gebhart/patrepeval huggingface dataset:
Chimpanzee Adenovirus Vector Ebola Vaccine (2014)

Reactogenicity and immune responses to cAd3-EBO vaccine were dose-dependent. At the 2×10<sup>11</sup> particle-unit dose, glycoprotein Zaire-specific antibody responses were in the range reported to be associated with vaccine-induced protective immunity in challenge studies involving nonhuman primates, and responses were sustained to week 48. Phase 2 studies and efficacy trials assessing cAd3-EBO are in progress. (Funded by the Intramural Research Program of the National Institutes of Health; VRC 207 ClinicalTrials.gov number, NCT02231866 .).
3-Chlorotyrosine, a specific marker of myeloperoxidase-catalyzed oxidation, is markedly elevated in low density lipoprotein isolated from human atherosclerotic intima. (1997)

Oxidation of LDL may be of pivotal importance in atherogenesis, but the mechanisms that promote oxidation in vivo remain poorly understood. We have explored the possibility that one pathway involves myeloperoxidase, a heme protein secreted by phagocytes. Myeloperoxidase is the only human enzyme known to generate hypochlorous acid (HOCl), a potent oxidizing agent, at physiological halide concentrations. LDL exposed to the complete myeloperoxidase-H2O2-Cl- system underwent chlorination of its protein tyrosyl residues. Treatment of LDL with reagent HOCl resulted in 3-chlorotyrosine formation, implicating HOCl as an intermediate in the enzymatic reaction pathway. In contrast, 3-chlorotyrosine was undetectable in LDL oxidized by hydroxyl radical, copper, iron, hemin, glucose, peroxynitrite, horseradish peroxidase, lactoperoxidase, or lipoxygenase. These results indicate that 3-chlorotyrosine is a specific marker for LDL oxidation by myeloperoxidase. To address the role of myeloperoxidase in promoting LDL oxidation in vivo, we used stable isotope dilution gas chromatography-mass spectrometry to quantify 3-chlorotyrosine in human aortic tissue and in LDL isolated from atherosclerotic lesions. The level of 3-chlorotyrosine in atherosclerotic tissue obtained during vascular surgery was sixfold higher than that of normal aortic intima. Moreover, the level of 3-chlorotyrosine was 30-fold higher in LDL isolated from atherosclerotic intima compared with circulating LDL. The detection of 3-chlorotyrosine in human atherosclerotic lesions indicates that halogenation reactions catalyzed by the myeloperoxidase system of phagocytes constitute one pathway for protein oxidation in vivo. These findings raise the possibility that the myeloperoxidase-H2O2-Cl- system plays a critical role in converting LDL into an atherogenic form.
The Mesolithic–Neolithic transition in southern Iberia (2012)

New data and a review of historiographic information from Neolithic sites of the Malaga and Algarve coasts (southern Iberian Peninsula) and from the Maghreb (North Africa) reveal the existence of a Neolithic settlement at least from 7.5 cal ka BP. The agricultural and pastoralist food producing economy of that population rapidly replaced the coastal economies of the Mesolithic populations. The timing of this population and economic turnover coincided with major changes in the continental and marine ecosystems, including upwelling intensity, sea-level changes and increased aridity in the Sahara and along the Iberian coast. These changes likely impacted the subsistence strategies of the Mesolithic populations along the Iberian seascapes and resulted in abandonments manifested as sedimentary hiatuses in some areas during the Mesolithic–Neolithic transition. The rapid expansion and area of dispersal of the early Neolithic traits suggest the use of marine technology. Different evidences for a Maghrebian origin for the first colonists have been summarized. The recognition of an early North-African Neolithic influence in Southern Iberia and the Maghreb is vital for understanding the appearance and development of the Neolithic in Western Europe. Our review suggests links between climate change, resource allocation, and population turnover.
Reusable immobilized enzyme/polyurethane sponge for removal and detoxification of localized organophosphate pesticide spills (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReusable immobilized enzyme/polyurethane sponge for removal and detoxification of localized organophosphate pesticide spillsPatrick L. Havens and Howard F. RaseCite this: Ind. Eng. Chem. Res. 1993, 32, 10, 2254–2258Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/ie00022a009https://doi.org/10.1021/ie00022a009research-articleACS PublicationsRequest reuse permissionsArticle Views540Altmetric-Citations46LEARN 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
Extraction and Characterization of Oil Bodies from Soy Beans: A Natural Source of Pre-Emulsified Soybean Oil (2007)

