gebhart/patrepeval huggingface dataset:
Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies (2020)

Neutralizing antibody responses to coronaviruses mainly target the receptor-binding domain (RBD) of the trimeric spike. Here, we characterized polyclonal immunoglobulin Gs (IgGs) and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their focus on RBD epitopes, recognition of alpha- and beta-coronaviruses, and contributions of avidity to increased binding/neutralization of IgGs over Fabs. Using electron microscopy, we examined specificities of polyclonal plasma Fabs, revealing recognition of both S1<sup>A</sup> and RBD epitopes on SARS-CoV-2 spike. Moreover, a 3.4 Å cryo-electron microscopy (cryo-EM) structure of a neutralizing monoclonal Fab-spike complex revealed an epitope that blocks ACE2 receptor binding. Modeling based on these structures suggested different potentials for inter-spike crosslinking by IgGs on viruses, and characterized IgGs would not be affected by identified SARS-CoV-2 spike mutations. Overall, our studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.
Defective vasculature in fibronectin‐receptor‐deficient cho cell tumors in nude mice (1993)

The level of expression of the alpha 5/beta 1 integrin fibronectin receptor (FnR) strongly affects the growth rate of CHO cell tumors in nude mice. Here we report that alpha 5/beta 1 expression also influences the organization of the tumor vasculature. Tumors formed from CHO clones defective in FnR expression have a leaky vasculature that gives them a hemorrhagic appearance. Tumors from wild-type CHO cells, or from FnR-deficient CHO clones transfected with constructs coding for the alpha 5 integrin subunit, have an intact, non-leaky vasculature. In tumors from FnR-deficient cells, the endothelial lining of blood vessels is sparse, and red cells and plasma proteins can be detected in the tumor parenchyma. In tumors from cells expressing the alpha 5/beta 1 FnR, tumor vessels are circumscribed by a lining of von-Willebrand-factor-positive endothelial cells, and blood cells and proteins are confined to the vessel lumina. Thus, the level of expression of the alpha 5/beta 1 FnR in the tumor parenchymal cells can influence the development of tumor vasculature. Since alpha 5/beta 1 is vital to the organization of the extracellular matrix, one possibility is that altered matrix assembly contributes to the defective vascularization seen in alpha 5/beta 1-deficient tumors.
Expression of functional CXCR4 chemokine receptors on human colonic epithelial cells (1999)

In addition to their role as regulators of leukocyte migration and activation, chemokines and their receptors also function in angiogenesis, growth regulation, and HIV-1 pathogenesis--effects that involve the action of chemokines on nonhematopoietic cells. To determine whether chemokine receptors are expressed in human colonic epithelium, HT-29 cells were examined by RT-PCR for the expression of the chemokine receptors for lymphotactin, fractalkine, CCR1-10, and CXCR1-5. The only receptor consistently detected was CXCR4 (fusin/LESTR), although HT-29 cells did not express mRNA for its ligand, stromal cell-derived factor (SDF-1alpha). Flow cytometric analysis with anti-CXCR4 antibody indicated that the CXCR4 protein was expressed on the surface of roughly half of HT-29 cells. CXCR4 was also expressed in colonic epithelial cells in vivo as shown by immunohistochemistry on biopsies from normal and inflamed human colonic mucosa. The mRNA for SDF-1alpha and other CC and CXC chemokines was present in normal colonic biopsies. The CXCR4 receptor in HT-29 cells was functionally coupled, as demonstrated by the elevation in [Ca2+]i, which occurred in response to 25 nM SDF-1alpha and by the SDF-1alpha-induced upregulation of ICAM-1 mRNA. Sodium butyrate downregulated CXCR4 expression and induced differentiation of HT-29 cells, suggesting a role for CXCR4 in maintenance and renewal of the colonic epithelium. This receptor, which also serves as a coreceptor for HIV, may mediate viral infection of colonic epithelial cells.
Growth and Carcass Characteristics of Cull Cows after Different Times-on-Feed (1987)

