gebhart/patrepeval huggingface dataset:
Comparative studies of duodenal and macrophage ferroportin proteins (2005)

Intestinal epithelial cells and reticuloendothelial macrophages are, respectively, involved in diet iron absorption and heme iron recycling from senescent erythrocytes, two critical processes of iron homeostasis. These cells appear to use the same transporter, ferroportin (Slc40a1), to export iron. The aim of this study was to compare the localization, expression, and regulation of ferroportin in both duodenal and macrophage cells. Using a high-affinity purified polyclonal antibody, we analyzed the localization and expression of ferroportin protein in the spleen, liver, and duodenum isolated from normal mice as well as from well-characterized mouse models of altered iron homeostasis. Ferroportin was found to be predominantly expressed in enterocytes of the duodenum, in splenic macrophages, and in liver Kupffer cells. Interestingly, the protein species detected in these cells migrated differently on SDS-PAGE. These differences in apparent molecular masses were partly explained by posttranslational complex N-linked glycosylations. In addition, in enterocytes, the transporter was mostly expressed at the basolateral membrane, whereas in bone marrow-derived macrophages, ferroportin was found predominantly localized in the intracellular vesicular compartment. However, some microdomains positive for ferroportin were also detected at the plasma membrane of macrophages. Despite these differences, we observed a parallel upregulation of ferroportin expression in tissue macrophages and enterocytes in response to iron-restricted erythropoiesis, suggesting that iron homeostasis is likely maintained through coordinate expression of the iron exporter in both intestinal and phagocytic cells. Our data also confirm a predominant regulation of ferroportin through systemic regulator(s) likely including hepcidin.
Coupled-wave analysis of lamellar metal transmission gratings for the visible and the infrared (1995)

We theoretically and experimentally investigate the response, in the visible and in the near infrared, of micrometer- and submicrometer-period lamellar metal transmission gratings in vacuum and on silica and GaAs substrates. We use a coupled-wave analysis to characterize the grating response as a function of wavelength, period, grating profile, and dielectric constant of the metal and the substrate. Losses to the metal, which have been neglected in prior studies, are shown to be as large as 80% of the incident optical power. Absorption in the metal and the substrate, associated with complex refractive indices, leads to a broadening and a reduction in amplitude of Rayleigh wavelength resonance features in the transmission efficiency and reduces the extinction between orthogonal polarizations in the wire-grid polarizer limit. The results of transmission and photocurrent studies performed on metal–semiconductor–metal photodiodes fabricated on GaAs or GaAs–AlGaAs heterostructure substrates demonstrate the rigorous nature of the coupled-wave analysis, indicate experimental limitations for the application of an infinite grating approximation to model finite-period structures, and provide evidence for the presence of surface electromagnetic waves in the forward-diffracted optical intensity distribution. Qualitative agreement is also obtained between coupled-wave analysis results and transmission data reported in the literature for gold gratings on silica.
Use of heteropolymeric monoclonal antibodies to attach antigens to the C3b receptor of human erythrocytes: a potential therapeutic treatment. (1991)

We have prepared bispecific, cross-linked monoclonal antibodies (heteropolymers) with specificity for both targeted antigens and the human erythrocyte (RBC) complement receptor. These heteropolymers facilitate binding of target antigens (human IgG and dinitrophenylated bovine gamma globulin) to human RBCs under conditions that either allow or preclude complement activation. Quantitative analyses of this binding agree well with the number of complement receptors per RBC. In vitro "whole-blood" model experiments indicate heteropolymer-facilitated binding of antigens to RBCs is rapid and stable at 37 degrees C. It may be possible to extend these prototype experiments to the in vivo situation and use heteropolymer-attached RBCs for the safe and rapid binding, neutralization, and removal from the circulation of pathogenic antigens associated with infectious disease.
Building a collaborative drug design system (1992)

