gebhart/patrepeval huggingface dataset:
Characterization of Protein Unfolding with Solid-state Nanopores (2014)

In this work, we review the process of protein unfolding characterized by a solid-state nanopore based device. The occupied or excluded volume of a protein molecule in a nanopore depends on the protein's conformation or shape. A folded protein has a larger excluded volume in a nanopore thus it blocks more ionic current flow than its unfolded form and produces a greater current blockage amplitude. The time duration a protein stays in a pore also depends on the protein's folding state. We use Bovine Serum Albumin (BSA) as a model protein to discuss this current blockage amplitude and the time duration associated with the protein unfolding process. BSA molecules were measured in folded, partially unfolded, and completely unfolded conformations in solid-state nanopores. We discuss experimental results, data analysis, and theoretical considerations of BSA protein unfolding measured with silicon nitride nanopores. We show this nanopore method is capable of characterizing a protein's unfolding process at single molecule level. Problems and future studies in characterization of protein unfolding using a solid-state nanopore device will also be discussed.
Synthesis and preliminary in vitro evaluation of DOTA-Tenatumomab conjugates for theranostic applications in tenascin expressing tumors (2019)

Tenatumomab is an anti-tenascin murine monoclonal antibody previously used in clinical trials for delivering radionuclides to tumors by both pre-targeting (biotinylated Tenatumomab within PAGRIT) and direct <sup>131</sup>Iodine labeling approaches. Here we present the synthesis and in vitro characterization of three Tenatumomab conjugates to bifunctional chelating agents (NHS-DOTA, NCS-DOTA and NCS-DTPA). Results indicate ST8198AA1 (Tenatumomab-DOTAMA, derived by conjugation of NHS-DOTA), as the most promising candidate in terms of conjugation rate and yield, stability, antigen immunoreactivity and affinity. Labeling efficiency of the different chelators was investigated with a panel of cold metals indicating DOTAMA as the best chelator. Labeling of Tenatumomab-DOTAMA was then optimized with several metals and stability performed confirms suitability of this conjugate for further development. ST8198AA1 represents an improvement of the previous antibody forms because the labeling with radionuclides like <sup>177</sup>Lu or <sup>64</sup>Cu would allow theranostic applications in patients bearing tenascin expressing tumors.
X-ray crystallographic analysis of inhibition of endothiapepsin by cyclohexyl renin inhibitors (1992)

The crystal structures of endothiapepsin, a fungal aspartic proteinase (EC 3.4.23.6), cocrystallized with two oligopeptide renin inhibitors, PD125967 and PD125754, have been determined at 2.0-A resolution and refined to R-factors of 0.143 and 0.153, respectively. These inhibitors, which are of the hydroxyethylene and statine types, respectively, possess a cyclohexylalanine side chain at P1 and have interesting functionalities at the P3 position which, until now, have not been subjected to crystallographic analysis. PD125967 has a bis(1-naphthylmethyl)acetyl residue at P3, and PD125754 possesses a hydroxyethylene analogue of the P3-P2 peptide bond for proteolytic stability. The structures reveal that the S3 pocket accommodates one naphthyl ring with conformational changes of the Asp 77 and Asp 114 side chains, the other naphthyl group residing in the S4 region. The P3-P2 hydroxyethylene analogue of PD125754 forms a hydrogen bond with the NH of Thr 219, thereby making the same interaction with the enzyme as the equivalent peptide groups of all inhibitors studied so far. The absence of side chains at the P2 and P1' positions of this inhibitor allows water molecules to occupy the respective pockets in the complex. The relative potencies of PD125967 and PD125754 for endothiapepsin are consistent with the changes in solvent-accessible area which take place on inhibitor binding.
The isolation and functional characterization of autoimmune clones expressing inappropriate Ia. (1984)

The MRL/lpr mouse is an inbred strain widely accepted as a model for autoimmune disease both in murine and human systems. Developed from a series of crosses involving four strains of mice, the MRL/lpr (H-2k) genome is a composite estimated to contain approximately 75% of its parental LG/J (H-2d) genome. To explore the cellular mechanism underlying lymphoproliferation in the MRL/lpr mouse, we have isolated a series of clones from the lymph nodes of MRL/lpr mice with autoimmune disease. Extensive immunofluorescent analyses of these clones, designated the PAC series, reveal expression of IAk and IEk (beta-chain) cell surface antigens, as well as inappropriate expression of IAd, IEd (beta-chain), and H-2d. PAC cells also express MAC-1, MAC-2, RA3-2C2, and RA3-6B2 and contain esterase-positive cytoplasmic granules. The capacity of PAC cells to present antigen was investigated by co-culturing PAC with IA-restricted, antigen-specific T cell hybridomas +/- antigen. These assays demonstrated the PAC inability to present antigen to IAk-restricted T cell hybridomas, as well as their capacity to present antigen to IAd-restricted T cell hybridomas. In addition, activation of MRL/lpr peritoneal macrophages using gamma-interferon resulted in increased fluorescent staining for IAd and IEd concomitant with decreased fluorescent staining for IAk. Based on these findings, we propose a model of lymphoproliferation in which Ly-1+, H-2K+ T cells proliferate to inappropriate d haplotype antigens expressed by a small subset of monocytes in the MRL/lpr lymph node. The major genomic contribution of the LG/J (H-2d) mouse may be in part responsible for inappropriate antigen expression either by age-dependent expansion of d haplotype cells or by age-regulated expression of Iad and H-2d genes.
RLIP76 Is a Major Determinant of Radiation Sensitivity (2005)