Cull cows (N = 48) of similar age from Angus and Hereford breed types were assigned to one of four feeding periods (0, 28, 56 or 84 d) and subdivided into two groups, one implanted with Synovex-H and a non-implanted control. Cows were fed a high energy diet and slaughtered at the end of each feeding period. Average daily gain and feed efficiency were evaluated on each animal during the trial. The following carcass traits were evaluated: USDA yield and quality grade characteristics, boning yield, muscle weights, bone weights, pH and Warner-Bratzler shear force of the longissimus muscle. The left side of each carcass was boned and proximate analysis was determined. No significant implant effects were encountered for any of the traits evaluated; therefore, data were pooled and evaluated by feeding period only. Carcass weight and boneless forequarter and hindquarter tissue weights increased significantly between each feeding period; percent kidney, pelvic and heart fat (KPH) and yield grade did not differ (P greater than .05) until d 56 and 84, respectively. Quality grade and marbling scores improved (P less than .05) between 28 and 56 d of feeding. Biceps femoris weight changed during the 84-d experiment from 4.1 kg on d 0 to 5.3 kg on d 84 (P less than .05). Proximate analysis of the boneless tissue indicated an increase (P less than .05) in extractable fat of approximately 6% for each feeding period (6.3% fat on d 0 to 25.4% on d 84).(ABSTRACT TRUNCATED AT 250 WORDS)
Identification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies (2007)

In Caenorhabditis elegans, the Mex-3 protein is a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. We have now identified a family of four homologous human Mex-3 genes, called hMex-3A to -3D that encode proteins containing two heterogeneous nuclear ribonucleoprotein K homology (KH) domains and one carboxy-terminal RING finger module. The hMex-3 are phosphoproteins that bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. Our analysis further revealed that hMex-3A and hMex-3B, but not hMex-3C, colocalize with both the hDcp1a decapping factor and Argonaute (Ago) proteins in processing bodies (P bodies), recently characterized as centers of mRNA turnover. Taken together, these findings indicate that hMex-3 proteins constitute a novel family of evolutionarily conserved RNA-binding proteins, differentially recruited to P bodies and potentially involved in post-transcriptional regulatory mechanisms.
SPECT and Lumbar MRI in Back Pain with Emphasis on Changes in End Plates in Association with Disc Degeneration (1998)

Over a two-year period, 48 sequential patients were selected because they showed type I or II end plate changes on magnetic resonance imaging (MRI) and/or had positive single-photon emission computerized tomography (SPECT) scan in the area of disc degeneration. They were selected out of a large group of patients who were being evaluated by MRI and SPECT scan for low back pain. In this group of 48 patients, 47 had positive SPECT scans at the disc space, which on MRI indicates degenerative disc disease. Of these, 38 had end plate changes on the MRI, but 10 did not have end plate changes on the MRI even though their SPECT was positive. None of the 48 patients had evidence of other pathology such as fracture, metastatic disease or spondylolysis. The MRI changes were both of type I and type II and thought to represent increased vascularization of the fibrous tissue or fatty replacement of marrow in the area of the end plate. Based on this study, we are proposing that a positive end plate SPECT in degenerative disc disease is related to marrow changes in the region of the end plate of the disc. Also, we are proposing that SPECT may be of value in delineating early end plate changes prior to the MRI showing type I or type II change in the same area.
Electrophysiological Studies of Salty Taste Modification by Organic Acids in the Labellar Taste Cell of the Blowfly (2002)