Describes a system that supports the drug designer in the search for compounds with desired biological properties. The system incorporates two design principles: it works in collaboration with the user, and it contains a variety of analytical tools. The tools, which share a common representational language with the drug designer, are used to construct predictive models of the domain from empirical data. The models are used to hypothesize sets of new compounds to by synthesized and tested.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Polymorphism of DNA sequence adjacent to human beta-globin structural gene: relationship to sickle mutation. (1978)

Restriction endonuclease mapping of the human globin genes revealed a genetic variation in a Hpa I recognition site about 5000 nucleotides from the 3' end of the beta-globin structural gene. Instead of a normal 7.6-kilobase (kb) fragment which contains the beta-globin structural gene, 7.0-kb and 13.0-kb variants were detected. Both variants were found in people of African origin and were not detected in Asians or Caucasians. The 13.0-kb variant is frequently associated with the sickle hemoglobin mutation and may be useful for the prediction of the sickle cell gene in prenatal diagnosis. Polymorphism in a restriction enzyme site could be considered as a new class of genetic marker and may offer a new approach to linkage analysis and anthropological studies.
SYBYL Line Notation (SLN):  A Versatile Language for Chemical Structure Representation (1997)

SYBYL Line Notation (SLN) is an ASCII language used to represent chemical structures, including common organic molecules, macromolecules, polymers, and combinatorial libraries. SLN is also used to express substructural (2D) queries and includes a complete facility for Markush representation. This concise language is ideal for database storage of chemical entities as well as for network communication of structures and queries.
Broadcast and Weight: An Integrated Network For Scalable Photonic Spike Processing (2014)

We propose an on-chip optical architecture to support massive parallel communication among high-performance spiking laser neurons. Designs for a network protocol, computational element, and waveguide medium are described, and novel methods are considered in relation to prior research in optical on-chip networking, neural networking, and computing. Broadcast-and-weight is a new approach for combining neuromorphic processing and optoelectronic physics, a pairing that is found to yield a variety of advantageous features. We discuss properties and design considerations for architectures for scalable wavelength reuse and biologically relevant organizational capabilities, in addition to aspects of practical feasibility. Given recent developments commercial photonic systems integration and neuromorphic computing, we suggest that a novel approach to photonic spike processing represents a promising opportunity in unconventional computing.
Polarizing beam splitter based on the anisotropic spectral reflectivity characteristic of form-birefringent multilayer gratings (1996)

We introduce a novel polarizing beam splitter that uses the anisotropic spectral reflectivity (ASR) characteristic of a high-spatial-frequency multilayer binary grating. Such ASR effects allow us to design an optical element that is transparent for TM polarization and reflective for TE polarization. For normally incident light our element acts as a polarization-selective mirror. The properties of this polarizing beam splitter are investigated with rigorous coupled-wave analysis. The design results show that an ASR polarizing beam splitter can provide a high polarization extinction ratio for optical waves from a wide range of incident angles and a broad optical spectral bandwidth.
Catalytic, Enantioselective Alkylation of α-Imino Esters Using Late Transition Metal Phosphine Complexes as Catalysts (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTCatalytic, Enantioselective Alkylation of α-Imino Esters Using Late Transition Metal Phosphine Complexes as CatalystsDana Ferraris, Brandon Young, Travis Dudding, and Thomas LectkaView Author Information Department of Chemistry, Johns Hopkins University 3400 North Charles Street, Baltimore, Maryland 21218 Cite this: J. Am. Chem. Soc. 1998, 120, 18, 4548–4549Publication Date (Web):May 13, 1998Publication History Received22 January 1998Published online13 May 1998Published inissue 1 May 1998https://pubs.acs.org/doi/10.1021/ja9802450https://doi.org/10.1021/ja9802450rapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views2085Altmetric-Citations226LEARN 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 SUBJECTS:Alcohols,Catalysts,Group 14 compounds,Organic compounds,Post-translational modification Get e-Alerts
A 5.2-GHz CMOS receiver with 62-dB image rejection (2001)