Soybeans contain oil bodies that are coated by a layer of oleosin proteins. In nature, this protein coating protects the oil bodies from environmental stresses and may be utilized by food manufacturers for the same purpose. In this study, oil bodies were extracted from soybean using an aqueous extraction method that involved blending, dispersion (pH 8.6), filtration, and centrifugation steps. The influence of NaCl (0-250 mM), thermal processing (30-90 degrees C, 20 min) and pH (2-8) on the properties and stability of the oil bodies was analyzed using zeta-potential, particle size, and creaming stability measurements. The extracted oil bodies were relatively small ( d 32 approximately 250 nm), and their zeta-potential went from around +12 mV to -20 mV as the pH was increased from 2 to 8, with an isoelectric point around pH 4. The oil bodies were stable to aggregation and creaming at low (pH = 2) and high (pH >/= 6) pH values but were unstable at intermediate values (3 </= pH </= 5), which was attributed to their relatively low zeta-potential. The oil bodies were stable to aggregation and creaming at relatively low salt concentrations (NaCl </= 25 mM, pH 7) but were unstable at higher values as a result of electrostatic screening effects. The oil bodies were stable to thermal processing from 30 to 90 degrees C (0 mM NaCl, pH 7), but there appeared to be a change in their interfacial properties (decrease in zeta-potential) at temperatures exceeding 60 degrees C. These results suggest that oil bodies extracted from soybeans have similar or improved stability compared to soybean oil emulsions produced from bulk ingredients and may provide a new way of creating functional soy products for the food industry.
Neurotensin receptors: a new marker for human ductal pancreatic adenocarcinoma (1998)

The selective and high expression of neurotensin receptors in ductal pancreatic adenocarcinomas could form the molecular basis for potential clinical applications, such as in vivo neurotensin receptor scintigraphy for early tumour diagnosis, radiotherapy with radiolabelled neurotensin analogues, and chemotherapy with neurotensin receptor antagonists.
Dynamic behavior of fully solvated β2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist (2006)

Recently we predicted the 3D structure of the human beta2-adrenergic receptor (beta2AR) and of the binding site of several agonists and antagonists to beta2AR. These predictions (MembStruk and HierDock) included no explicit water and only a few lipid molecules. Here we include explicit H(2)O and an infinite lipid bilayer membrane in molecular dynamics (MD) simulations of three systems: apo-beta2AR, epinephrine-bound beta2AR, and butoxamine-bound beta2AR (epinephrine is an endogenous agonist, and butoxamine is a beta2AR selective antagonist). The predicted structures for apo-beta2AR and butoxamine-beta2AR are stable in MD, but in epinephrine-beta2AR, extracellular water trickles into the binding pocket to mediate hydrogen bonding between the catechol of epinephrine and Ser-204 on helix 5. The epinephrine-beta2AR structure shows dynamic flexibility with small, piston-like movements of helices 3 and 6 and transient interhelical hydrogen bonding between Ser-165 on transmembrane 4 and Ser-207 on transmembrane 5. These couplings and motions may play a role in protein activation. The apo-beta2AR shows less dynamic flexibility, whereas the antagonist-beta2AR structure is quite rigid. This MD validation of the structure predictions for G protein-coupled receptors in explicit lipid and water suggests that these methods can be trusted for studying the mechanism of activation and the design of subtype-specific agonists and antagonists.
Imaging through scattering media with depth resolution by use of low-coherence gating in spatiotemporal digital holography (2000)