Using the labellar salt receptor cells of the blowfly, Phormia regina, we electrophysiologically showed that the response to NaCl and KCl aqueous solutions was enhanced and depressed by acetic, succinic and citric acids. The organic acid concentrations at which the most enhanced salt response (MESR) was obtained were found to be different: 0.05-1 mM citric acid, 0.5-2 mM succinic acid and 5-50 mM acetic acid. Moreover, the degree of the salt response was not always dependent on the pH values of the stimulating solutions. The salt response was also enhanced by HCl (pH 3.5-3.0) only when the NaCl concentration was greater than the threshold, indicating that the salty taste would be enhanced by the comparatively lower concentrations of hydrogen ions. Another explanation for the enhancement is that the salty taste may also be enhanced by undissociated molecules of the organic acids, because the MESRs were obtained at the pH values lower than the pKa(1) or pKa(2) values of these organic acids. On the other hand, the salty taste could be depressed by both the lower pH range (pH 2.5-2.0) and the dissociated organic anions from organic acid molecules with at least two carboxyl groups.
ChemInform Abstract: Combination of Vitamin E with a Carotenoid: α‐Tocopherol and Trolox Linked to β‐Apo‐8′‐carotenoic Acid. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Treatment of acquired factor X inhibitor by plasma exchange with concomitant intravenous immunoglobulin and corticosteroids (2007)

A patient with spontaneous hemorrhage from multiple body sites was found to have markedly prolonged international normalized ratio (INR) and activated partial thromboplastin times (aPTT) with incomplete correction of aPTT on mixing studies using normal plasma. The cause of this severe hemorrhage was due to a specific factor X inhibitor. No underlying or associated diseases were found. Initial treatment with fresh frozen plasma, vitamin K, and recombinant activated factor VII (rFVIIa) was unsuccessful. However, therapy utilizing plasma exchange with concomitant intravenous immunoglobulin and corticosteroids resulted in a rapid and sustained normalization of factor X levels with a clinical hemostatic response.
Antitumor Imidazotetrazines. 32.1 Synthesis of Novel Imidazotetrazinones and Related Bicyclic Heterocycles To Probe the Mode of Action of the Antitumor Drug Temozolomide (1995)

A series of new imidazo[5,1-d]-1,2,3,5-tetrazinones with additional hydrogen-bonding or ionic substituents at the 8-carboxamide position of the antitumor drugs temozolomide (1) and mitozolomide (2) has been prepared. None of these compounds were significantly more cytotoxic in vitro against the mouse TLX5 lymphoma than the lead structures. Molecular modeling techniques have been used to design benzo- and pyrazolo[4,3-d]-1,2,3-triazinones bearing carboxamide groups in appropriate positions which are isosteric with temozolomide and mitozolamide but which cannot ring open to alkylating species. As predicted, these compounds have no inhibitory properties against human GM892A or Raji cell lines in vitro. Temozolomide and the spermidine-temozolomide conjugate 28 preferentially methylate guanines within guanine-rich sequences in DNA, but no experimental evidence has been found to support the hypothesis that such regions are involved in catalyzing the ring opening of the imidazotetrazinone prodrugs to their active forms.
Identification of G protein-coupled receptors for Drosophila PRXamide peptides, CCAP, corazonin, and AKH supports a theory of ligand-receptor coevolution (2002)

G-protein coupled receptors (GPCRs) are ancient, ubiquitous sensors vital to environmental and physiological signaling throughout organismal life. With the publication of the Drosophila genome, numerous "orphan" GPCRs have become available for functional analysis. Here we characterize two groups of GPCRs predicted as receptors for peptides with a C-terminal amino acid sequence motif consisting of -PRXamide (PRXa). Assuming ligand-receptor coevolution, two alternative hypotheses were constructed and tested. The insect PRXa peptides are evolutionarily related to the vertebrate peptide neuromedin U (NMU), or are related to arginine vasopressin (AVP), both of which have PRXa motifs. Seven Drosophila GPCRs related to receptors for NMU and AVP were cloned and expressed in Xenopus oocytes for functional analysis. Four Drosophila GPCRs in the NMU group (CG14575 [corrected], CG8795, CG9918, CG8784) are activated by insect PRXa pyrokinins, (-FXPRXamide), Cap2b-like peptides (-FPRXamide), or ecdysis triggering hormones (-PRXamide). Three Drosophila GPCRs in the vasopressin receptor group respond to crustacean cardioactive peptide (CCAP), corazonin, or adipokinetic hormone (AKH), none of which are PRXa peptides. These findings support a theory of coevolution for NMU and Drosophila PRXa peptides and their respective receptors.
Magnesiation of indoles with magnesium amide bases (1996)