A 5.2-GHz CMOS receiver employs a double downconversion heterodyne architecture with a local oscillator frequency of 2.6 GHz and applies offset cancellation to the baseband amplifiers. Placing the image around the zero frequency, the receiver achieves an image rejection of 62 dB with no external components while minimizing the flicker noise upconversion in the first mixing operation. Realized in a 0.25-/spl mu/m digital CMOS technology, the circuit exhibits a noise figure of 6.4 dB, an IP/sub 3/ of -15 dBm, and a voltage conversion gain of 43 dB, while draining 29 mW from a 2.5-V supply.
STEROL METHYLTRANSFERASE 1 Controls the Level of Cholesterol in Plants (2000)

Andrew C. Diener, Haoxia Li, Wen-xu Zhou, Wendy J. Whoriskey, W. David Nes, Gerald R. Fink, STEROL METHYLTRANSFERASE 1 Controls the Level of Cholesterol in Plants, The Plant Cell, Vol. 12, No. 6 (Jun., 2000), pp. 853-870
Lack of expression of c-KIT in ovarian cancers is associated with poor prognosis (2000)

The c-KIT protooncogene encodes a tyrosine kinase receptor, KIT, that is expressed in many normal and cancerous tissues. In this study, we have examined the expression of c-KIT and its ligand, stem cell factor (SCF), in human epithelial ovarian tumors, in normal ovaries and in cultured ovarian surface epithelium (OSE). Cultured cells, normal tissues and tumors were analyzed by Northern and Western blot analyses, reverse transcription-polymerase chain reaction and immunohistochemistry. Normal OSE expressed SCF, but not c-KIT; however, epithelial invaginations and inclusion cysts often expressed KIT protein. Of 15 benign ovarian tumors and tumors of low malignant potential, 87% expressed c-KIT, and 92% of these co-expressed SCF, suggesting the possibility of autocrine growth regulation. Of 35 malignant ovarian cancers, 71% expressed c-KIT (92% co-expressed SCF), with a trend for decreased c-KIT expression in advanced stage disease. Of 34 patients with malignant tumors for whom follow-up information was available (median follow-up time of 24 months), 9 had tumors that did not express c-KIT, 8 (89%) of whom have died and the remaining 1 has recurrent disease. Of the 25 patients with tumors expressing c-KIT, 56% are still alive. Eight of the patients have no evidence of disease and all had KIT-expressing tumors. Statistical analysis indicated that patients whose tumors did not express c-KIT had a significantly shorter (p < 0.05) disease-free survival time than patients who had KIT-expressing tumors. Our results suggest that c-KIT may play a role in early ovarian tumorigenesis, and that loss of c-KIT expression is associated with poor prognosis.
Decision Analysis: Practice and Promise (1988)

Decision analysis stands on a foundation of hundreds of years of philosophical and practical thought about uncertainty and decision-making. The accomplishments and promise of the field are impressive, yet it has not become commonplace even in very important decisions. While human nature may pose an ultimate limitation, maintaining clarity of concept and exploiting progress in the realms of scope, skill, and efficiency should lead to more widespread use. A central conceptual distinction is that between normative and descriptive views of decision-making. We discuss the importance of maintaining this distinction in the face of attempts to compromise. The procedures for formulating, eliciting, evaluating, and appraising the decision problem are all experiencing major improvements. The strategy-generation table helps in finding creative alternatives. Decision quality concepts permit us to assure both effectiveness and efficiency in analyzing decision problems. The influence diagram provides new clarity to the conversation between decision-maker and analyst, allowing representations that are both easily understandable and mathematically consistent. The clarity test makes sure we know what we are talking about regardless of what we are saying about it. Direct and indirect values illuminate preferences. Generic risk attitude considerations indicate how to relate corporate risk tolerance to the financial measures of the corporation. Spreadsheet, decision tree, and influence diagram programs speed evaluation. Intelligent decision systems realized in computers offer promise of providing the benefits of decision analysis on a broader scale than ever before. Decision analysis is now poised for a breakthrough in its usefulness to human beings.
Antigenic Determinants on Rat Metallothionein: Fine Epitope Mapping for a Murine Monoclonal Antibody and Rabbit Polyclonal Antisera1 (1990)

