gebhart/patrepeval huggingface dataset:
Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2 (2020)

Abstract The coronavirus SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Therapeutic neutralizing antibodies constitute a key short-to-medium term approach to tackle COVID-19. However, traditional antibody production is hampered by long development times and costly production. Here, we report the rapid isolation and characterization of nanobodies from a synthetic library, known as sybodies (Sb), that target the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Several binders with low nanomolar affinities and efficient neutralization activity were identified of which Sb23 displayed high affinity and neutralized pseudovirus with an IC 50 of 0.6 µg/ml. A cryo-EM structure of the spike bound to Sb23 showed that Sb23 binds competitively in the ACE2 binding site. Furthermore, the cryo-EM reconstruction revealed a novel conformation of the spike where two RBDs are in the ‘up’ ACE2-binding conformation. The combined approach represents an alternative, fast workflow to select binders with neutralizing activity against newly emerging viruses.
Shade Matching Assisted by Digital Photography and Computer Software (2008)

Shade matching assisted by digital photographs and computer software was significantly more reliable than by conventional visual methods.
Tensegrity of Cell Structure (2001)

Tensegrity structure is comprised of compression resistant elements and a set of continuous tensile elements that are interconnected with each other. The stability of such system depends on maintenance of tensional integrity inside the structure, or what has come to be termed “tensegrity”. According to studies on biology, cell structures are assembled on the basis of tensegrity mechanism. Tensegrity of cytoskeleton can affect cell shape and function. Furthermore, some basic rules of mechanochemical transduction in cells can be well explained using tensegrity theory.
Conformational Changes in Talin on Binding to Anionic Phospholipid Membranes Facilitate Signaling by Integrin Transmembrane Helices (2013)

Integrins are heterodimeric (αβ) cell surface receptors that are activated to a high affinity state by the formation of a complex involving the α/β integrin transmembrane helix dimer, the head domain of talin (a cytoplasmic protein that links integrins to actin), and the membrane. The talin head domain contains four sub-domains (F0, F1, F2 and F3) with a long cationic loop inserted in the F1 domain. Here, we model the binding and interactions of the complete talin head domain with a phospholipid bilayer, using multiscale molecular dynamics simulations. The role of the inserted F1 loop, which is missing from the crystal structure of the talin head, PDB:3IVF, is explored. The results show that the talin head domain binds to the membrane predominantly via cationic regions on the F2 and F3 subdomains and the F1 loop. Upon binding, the intact talin head adopts a novel V-shaped conformation which optimizes its interactions with the membrane. Simulations of the complex of talin with the integrin α/β TM helix dimer in a membrane, show how this complex promotes a rearrangement, and eventual dissociation of, the integrin α and β transmembrane helices. A model for the talin-mediated integrin activation is proposed which describes how the mutual interplay of interactions between transmembrane helices, the cytoplasmic talin protein, and the lipid bilayer promotes integrin inside-out activation.
Chitin Whisker Reinforced Thermoplastic Nanocomposites (2001)

ADVERTISEMENT RETURN TO ISSUECommunication to the...Communication to the EditorNEXTChitin Whisker Reinforced Thermoplastic NanocompositesMichel Paillet and Alain DufresneView Author Information Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS), Université Joseph Fourier, BP 53, 38041 Grenoble, Cedex 9, France Cite this: Macromolecules 2001, 34, 19, 6527–6530Publication Date (Web):August 11, 2001Publication History Received1 December 2000Revised25 May 2001Published online11 August 2001Published inissue 1 September 2001https://pubs.acs.org/doi/10.1021/ma002049vhttps://doi.org/10.1021/ma002049vrapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views2562Altmetric-Citations262LEARN 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 SUBJECTS:Biopolymers,Cellulose,Composites,Fluid dynamics,Suspensions Get e-Alerts
Microfabricated Devices for Integrated Dna Analysis (2001)

