transition metal formates, [NH4][M(HCOO)3], where M = divalent Mn, Co, or Ni. They crystallize in the hexagonal chiral space group P6(3)22. The structure consists of octahedral metal centers connected by the anti-anti formate ligands, and the ammonium cations sit in the channels. The chiral structure is a framework with the rarely observed 49.66 topology, and the chirality is derived from the handedness imposed by the formate ligands around the metals and the presence of units with only one handedness. The thermal properties are characterized by a decomposition at ca. 200 degrees C. The three compounds exhibit an antiferromagnetic ground state at 8.4, 9.8, and 29.5 K for Mn, Co, and Ni, respectively. The last two display a weak spontaneous magnetization due to a small canting of the moments below the critical temperature, and the Co compound shows a further transition at lower temperatures. The isothermal magnetizations at 2 K show spin-flop fields of 600 Oe (Mn), 14 kOe (Co), and above 50 kOe (Ni) and a small hysteresis with a remnant magnetization of 25 cm3 G mol(-1) (Co) and 50 cm3 G mol(-1) (Ni) and coercive field of 400 Oe (Co) and 830 Oe (Ni).
Prediction of the Localization of High-Risk Coronary Atherosclerotic Plaques on the Basis of Low Endothelial Shear Stress (2008)

The magnitude of low ESS determines the complexity and heterogeneity of atherosclerotic lesions and predicts the development of high-risk plaque.
A Capacitive MEMS Viscometric Sensor for Affinity Detection of Glucose (2009)

This paper presents a capacitively based microelectromechanical systems affinity sensor for continuous glucose monitoring (CGM) applications. This sensor consists of a vibrating Parylene diaphragm, which is remotely driven by a magnetic field and situated inside a microchamber. A solution of poly(acrylamide-ran-3-acrylamidophenylboronic acid) (PAA-<i>ran</i>-PAAPBA), a biocompatible glucose-sensitive polymer, fills the microchamber, which is separated from its surroundings by a semipermeable membrane. Glucose permeates through the membrane and binds reversibly to the phenylboronic acid moiety of the polymer. This results in a viscosity change of the sensing solution, causing a detectable change in the Parylene diaphragm vibration which can be measured capacitively. Experimental results demonstrate that the device is capable of detecting glucose at physiologically relevant concentrations ranging from 30 to 360 mg/dL. The response time of the sensor to glucose concentration changes is approximately 1.5 min, which can be further improved with optimized device designs. Excellent reversibility and stability are observed in sensor responses, as highly desired for long-term CGM.
Production of Incomplete Vi Antibody in Mice (1960)

Immunization with purified Vi antigen elicited incomplete Vi antibody in the Cinnamon strain, and complete Vi antibody in BALB/c mice. Incomplete Vi antibody alone accounted for protection afforded by serum from Cinnamon mice against challenge with fully virulent typhoid bacilli. Absorption tests verified the specificity of incomplete Vi antibody and protection it afforded.
Blue-Light-Activated Histidine Kinases: Two-Component Sensors in Bacteria (2007)

Histidine kinases, used for environmental sensing by bacterial two-component systems, are involved in regulation of bacterial gene expression, chemotaxis, phototaxis, and virulence. Flavin-containing domains function as light-sensory modules in plant and algal phototropins and in fungal blue-light receptors. We have discovered that the prokaryotes Brucella melitensis, Brucella abortus, Erythrobacter litoralis, and Pseudomonas syringae contain light-activated histidine kinases that bind a flavin chromophore and undergo photochemistry indicative of cysteinyl-flavin adduct formation. Infection of macrophages by B. abortus was stimulated by light in the wild type but was limited in photochemically inactive and null mutants, indicating that the flavin-containing histidine kinase functions as a photoreceptor regulating B. abortus virulence.
Bowel necrosis induced by tumor necrosis factor in rats is mediated by platelet-activating factor. (1988)

We have developed a rat model of ischemic bowel necrosis associated with shock by injection of platelet-activating factor (PAF) or a combination of PAF and endotoxin. Recent investigations have shown that tumor necrosis factor (TNF) also induces shock and necrosis of the gastrointestinal tract. The morphological changes of TNF-induced bowel lesions are indistinguishable from those caused by PAF. The mechanism of TNF-induced bowel necrosis is unclear. In the present study, we have shown that (a) TNF caused PAF production in bowel tissue; (b) the effects of TNF and LPS on PAF production in the intestine are additive; (c) TNF and LPS are synergistic in inducing bowel necrosis; and (d) TNF-induced bowel necrosis is due to PAF release and can be prevented by pretreatment with PAF antagonists.
Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation (2014)

Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. We report 2.6 and 2.2 angstrom resolution crystal structures of two major Cas9 enzyme subtypes, revealing the structural core shared by all Cas9 family members. The architectures of Cas9 enzymes define nucleic acid binding clefts, and single-particle electron microscopy reconstructions show that the two structural lobes harboring these clefts undergo guide RNA-induced reorientation to form a central channel where DNA substrates are bound. The observation that extensive structural rearrangements occur before target DNA duplex binding implicates guide RNA loading as a key step in Cas9 activation.
High-throughput 3D spheroid culture and drug testing using a 384 hanging drop array (2010)

Culture of cells as three-dimensional (3D) aggregates can enhance in vitro tests for basic biological research as well as for therapeutics development. Such 3D culture models, however, are often more complicated, cumbersome, and expensive than two-dimensional (2D) cultures. This paper describes a 384-well format hanging drop culture plate that makes spheroid formation, culture, and subsequent drug testing on the obtained 3D cellular constructs as straightforward to perform and adapt to existing high-throughput screening (HTS) instruments as conventional 2D cultures. Using this platform, we show that drugs with different modes of action produce distinct responses in the physiological 3D cell spheroids compared to conventional 2D cell monolayers. Specifically, the anticancer drug 5-fluorouracil (5-FU) has higher anti-proliferative effects on 2D cultures whereas the hypoxia activated drug commonly referred to as tirapazamine (TPZ) are more effective against 3D cultures. The multiplexed 3D hanging drop culture and testing plate provides an efficient way to obtain biological insights that are often lost in 2D platforms.
Cloning and Functional Expression of UGT Genes Encoding Sterol Glucosyltransferases from Saccharomyces cerevisiae, Candida albicans, Pichia pastoris, and Dictyostelium discoideum (1999)

Sterol glucosides, typical membrane-bound lipids of many eukaryotes, are biosynthesized by a UDP-glucose:sterol glucosyltransferase (EC 2. 4.1.173). We cloned genes from three different yeasts and from Dictyostelium discoideum, the deduced amino acid sequences of which all showed similarities with plant sterol glucosyltransferases (Ugt80A1, Ugt80A2). These genes from Saccharomyces cerevisiae (UGT51 = YLR189C), Pichia pastoris (UGT51B1), Candida albicans (UGT51C1), and Dictyostelium discoideum (ugt52) were expressed in Escherichia coli. In vitro enzyme assays with cell-free extracts of the transgenic E. coli strains showed that the genes encode UDP-glucose:sterol glucosyltransferases which can use different sterols such as cholesterol, sitosterol, and ergosterol as sugar acceptors. An S. cerevisiae null mutant of UGT51 had lost its ability to synthesize sterol glucoside but exhibited normal growth under various culture conditions. Expression of either UGT51 or UGT51B1 in this null mutant under the control of a galactose-induced promoter restored sterol glucoside synthesis in vitro. Lipid extracts of these cells contained a novel glycolipid. This lipid was purified and identified as ergosterol-beta-D-glucopyranoside by nuclear magnetic resonance spectroscopy. These data prove that the cloned genes encode sterol-beta-D-glucosyltransferases and that sterol glucoside synthesis is an inherent feature of eukaryotic microorganisms.
The Evolution in Coal Mine Gas Extraction - A Response to Economic, Environmental and Community Pressures (2008)

Effective gas management is vital to the success of the longwall mines operating in the Bulli seam, located in the Southern Sydney Basin, Australia. High gas emissions are characteristic of the region with specific gas emissions typically in the order of 30-45 m3/t. The mines that operate in this area have, since 1980, relied on the use of extensive underground to inseam (UIS) drilling to drain gas both ahead of advancing roadway development and following longwall coal extraction. With the ever increasing production capacity of modern mining machinery the UIS methods are struggling to drain sufficient gas from the coal ahead of mining to avoid gas related production delays. A further consideration for the operations in this region is the rapid rate of urban development extending to the south of Sydney and the increasing pressure to reduce greenhouse gas emissions. This paper discusses the evolution of gas drainage methods in the Southern Sydney Basin along with a range of developments that have the potential to significantly reduce both the community impact and mine green house gas (GHG) emissions.
Glutathione in gingival crevicular fluid and its relation to local antioxidant capacity in periodontal health and disease (2002)

GSH values and total antioxidant capacity are reduced in chronic periodontal disease. The high concentrations of GSH present in GCF in health are similar to those found extracellularly in the lung and may represent an important antioxidant and anti-inflammatory defence strategy common to exposed epithelial surfaces.