In order to determine the epitope of metallothionein (MT) to a murine monoclonal antibody (MT 189-14-7) which had been produced by immunization with rat MT 2 (Kikuchi et al. (1988) Mol. Immunol. 25, 1033-1036), various lengths of synthetic oligopeptides were tested for their inhibitory activities in competitive radioimmunoassay (RIA). The amino-terminal acetylated pentapeptide, AcMDPNC, exhibited an inhibitory activity comparable to that of native MTs, whereas the acetylated tetrapeptide, AcMDPN, and the deacetylated heptapeptide, MDPNCSC, were much less inhibitory. The results suggest that the major part of the epitope structure of MT to the MT 189-14-7 monoclonal antibody is located within the amino-terminal acetylated pentapeptide, AcMDPNC. The specificities of polyclonal rabbit anti-MT antisera raised against the same immunogen were also determined by using various animal MTs and synthetic peptides as inhibitors in the RIA. Among three antisera tested, two reacted with several amino-terminal oligopeptides similarly to the MT 189-14-7 antibody. The major epitope structures to these polyclonal antibodies were shown to be located within the acetylated tetrapeptide, AcMDPN. Another antiserum contained at least two different populations of antibodies: one consisted of antibodies reactive with the amino-terminal synthetic peptides, while the other was not reactive with them. These results suggest that, in the rabbit also, the amino-terminal region common to various animal MTs can be an epitope to antibodies raised against rat MT, as shown in the mouse. Moreover, the results indicate that the synthetic amino-terminal peptides are useful for determination of the specificity of polyclonal rabbit anti-MT antibodies, which have been widely used for the quantification of MTs.
The TILDE File Naming Scheme (1985)

ABSTRACfHierarchical directory systems permit users of a computer system to organize files into meaningful sets.A key part of the directory's usefulness lies in the way it partitions names.A hierarchical directory system supports short mnemonic names by keeping the names of files in one directory independent of those in other directories.Most hierarchical directory systems, which were designed for single-processor time sharing systems, place files in a sin- gle directory tree.The disadvantages of the single tree scheme become apparent when two such systems are interconnected by a computer network.or when soft\\are is transported from one machine to another.This report proposes an alternative to the single-tree naming scheme in which files are organized in a forest of tree-structwed directories and each user chases his own view of the forest.~i.~~omes necessaI)' to divorce the directory tree from the processor in order !o provide meaningful file naming in a distributed environment.Separating directory trees from processors also has advantages in single-processor systems.
Facile Preparation of Carbohydrate Microarrays by Site-Specific, Covalent Immobilization of Unmodified Carbohydrates on Hydrazide-Coated Glass Slides (2005)

[reaction: see text] A new, simple and efficient immobilization method to attach mono-, di-, oligo-, and polysaccharides to hydrazide-coated glass slides was developed. Protein and cell-binding experiments show that the carbohydrate microarrays prepared by this method are applicable for the rapid analysis of protein-carbohydrate interactions and fast detection of pathogens.
Mechanical Properties of Electrospun Silk Fibers (2004)

The morphology and microstructure of electrospun B. mori silk/poly(ethylene oxide) (PEO) fibers with diameters less than 1 μm were characterized using birefringence, wide-angle X-ray diffraction, differential scanning calorimetry, and atomic force microscopy (AFM). In the as-spun fibers, silk fibroin is present in a coil conformation due to rapid fiber formation during electrospinning. After treatment with methanol, the silk fibroin was transformed into a β-sheet-containing structure. Evidence for nanofibrils within the as-spun fibers was observed by AFM, and the PEO phase was dispersed as small, elongated islands within the silk fibroin matrix and oriented along the fiber direction. The mechanical properties of single fibers were characterized by AFM nanoindentation. The results were consistent with uniaxial tensile tests and with the morphological analysis. After methanol treatment and extraction with water, the electrospun silk fiber exhibits a lateral modulus of 8.0 GPa, within a factor of 2 of degummed native silk. The results provide additional insight into the nature of these reconstituted silk fibroin submicron diameter fibers, which have potential utility in a range of materials science and engineering applications.
A Molecular Framework for Plant Regeneration (2006)