Y. Kondo, A. Yoshida and T. Sakamoto, J. Chem. Soc., Perkin Trans. 1, 1996, 2331 DOI: 10.1039/P19960002331
The Library of Congress Classification System in an Online Environment (1990)

Advantages and disadvantages of online classification access are presented with special attention to LCC features for subject browsing, known item-searching, enhancement of keyword and controlled vocabulary searching, and other unique retrieval capabilities.
A new generation of protein display scaffolds for molecular recognition (2005)

Engineered antibodies and their fragments are invaluable tools for a vast range of biotechnological and pharmaceutical applications. However, they are facing increasing competition from a new generation of protein display scaffolds, specifically selected for binding virtually any target. Some of them have already entered clinical trials. Most of these nonimmunoglobulin proteins are involved in natural binding events and have amazingly diverse origins, frameworks, and functions, including even intrinsic enzyme activity. In many respects, they are superior over antibody-derived affinity molecules and offer an ever-extending arsenal of tools for, e.g., affinity purification, protein microarray technology, bioimaging, enzyme inhibition, and potential drug delivery. As excellent supporting frameworks for the presentation of polypeptide libraries, they can be subjected to powerful in vitro or in vivo selection and evolution strategies, enabling the isolation of high-affinity binding reagents. This article reviews the generation of these novel binding reagents, describing validated and advanced alternative scaffolds as well as the most recent nonimmunoglobulin libraries. Characteristics of these protein scaffolds in terms of structural stability, tolerance to multiple substitutions, ease of expression, and subsequent applications as specific targeting molecules are discussed. Furthermore, this review shows the close linkage between these novel protein tools and the constantly developing display, selection, and evolution strategies using phage display, ribosome display, mRNA display, cell surface display, or IVC (in vitro compartmentalization). Here, we predict the important role of these novel binding reagents as a toolkit for biotechnological and biomedical applications.
Radionuclide imaging of infection. (2004)

Although our understanding of microorganisms has advanced significantly and antimicrobial therapy has become increasingly available, infection remains a major cause of patient morbidity and mortality. The role of radionuclide imaging in the evaluation of the patient suspected of harboring an infection varies with the situation. For example, in the postoperative patient, radionuclide imaging is complementary to CT and is used to help differentiate postoperative changes from infection. In the case of the painful joint replacement, in contrast, radionuclide studies are the primary diagnostic imaging modality for differentiating infection from other causes of prosthetic failure. Several tracers are available for imaging infection: (99m)Tc-diphosphonates, (67)Ga-citrate, and (111)In- and (99m)Tc-labeled leukocytes. At the moment, in immunocompetent patients, labeled leukocyte imaging is the radionuclide procedure of choice for detecting most infections. There are, unfortunately, significant limitations to the use of labeled leukocytes. The in vitro labeling process is labor intensive, is not always available, and involves direct handling of blood products. For musculoskeletal infection, the need to frequently perform complementary marrow or bone imaging adds complexity and expense to the procedure and is an inconvenience to patients. Considerable effort has therefore been devoted to the search for alternatives to this procedure, including in vivo methods of labeling leukocytes, (18)F-FDG PET, and radiolabeled antibiotics. This article reviews the current status of nuclear medicine infection imaging and the potential of a murine monoclonal antigranulocyte antibody, fanolesomab, that is currently under investigation. Upon completion of this article, the reader will be familiar with the physical characteristics and uptake mechanisms of tracers currently approved for infection imaging, the indications for the uses of these tracers, and the characteristics and potential indications for a murine monoclonal antigranulocyte antibody under investigation.
Au micro-pattern fabrication on cellulose paper: comparison of μ-contact printing and liftoff techniques (2007)