We demonstrate optical gating through scattering media based on low-coherence spatiotemporal digital holography. The method combines the advantages of low-coherence gating, both temporal and spatial, with the advantages of methods using heterodyning and phase-sensitive detection. Spatiotemporal data are captured on a CCD detector in a single exposure, without mechanical scans, and processed digitally. Examples of reconstructions and sectioning of objects hidden behind a ground-glass diffuser are shown.
Misfocus tolerance seen by simple inspection of the ambiguity function (1984)

Since Woodward’s ambiguity function contains all the optical transfer functions with varying focus error, it can be applied to display visually the tolerance to focus error. We compare the tolerance to defocus of a transparent but finite extended pupil and a pupil with a central obscuration.
Strontium phosphate transfection of human cells in primary culture: stable expression of the simian virus 40 large-T-antigen gene in primary human bronchial epithelial cells. (1987)

Strontium ion formed DNA-phosphate precipitates analogous to those formed by calcium but lacking the lethal and differentiation-inducing effects of calcium on many epithelial cell types in primary culture. Human primary bronchial epithelial cells were transiently and stably transfected by using strontium phosphate; the frequency of stable transformation with a plasmid carrying the simian virus 40 large-T-antigen gene was greater than 10(-4).
Dietary Fat and Fish Intake and Age-Related Maculopathy (2000)

The amount and type of dietary fat intake may be associated with ARM.
Nodular hepatocellular carcinoma. Treatment with subsegmental intraarterial injection of iodine 131-labeled iodized oil (1991)

Internal radiation therapy with subsegmental arterial injection of iodine 131(131I)-labeled iodized oil (Lipiodol; Laboratorie, Guerbet, France) was evaluated in 24 patients with nodular hepatocellular carcinoma (HCC) ranging from 2.5 to 8.0 cm in size. 131I Lipiodol (555 to 2220 MBq in 3 to 8 ml) was injected depending on the tumor size. Tumor reduction was seen in 88.9% of tumors smaller than 4.0 cm in diameter, 65.5% of tumors between 4.1 to 6.0 cm, and 25.0% of tumors larger than 5.1 cm. The tumor size reduction corresponded to the gradual drop of serum alpha-fetoprotein (AFP) levels and devascularization on follow-up angiography. Adverse reactions from treatment included fever, mild abdominal pain, nausea, and elevation of transaminases. These were mild and well tolerated by patients. This method provided long-term local control without complications related to the thyroid, lung, gastrointestinal tract, and bone marrow.
Hemostatic Factors and the Risk of Myocardial Infarction or Sudden Death in Patients with Angina Pectoris (1995)

In patients with angina pectoris, the levels of fibrinogen, von Willebrand factor antigen, and t-PA antigen are independent predictors of subsequent acute coronary syndromes. In addition, low fibrinogen concentrations characterize patients at low risk for coronary events despite increased serum cholesterol levels. Our data are consistent with a pathogenetic role of impaired fibrinolysis, endothelial-cell injury, and inflammatory activity in the progression of coronary artery disease.
Biofilm Formation in Medical Device-Related Infection (2006)

Medical device-associated infections, most frequently caused by coagulase-negative staphylococci, especially Staphylococcus epidermidis, are of increasing importance in modern medicine. Regularly, antimicrobial therapy fails without removal of the implanted device. The most important factor in the pathogenesis of medical device-associated staphylococcal infections is the formation of adherent, multilayered bacterial biofilms. There is urgent need for an increased understanding of the functional factors involved in biofilm formation, the regulation of their expression, and the interaction of those potential virulence factors in device related infection with the host. Significant progress has been made in recent years which may ultimately lead to new rational approaches for better preventive, therapeutic, and diagnostic measures.
Low bit-rate scalable video coding with 3-D set partitioning in hierarchical trees (3-D SPIHT) (2000)