Over the last two decades, few areas have witnessed changes of the magnitude observed in molecular biology in general and DNA/RNA analysis in particular (Burke et al., 1997). This progress has been catalyzed by the discoveries of techniques for synthesis, analysis, and manipulation of nucleic acids. Genetic tests and assays have an enormous scope of applications in biotechnology and medicine, ranging from agriculture and farming (Buitkamp and Epplen, 1996) to the detection of pathogens in foods (Feng, 1997), to genetic diagnostics on human subjects (Reiss, 1991). The benefits of this progress include the commercial availability of improved drugs produced by genetic engineering and new techniques for diagnosis of genetic diseases. Currently more than 400 diseases are diagnosable by molecular analysis of nucleic acids, and many more assays will undoubtedly follow in the near future as more genetic information is made available by major research undertakings such as the Human Genome Project (Olson, 1993).
Display of β-lactamase on the Escherichia coli surface: outer membrane phenotypes conferred by Lpp′–OmpA′–β-lactamase fusions (1996)

Bacterial cell-surface exposure of foreign peptides and soluble proteins has been achieved recently by employing a fusion protein methodology. An Lpp'-OmpA(46-159)-Bla fusion protein has been shown previously to display the normally periplasmic enzyme beta-lactamase (Bla) on the cell surface of the Gram-negative bacterium Escherichia coli. Here, we have investigated the role of the OmpA domain of the tripartite fusion protein in the surface display of the passenger domain (Bla) and have characterized the effects of the fusion proteins on the integrity and permeability of the outer membrane. We show that in addition to OmpA(46-159), a second OmpA segment, consisting of amino acids 46-66, can also mediate the display of Bla on the cell surface. Other OmpA domains of various lengths (amino acids 46-84, 46-109, 46-128, 46-141 and 46-145) either anchored the Bla domain on the periplasmic face of the outer membrane or caused a major disruption of the outer membrane, allowing the penetration of antibodies into the cell. Detergent and antibiotic sensitivity and periplasmic leakage assays showed that changes in the permeability of the outer membrane are an unavoidable consequence of displaying a large periplasmic protein on the surface of E. coli. This is the first systematic report on the effects that cell surface engineering may have on the integrity and permeability properties of bacterial outer membranes.
Glycation, Inflammation, and RAGE (2003)

The cardiovascular complications of diabetes represent the leading cause of morbidity and mortality in affected subjects. The impact of hyperglycemia may be both direct and indirect: indirect consequences of elevated blood glucose lead to generation of advanced glycation endproducts, the products of nonenzymatic glycation/oxidation of proteins/lipids that accumulate in the vessel wall, and are signal transduction ligands for Receptor for AGE (RAGE). Although enhanced in diabetes, AGE accumulation also occurs in euglycemia and aging, albeit to lower degrees, driven by oxidant stress and inflammation. In hyperglycemia, production of 3-deoxyglucosone, at least in part via the polyol pathway, provides an amplification loop to sustain AGE generation, oxidant stress, and vascular activation. Furthermore, recruitment of inflammatory cells bearing S100/calgranulins, also ligands for RAGE, augments vascular dysfunction. We hypothesize that activation of RAGE is a final common pathway that transduces signals from these diverse biochemical and molecular species, leading to cardiovascular perturbation. Ultimately, these pathways synergize to construct a scaffold on which the complications of diabetes in the vasculature and heart may be built. We propose that antagonism of RAGE will provide a unique means to dismantle this scaffold and, thereby, suppress initiation/progression of vascular disease and cardiac dysfunction that accompany diabetes and aging.
Increased Collagen Gene Expression in Vascular Smooth Muscle Cells Cultured in Serum or Isoleucine Deprived Medium (1991)