Micro-contact printing (μ-CP) and liftoff techniques were employed to fabricate Au micro-patterns onto electro-active paper (EAPap) for biodegradable and flexible microelectromechanical system (MEMS) application. Conventional lithography and etching techniques cannot be utilized to fabricate micropatterns on EAPap having interesting actuating properties due to its hydrophilic and flexible characteristics. The cause of nanodefects on the Au pattern after the μ-CP process was investigated to enhance the pattern quality. Three different solvents were utilized to investigate the consequence of the solvent polarity during the 3-mercaptopropyltrimethoxysilane (MPTMS) self-assembled monolayer (SAM) fabrication and after the μ-CP process. The defects, such as microcracks and nanograins, were closely related to the solvent polarity. The higher polar solvent turned out smaller defects than the lower polar solvent due to the reduction of the solvent swell onto the PDMS stamp during SAM layer formation. The liftoff technique exhibited a new way of fabricating various metal patterns on EAPap without any nanodefects.
Supporting Data Integration Tasks with Semi-Automatic Ontology Construction (2015)

Data integration aims to facilitate the exploitation of heterogeneous data by providing the user with a unified view of data residing in different sources. Currently, ontologies are commonly used to represent this unified view in terms of a global target schema due to their flexibility and expressiveness. However, most approaches still assume a predefined target schema and focus on generating the mappings between this schema and the sources.
Predictive Value of Reactive Hyperemia for Cardiovascular Events in Patients With Peripheral Arterial Disease Undergoing Vascular Surgery (2007)

Thus, lower reactive hyperemia is associated with increased cardiovascular risk in patients with peripheral arterial disease. Furthermore, flow-mediated dilation and reactive hyperemia incrementally relate to cardiovascular risk, although impaired flow-mediated dilation was the stronger predictor in this population. These findings further support the clinical relevance of vascular function measured in the microvasculature and conduit arteries in the upper extremity.
Initiation and Propagation of Blood Coagulation at Artificial Surfaces Studied in a Capillary Flow Reactor (1998)

We have made use of a novel flow reactor to study the initiation and propagation of the ex vivo blood coagulation processes at artificial surfaces. The flow reactor consisted of a primary glass or polymer capillary that is connected to a secondary glass capillary, which inner wall was coated with a phospholipid bilayer of 25 mol% dioleoylphosphatidylserine/75 mol% dioleoylphosphatidylcholine (DOPS/DOPC). Citrated platelet free plasma and a CaCl2 solution were delivered by syringe pumps and mixed just before the entrance of the flow reactor. The outflowing plasma was assayed for factor XIa, factor IXa, factor Xa and thrombin activity. Perfusion of recalcified plasma through a bare glass capillary resulted in a transient generation of fluid phase factor XIa. In contrast, factor IXa production increased slowly to attain a stable steady-state level. We established that surface-bound factor XIa was responsible for a continuous production of factor IXa. Factor IXa-induced generation of factor Xa and thrombin was only observed when contact activated plasma was subsequently perfused through a DOPS/DOPC-coated capillary, showing that propagation of the factor IXa trigger requires a procoagulant, phosphatidylserine-containing, phospholipid membrane. The negatively charged inner surface of a heparin-coated polyurethane capillary, generated like the glass capillary significant amounts of factor XIa and factor IXa when perfused with recalcified plasma. No differences were found between unfractionated heparin and heparin devoid of anticoagulant activity. Thus, it is concluded that contact activation and factor IXa generation in flowing plasma is not inhibited by immobilised anticoagulant active heparin. Consequently, factor IXa-dependent thrombin generation at a downstream located phospholipid membrane was similar, regardless the specific anticoagulant activity of immobilised heparin.