We propose a low bit-rate embedded video coding scheme that utilizes a 3-D extension of the set partitioning in hierarchical trees (SPIHT) algorithm which has proved so successful in still image coding. Three-dimensional spatio-temporal orientation trees coupled with powerful SPIHT sorting and refinement renders 3-D SPIHT video coder so efficient that it provides comparable performance to H.263 objectively and subjectively when operated at the bit rates of 30 to 60 kbits/s with minimal system complexity. Extension to color-embedded video coding is accomplished without explicit bit allocation, and can be used for any color plane representation. In addition to being rate scalable, the proposed video coder allows multiresolutional scalability in encoding and decoding in both time and space from one bit stream. This added functionality along with many desirable attributes, such as full embeddedness for progressive transmission, precise rate control for constant bit-rate traffic, and low complexity for possible software-only video applications, makes the proposed video coder an attractive candidate for multimedia applications.
A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. (1989)

Among the fundamental problems in molecular evolution and in the analysis of homologous sequences are alignment, phylogeny reconstruction, and the reconstruction of ancestral sequences. This paper presents a fast, combined solution to these problems. The new algorithm gives an approximation to the minimal history in terms of a distance function on sequences. The distance function on sequences is a minimal weighted path length constructed from substitutions and insertions-deletions of segments of any length. Substitutions are weighted with an arbitrary metric on the set of nucleotides or amino acids, and indels are weighted with a gap penalty function of the form gk = a + (bxk), where k is the length of the indel and a and b are two positive numbers. A novel feature is the introduction of the concept of sequence graphs and a generalization of the traditional dynamic sequence comparison algorithm to the comparison of sequence graphs. Sequence graphs ease several computational problems. They are used to represent large sets of sequences that can then be compared simultaneously. Furthermore, they allow the handling of multiple, equally good, alignments, where previous methods were forced to make arbitrary choices. A program written in C implemented this method; it was tested first on 22 5S RNA sequences.
Analysis of Ubiquitination In Vivo Using a Transgenic Mouse Model (2001)

The primary pathway for the proteolytic destruction of cellular proteins is through ubiquitin-mediated targeting to the proteasome. This pathway is pivotal not only in the elimination of damaged or misfolded proteins but also in the temporal, developmental, or signal-mediated destruction of normal cellular substrates. The list of known substrates of the ubiquitin/proteasome pathway is long, but most substrates have been identified in yeast or, more recently, in cultured mammalian cells. It is likely that many mammalian substrates with developmental or disease relevance have yet to be identified because their ubiquitination occurs in tissue or organ systems that cannot be adequately modeled in vitro. We have developed a transgenic mouse model that will allow the isolation and identification of these substrates. The human UbC promoter was used to drive expression of a hexahistidine-tagged version of human ubiquitin in a variety of mouse tissues from early embryonic stages, as assessed by a green fluorescent protein marker. Cleavage of the fusion protein by endogenous enzymes produced epitope-tagged ubiquitin that was detected both in monomeric form and conjugated to cellular proteins. This mouse model should facilitate in the analysis of normal and disease-related ubiquitination events in vivo.
Growth of Gold Nanorods on Surfaces (2003)

The surfactant-assisted seeded growth method was adapted for growth of gold nanorods directly on mica surfaces. Spherical gold seed particles were first linked to the surface and then dipped in a cationic surfactant growth solution. Part of the grown particles were nanorods with a typical length of several hundred nanometers and diameter of 10−20 nm. The probability to grow elongated particles out of a seed on the surface was found to be larger than the comparable solution growth process. Successive dipping in the growth solution was found to increase the length and thickness of the gold nanorods without a significant increase in aspect ratio.
X-ray Snapshot of the Mechanism of Inactivation of Human Neutrophil Elastase by 1,2,5-Thiadiazolidin-3-one 1,1-Dioxide Derivatives (2008)

The mechanism of action of a general class of mechanism-based inhibitors of serine proteases, including human neutrophil elastase (HNE), has been elucidated by determining the X-ray crystal structure of an enzyme-inhibitor complex. The captured intermediate indicates that processing of inhibitor by the enzyme generates an N-sulfonyl imine functionality that is tethered to Ser195, in accordance with the postulated mechanism of action of this class of inhibitors. The identity of the HNE-N-sulfonyl imine species was further corroborated using electrospray ionization mass spectrometry.
Urban sensing systems (2008)