RLIP76 (RALBP1) is a glutathione-conjugate transporter that is a critical component of clathrin-coated pit-mediated endocytosis, as well as in stress responses. In cultured cells, it provides protection from stressors including heat, oxidant chemicals, chemotherapeutic agents, UV irradiation, and X-irradiation. Here, we show marked reduction in glutathione conjugate transport capacity and stepwise increase in radiation sensitivity associated with heterozygous or homozygous loss of the RLIP76 gene in mice. Survival after radiation in homozygous knockout animals was significantly shorter than either the heterozygous knockouts or the wild type. Delivery of recombinant RLIP76 to mice lacking RLIP76 via a liposomal delivery system rescued radiation sensitivity. Furthermore, treatment of wild-type mice with RLIP76-containing liposomes conferred resistance to radiation. These findings suggest that inhibiting RLIP76 could be used for sensitization to radiation during cancer therapy and that RLIP76 liposomes could be radioprotective agents useful for treatment of iatrogenic or catastrophic radiation poisoning.
In Situ Analysis of Lymphocyte Migration to Lymph Nodes (1998)

Blood-borne lymphocytes migrate continuously to peripheral lymph nodes (PLN) and other organized lymphoid tissues where they are most likely to encounter their cognate antigen. Lymphocyte homing to PLN is a highly regulated process that occurs exclusively in specialized high endothelial venules (HEV) in the nodal paracortex. Recently, it has become possible to explore this vital aspect of peripheral immune surveillance by intravital microscopy of the subiliac lymph node microcirculation in anesthetized mice. This paper reviews technical and experimental aspects of the new model and summarizes recent advances in our understanding of the molecular mechanisms of lymphocyte homing to PLN which were derived from its use. Both lymphocytes and granulocytes initiate rolling interactions via L-selectin binding to the peripheral node addressin (PNAd) in PLN HEV. Subsequently, a G protein-coupled chemoattractant stimulus activates LFA-1 on rolling lymphocytes, but not on granulocytes. Thus, granulocytes continue to roll through the PLN, whereas LFA-1 activation allows lymphocytes to arrest and emigrate into the extravascular compartment. We have also identified a second homing pathway that allows L-selectin low/(activated/memory) lymphocytes to home to PLN. P-selectin on circulating activated platelets can mediate simultaneous platelet adhesion to PNAd in HEV and to P-selectin glycoprotein ligand (PSGL)-1 on lymphocytes. Through this mechanism, platelets can form a cellular bridge which can effectively substitute for the loss of L-selectin on memory cell subsets.
Geranyl 6-O-α-L-Arabinopyranosyl-β-D-glucopyranoside Isolated as an Aroma Precursor from Leaves of a Green Tea Cultivar (1996)

A new glycosidic aroma precursor was isolated from green tea leaves (Camellia sinensis var. sinensis cv. Yabukita) along with the known primeverosides of cis-linalool 3,6-oxide, linalool and geraniol. These glycosides were separated by chromatographic isolation on Amberlite XAD-2, ODS flash chromatography, and finally HPLC. The chemical structure of the new unknown glycoside was confirmed as geranyl 6-O-alpha-L-arabinopyranosyl-beta-D-glucopyranoside (geranyl beta-vicianoside) by spectrometric analyses and by an enzymatic hydrolysis with glycosidase followed by GC-MS and HPLC analyses. Moreover the vicianoside was hydrolyzed with acetone powder obtained from fresh tea leaves to generate the same compounds, suggesting this glycoside to be a tea aroma precursor.
HUMAN CARBONIC ANHYDRASES AND CARBONIC ANHYDRASE DEFICIENCIES (1995)

Carbonic anhydrases (CAs I-VII) are products of a gene family that encodes seven isozymes and several homologous, CA- related proteins. All seven isozymes have been cloned, sequenced, and mapped, and the intron-exon organization of five genes established. They differ in subcellular localizations, being cytoplasmic (CA I, II, III, and VII), GPI-anchored to plasma membranes of specialized epithelial and endothelial cells (CA IV), in mitochondria (CA V), or in salivary secretions (CA VI). They also differ in kinetic properties, susceptibility to inhibitors, and tissue-specific distribution. Structural and kinetic studies of recombinant natural and mutant CAs have greatly increased our understanding of the structural requirements for catalysis. Studies of the effects of CA inhibitors over many years have implicated CAs in a variety of physiological processes. Analyses of human and animal CA deficiencies provide unique opportunities to understand the individual contributions of different isozymes to these processes.
Complete genome of the onion pathogen Enterobacter cloacae EcWSU1 (2011)