The relationship between type I and type III collagen gene expression and the growth state of cultured bovine vascular smooth muscle cells has been investigated. Growth was modulated by incubation of subconfluent cultures of smooth muscle cells in media containing concentrations of fetal calf serum ranging from 10% to 0.5%. As the serum concentration was lowered, the doubling time increased from 17 hours to 70 hours, and collagen mRNA levels increased as judged by Northern blot analysis. The levels of induction were 5- to 15-fold for alpha 1(I), 2- to 3-fold for alpha 2(I), and 4- to 7-fold for alpha 1(III). Metabolic cell labelling with precursor amino acids indicated that type I and type III procollagen synthesis was elevated approximately 2-fold as growth slowed. A similar 2-fold increase occurred upon translation of isolated RNAs in a rabbit reticulocyte cell-free system. Nuclear run-on analysis indicated that increased collagen transcription can account for part of the increase in mRNA levels following incubation in lowered fetal calf serum. To further examine the influence of proliferation on collagen gene expression, smooth muscle cells were cultured in isoleucine-free medium, which resulted in quiescence within 36 hours. Induction of collagen mRNA levels was observed within 24 hours of incubation in isoleucine-free medium. Thus, collagen gene expression increases as the growth of vascular smooth muscle cells is slowed by either deprivation of growth factors or essential amino acids. Regulation is mediated at several sites, including gene transcription and mRNA translation, and possibly post-transcriptional steps.
Kekule index for valence bond structures of conjugated polycyclic systems (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKekule index for valence bond structures of conjugated polycyclic systemsA. Graovac, I. Gutman, M. Randic, and N. TrinajsticCite this: J. Am. Chem. Soc. 1973, 95, 19, 6267–6273Publication Date (Print):September 1, 1973Publication History Published online1 May 2002Published inissue 1 September 1973https://pubs.acs.org/doi/10.1021/ja00800a019https://doi.org/10.1021/ja00800a019research-articleACS PublicationsRequest reuse permissionsArticle Views114Altmetric-Citations44LEARN 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
UNTERSUCHUNGEN DER SCHWANGERSCHAFTSERHALTENDEN WIRKUNG VON 17α HYDROXYPROGESTERONCAPRONAT AN KASTRIERTEN TRÄCHTIGEN KANINCHEN (1958)

Zu einer Weiterverfolgung der schwangerschaftserhaltenden Wirkung von 17α-Hydroxyprogesteroncapronat sahen wir uns nach den negativen Ergebnissen an kastrierten trächtigen Ratten veranlasst (Junkmann, 1957, Suchowsky & Junkmann, 1957), zumal klinische Befunde beim Menschen eine deutliche und gute Wirkung aufweisen (Boschann, 1954, 1955 a, 1955 b, Davis & Wied, 1955, Cohen et al, 1956, Tyler, 1956, Reifenstein, Jr., 1957). Nach dem Schrifttum gelingt es, an 20 Stdn. nach der Begattung kastrierten Kaninchen mit zweimaliger Gabe von 0,5 mg Progesteron tägl. die Foeten bis zum 11. Tag zu erhalten, von diesem Zeitpunkt werden 2 × tägl. I mg Progesteron benötigt, um eine zeitgerechte Geburt lebender Jungen zu erzielen (Hafez & Pincus, 1956). Dies legte uns nahe zu unseren Untersuchungen Kaninchen zu verwenden. In unserer Versuchsanordnung haben wir ein ähnliches Behandlungsregime wie bei den Versuchen der Schwangerschaftserhaltung bei trächtig kastrierten Ratten zur Anwendung gebracht. Der Kopulationstermin wurde an 2800–3500 g schweren weiblichen Kaninchen durch Nachweis
ALIS: An Affinity Selection–Mass Spectrometry System for the Discovery and Characterization of Protein–Ligand Interactions (2007)

This chapter contains sections titled: Introduction State of the Art Spectroscopic and Biophysical Methods Mass Spectrometry-based Methods ALIS: An Affinity Selection–Mass Spectrometry System based on Continuous SEC ALIS System Design Discovery of Ligands from Combinatorial Libraries Quantitative Binding Affinity Measurement Theory Simulations and Experimental Results Competition-based Binding Site Determination and Affinity Ranking in Mixtures Binding Site Classification Affinity Ranking in Compound Mixtures Protein–Ligand Dissociation Rate Measurement Theory Simulations Experimental Results Conclusions Future Directions
Metabolism of erythritol in humans: Comparison with glucose and lactitol (1993)