The development of sensing systems for urban deployments is still in its infancy. An interesting unresolved issue is the precise role assumed by people within such systems. This issue has significant implications as to where the complexity and the main challenges in building urban sensing systems will reside. This issue will also impact the scale and diversity of applications that are able to be supported. We contrast two end-points of the spectrum of conscious human involvement, namely participatory sensing, and opportunistic sensing. We develop an evaluation model and argue that opportunistic sensing more easily supports larger scale applications and broader diversity within such applications. In this paper, we provide preliminary analysis which supports this conjecture, and outline techniques we are developing in support of opportunistic sensing systems.
Listeria monocytogenes p60 supports host cell invasion by and in vivo survival of attenuated Salmonella typhimurium (1995)

The extracellular protein p60 is a major virulence factor of the intracellular bacterium Listeria monocytogenes. Its roles in pathogen survival in vivo and host cell invasion in vitro were studied. To this end, Salmonella typhimurium SL7207 was used as carrier for secreted p60-HlyA fusion protein by Escherichia coli HlyB and HlyD transport proteins. C57BL/6 mice infected intravenously with this strain suffered from increased bacterial numbers in livers and spleens compared with the p60-nonexpressing control strain, but only transiently. In vitro experiments showed that p60 promotes invasion of recombinant S. typhimurium SL7207 p60 into hepatocytes and resting macrophages independent from complement. Moreover, the uptake of wild-type L. monocytogenes EGD and L. monocytogenes BUG 8, an internalin-deficient strain, into hepatocytes was partially blocked by anti-p60 antibodies. The impaired invasion of dissociated bacterial chains of L. monocytogenes RIII, a p60 expression mutant, into hepatocytes and macrophages was partially restored by addition of p60- or p60-HlyA-enriched bacterial supernatants. These data suggest that the L. monocytogenes surface-associated proteins, p60 and internalin, act in concert to achieve optimal uptake into nonprofessional phagocytes and macrophages. Together, these experiments reveal a substantial impact of p60 on cell invasion and virulence and thus emphasize the importance of the intracellular habitat for survival of L. monocytogenes in the host.
Stage-specific expression of B cell translocation gene 1 in rat testis (1995)

B Cell translocation gene 1 (BTG1) is a member of a new family of putative antiproliferative factors. They are characterized by their rapid, but transient, expression in response to factors that induce growth arrest and subsequent differentiation. In immature rat Sertoli cell cultures, BTG1 messenger RNA (mRNA) increases rapidly after FSH stimulation. We obtained the full-length coding sequence of rat BTG1 complementary DNA for Northern blot analysis and in situ hybridization to determine the temporal expression and spatial distribution of BTG1 mRNA in the rat testis. Northern analysis of isolated adult germ cells and in situ hybridization analysis of adult seminiferous epithelium demonstrated that BTG1 expression was first evident in late primary spermatocytes. The level of BTG1 mRNA was also elevated in secondary spermatocytes, but was maximal in postmeiotic round spermatids where levels were 5 times the background. BTG1 mRNA was not detectable in cells in the M phase of meiosis or spermatids undergoing nuclear elongation and condensation. The oscillation of BTG1 expression from the late prophase of the first meiotic division through spermatozoa release suggests BTG1 involvement in spermatogenesis. High levels of BTG1 mRNA at entry into terminal spermatid differentiation suggests a role consistent with that proposed for the BTG1 family of antiproliferative factors.
Analysis of brain biocompatibility of drug-releasing biodegradable microspheres by scanning and transmission electron microscopy (2001)

The progressive degradation of the microspheres, with vacuolization, deformation, and shrinkage, was well visualized. This degradation was identical in microspheres implanted in the inert material and in the rat brain tissue, independent of the presence of macrophages. The studies preformed in the striatum permitted the authors to demonstrate the structural integrity of axons in contact with microspheres, confirming the biocompatibility of the polymer. Furthermore, scanning electron microscopy showed the preservation of the 3D ultrastructure of the striatum around the microparticles. These microparticles, which can be stereotactically implanted in functional areas of the brain and can release neurotrophic factors, could represent, for some indications, an alternative to gene therapy.