Plants and some animals have a profound capacity to regenerate organs from adult tissues. Molecular mechanisms for regeneration have, however, been largely unexplored. Here we investigate a local regeneration response in Arabidopsis roots. Laser-induced wounding disrupts the flow of auxin-a cell-fate-instructive plant hormone-in root tips, and we demonstrate that resulting cell-fate changes require the PLETHORA, SHORTROOT, and SCARECROW transcription factors. These transcription factors regulate the expression and polar position of PIN auxin efflux-facilitating membrane proteins to reconstitute auxin transport in renewed root tips. Thus, a regeneration mechanism using embryonic root stem-cell patterning factors first responds to and subsequently stabilizes a new hormone distribution.
Vaccination against Anthrax with Attenuated Recombinant Strains of Bacillus anthracis That Produce Protective Antigen (1999)

The protective efficacy of several live, recombinant anthrax vaccines given in a single-dose regimen was assessed with Hartley guinea pigs. These live vaccines were created by transforming DeltaANR and DeltaSterne, two nonencapsulated, nontoxinogenic strains of Bacillus anthracis, with four different recombinant plasmids that express the anthrax protective antigen (PA) protein to various degrees. This enabled us to assess the effect of the chromosomal background of the strain, as well as the amount of PA produced, on protective efficacy. There were no significant strain-related effects on PA production in vitro, plasmid stability in vivo, survival of the immunizing strain in the host, or protective efficacy of the immunizing infection. The protective efficacy of the live, recombinant anthrax vaccine strains correlated with the anti-PA antibody titers they elicited in vivo and the level of PA they produced in vitro.
Tumoral Angiogenesis: Review of the Literature (2008)

Tumoral angiogenesis is necessary for the growth of neoplasms and the production of metastasis. The vascular endothelial growth factor (VEGF) is a homodimeric heparin-binding glycoprotein that binds to VEGF-receptors and can induce endothelial cell mitosis, invasion, and eventually capillary tube formation. Bevacizumab, a humanized monoclonal antibody against VEGF, inhibits tumoral angiogenesis and may also improve the delivery of chemotherapy to the tumor mass. Some new antiangiogenic agents, called multi-kinase inhibitors (sorafenib and sunitinib), have also activity against other receptors, such as epidermal growth factor-receptor or platelet-derived growth factor-receptor. A new schedule of treatment (metronomic chemotherapy) also has antiangiogenic activity.
Site-directed mutagenesis of the phosphorylatable serine (Ser8) in C4 phosphoenolpyruvate carboxylase from sorghum. The effect of negative charge at position 8. (1992)

The properties of the dephospho and in vitro phosphorylated forms of recombinant sorghum phosphoenolpyruvate carboxylase have been compared with those of the authentic dark (dephospho) and light (phospho) leaf enzyme forms and two mutant enzymes in which the phosphorylatable serine residue (Ser8) has been changed by site-directed mutagenesis to Cys (S8C) or Asp (S8D). Kinetic analysis of the purified recombinant, mutant, and leaf enzyme forms at pH 8.0 indicated virtually identical Vmax, apparent Km (phosphoenolpyruvate), and half-maximal activation (glucose 6-P) values of about 44 units/mg, 1.1 mM, and 0.23 mM, respectively. In contrast, the Ser8, S8C, and dark leaf enzymes were about 3-fold more sensitive to inhibition by L-malate at pH 7.3 than the Ser8-P, S8D, and light leaf enzyme forms. These comparative results indicate that: (i) Ser8 is an important determinant in the regulation of sorghum phosphoenolpyruvate carboxylase activity by negative (L-malate), but not positive (glucose 6-phosphate) metabolite effectors, (ii) phosphorylation of this target residue can be functionally mimicked by Asp, but not Cys, and (iii) negative charge contributes to the effect of regulatory phosphorylation on this C4-photosynthesis enzyme.