The metabolism of erythritol was assessed in six normal volunteers by measuring the amount of 13CO2 excretion and H2 excretion in breath, and erythritol in urine after intake of 25 g 13C-labelled erythritol. The results were compared with the same variables obtained after intake of 25 g 13C-labelled glucose and 13C-labelled lactitol. In addition, the H2 production by faecal flora supplemented with small amounts of erythritol, glucose and lactitol was measured in vitro, as an index of bacterial metabolism of non-absorbed substrate. In contrast to the results obtained after intake of glucose and lactitol, no increase in breath 13CO2 and H2 was observed after intake of erythritol, and erythritol was nearly completely recovered in urine. The in vitro experiments showed that no H2 was formed by faecal flora from erythritol as compared with glucose and lactitol. It is concluded that erythritol is a substrate that is readily absorbed, and undergoes no metabolism by the host. If part of it escapes absorption, it is not metabolized by faecal flora.
Cell Surface P-Glycoprotein Associated with Multidrug Resistance in Mammalian Cell Lines (1983)

The plasma membranes of hamster, mouse, and human tumor cell lines that display multiple resistance to drugs were examined by gel electrophoresis and immunoblotting. In every case, increased expression of a 170,000-dalton surface antigen was found to be correlated with multidrug resistance. This membrane component is of identical molecular size and shares some immunogenic homology with the previously characterized P-glycoprotein of colchicine-resistant Chinese hamster ovary cells. This finding may have application to cancer therapy.
Magnetic and optical tunable microspheres with a magnetite/gold nanoparticle shell (2005)

Multifunctional core-shell microspheres consisting of a polystyrene 640 nm diameter core covered with a selectable number of layers of magnetite (12 nm) and silica-coated gold (15 nm) nanoparticles have been fabricated using the layer-by-layer (LbL) technique in aqueous solution. By varying the shell thickness and layer composition the magnetic and optical properties and the diameter of the colloids can be controlled independently. Optical spectra of the core-shell colloidal microspheres show a well-resolved Au surface plasmon peak in the visible which red-shifts with the number of adsorbed Au nanoparticle layers. The magnetic moment per sphere increases nearly linearly with the number of adsorbed magnetite nanoparticle layers, and the spheres can be assembled into chains of up to 1 mm length by deposition in a magnetic field.
The Eden System: A Technical Review (1985)

The Eden project is a five year experiment in designing, building, and using an "integrated distributed" computing system. We are attempting to combine the benefits of integration and distribution by supporting an object based style of programming on top of a node machine/local network hardware base. Our experimental hypothesis is that such an architecture will provide an environment conducive to building distributed applications.
Protection against apoptosis by the vaccinia virus SPI-2 (B13R) gene product (1996)

Vaccinia virus contains a gene, termed SPI-2 or B13R, that is closely related in its sequence to a potent inhibitor of apoptosis from cowpox virus (crmA). Infection by vaccinia virus protects HeLa cells against apoptosis that is induced by an immunoglobulin M antibody against the fas receptor or by tumor necrosis factor alpha. This effect is profoundly reduced when the SPI-2 gene is deleted. The SPI-2 gene, when transiently expressed in these cells, can also protect against apoptosis mediated by these agents. Given the similarity to crmA, it seems likely that SPI-2 functions in an analogous fashion, inhibiting the activity of ICE protease family members and blocking the onset of apoptosis.
Arabidopsis LEAFY COTYLEDON1 represents a functionally specialized subunit of the CCAAT binding transcription factor (2003)

LEAFY COTYLEDON1 (LEC1) is a central regulator that is required for many aspects of Arabidopsis embryogenesis and sufficient to induce embryo development in vegetative cells when expressed ectopically. We previously showed that LEC1 encodes an HAP3 subunit of the CCAAT binding factor and that the 10 Arabidopsis HAP3 (AHAP3) subunits can be divided into two classes, the LEC1-type and the non-LEC1-type, based on sequence similarity within their B domains. By analyzing the ability of chimeric HAP3 subunits containing different combinations of domains from LEC1 and a non-LEC1-type AHAP3 subunit to suppress genetically the lec1 mutation, we show that the B domain of LEC1 is necessary and sufficient within the context of the protein for its activity in embryogenesis. Moreover, we identify one amino acid residue, Asp-55, specific to the LEC1-type B domain that is required for LEC1 activity in embryogenesis and sufficient to confer partial LEC1 activity to a non-LEC1-type B domain. Based on structural similarities between the HAP3 B domain and histone fold motif, we discuss how the Asp-55 residue may functionally differentiate LEC1 from the non-LEC1-type AHAP3 subunits.
Previous asthma and methacholine reactivity in defence force recruit screening (2005)

Screening for bronchial asthma remains a difficult but important aspect in the evaluation of health in potential recruits for the Australian Defence Force (ADF). Current regulations allow acceptance of subjects with a past history of asthma but who have been asymptomatic and have not required treatment for three years. Bronchial challenge tests may be used in an attempt to clarify a doubtful diagnosis. The findings of methacholine reactivity assessment in a group of 310 potential recruits referred for a consultant opinion have been examined. Despite being asymptomatic and demonstrating normal spirometry, half the group showed an abnormal degree of reactivity with 17% having brisk reactivity. Importantly, 17% of a group currently acceptable under current regulations showed brisk reactivity. In determining whether the current guidelines are appropriate, it is essential to determine the subsequent service record of those recruits with persisting brisk reactivity who commence military service. (author abstract)
Channel status prediction for cognitive radio networks (2010)

Abstract The cognitive radio (CR) technology appears as an attractive solution to effectively allocate the radio spectrum among the licensed and unlicensed users. With the CR technology the unlicensed users take the responsibility of dynamically sensing and accessing any unused channels (frequency bands) in the spectrum allocated to the licensed users. As spectrum sensing consumes considerable energy, predictive methods for inferring the availability of spectrum holes can reduce energy consumption of the unlicensed users to only sense those channels which are predicted to be idle. Prediction‐based channel sensing also helps to improve the spectrum utilization (SU) for the unlicensed users. In this paper, we demonstrate the advantages of channel status prediction to the spectrum sensing operation in terms of improving the SU and saving the sensing energy. We design the channel status predictor using two different adaptive schemes, i.e., a neural network based on multilayer perceptron (MLP) and the hidden Markov model (HMM). The advantage of the proposed channel status prediction schemes is that these schemes do not require a priori knowledge of the statistics of channel usage. Performance analysis of the two channel status prediction schemes is performed and the accuracy of the two prediction schemes is investigated. Copyright © 2010 John Wiley &amp; Sons, Ltd.
Neural Network and Fuzzy Logic Applications in C/C++ (1994)

From the Publisher:
Many books discuss the theory of neural and fuzzy systems, but this is the only one that gives you everything you need to actually design and implement neural and fuzzy programs for real-world scientific, engineering, and financial applications. Each chapter is self-contained and takes the reader through all the steps - from data preparation to the presentation of results - necessary to develop a complete working application, many of which feature interactive graphics. In addition to basics such as backpropagation for feedforward networks, the book also covers a number of advanced methods, including genetic algorithms, simulated annealing, and conjugate gradient methods. A complete, step-by-step guide to developing fuzzy and neural applications; applications for financial forecasting, modeling of chaotic dynamics, pattern classification, and control of unstable systems; provides a wealth of sample code for all applications; critically evaluates how well each application works; and features a guide to creating a complete object-oriented interactive interface framework through which all applications can be run.