Previous studies have shown that the members of the Enterobacter cloacae complex are difficult to differentiate with biochemical tests and in phylogenetic studies using multilocus sequence analysis, strains of the same species separate into numerous clusters. There are only a few complete E. cloacae genome sequences and very little knowledge about the mechanism of pathogenesis of E. cloacae on plants and humans. Enterobacter cloacae EcWSU1 causes Enterobacter bulb decay in stored onions (Allium cepa). The EcWSU1 genome consists of a 4,734,438 bp chromosome and a mega-plasmid of 63,653 bp. The chromosome has 4,632 protein coding regions, 83 tRNA sequences, and 8 rRNA operons.
Human and murine anti-DNA antibodies induce the production of anti-idiotypic antibodies with autoantigen-binding properties (epibodies) through immune-network interactions. (1990)

To examine the potential role of immune-network interactions in the production of lupus autoantibodies, normal NZW rabbit antibody responses were analyzed after immunization with one of the following Ig preparations: human lupus serum anti-dsDNA antibodies, human lupus serum anti-ssDNA antibodies, a mixture of human lupus serum anti-dsDNA and anti-ssDNA antibodies, the MRL-lpr/lpr anti-dsDNA mAb H241, and the MRL-lpr/lpr anti-ssDNA mAb H130. Four of five rabbits produced Ig typical of lupus autoantibodies: individual rabbit Ig cross-reacted with multiple autoantigens including nucleic acids, cardiolipin, SmRNP, glomerular extract, laminin, and exogenous Ag. Rabbit anti-Id against human anti-dsDNA antibodies were highly specific for dsDNA. Notably, in each serum the autoantibody activity was confined to the anti-Id Ig fraction. A similar spontaneously occurring Id-anti-Id interaction was also found between anti-ssDNA and anti-dsDNA antibodies isolated from an individual lupus patient. These results indicate that lupus autoantibodies which share Ag binding properties with pathogenic Ig, including both cross-reactive and anti-dsDNA antibodies, can induce the production of Ig with similar autoantigen binding properties through immune-network interactions. This phenomenon, if unregulated, could lead to the amplification of pathogenic autoantibody production in individuals with systemic lupus.
Solution Structure of the Squash Trypsin Inhibitor MCoTI-II. A New Family for Cyclic Knottins, (2001)

The "knottin" fold is a stable cysteine-rich scaffold, in which one disulfide crosses the macrocycle made by two other disulfides and the connecting backbone segments. This scaffold is found in several protein families with no evolutionary relationships. In the past few years, several homologous peptides from the Rubiaceae and Violaceae families were shown to define a new structural family based on macrocyclic knottin fold. We recently isolated from Momordica cochinchinensis seeds the first known macrocyclic squash trypsin inhibitors. These compounds are the first members of a new family of cyclic knottins. In this paper, we present NMR structural studies of one of them, MCoTI-II, and of a beta-Asp rearranged form, MCoTI-IIb. Both compounds display similar and well-defined conformations. These cyclic squash inhibitors share a similar conformation with noncyclic squash inhibitors such as CPTI-II, and it is postulated that the main effect of the cyclization is a reduced sensitivity to exo-proteases. On the contrary, clear differences were detected with the three-dimensional structures of other known cyclic knottins, i.e., kalata B1 or circulin A. The two-disulfide cystine-stabilized beta-sheet motif [Heitz et al. (1999) Biochemistry 38, 10615-10625] is conserved in the two families, whereas in the C-to-N linker, one disulfide bridge and one loop are differently located. The molecular surface of MCoTI-II is almost entirely charged in contrast to circulin A that displays a well-marked amphiphilic character. These differences might explain why the isolated macrocyclic squash inhibitors from M. cochinchinensis display no significant antibacterial activity, whereas circulins and kalata B1 do.
H. C. Brown (1979)

Abstract “As mentioned below, I had rough times and frustating moments during my first year at Purdue. However, nothing has been more frustating than the fact that the Nobel Committee has kept mistreating H. C. Brown. While there can be chemists who are worthy of all prizes except Nobel Prize, H. C. Brown is definitely not one of them.”
Organic Reactions with Boron Fluoride. XI. The Condensation of Propylene with m-and p-Hydroxybenzoic Acids (1935)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganic Reactions with Boron Fluoride. XI. The Condensation of Propylene with m-and p-Hydroxybenzoic AcidsW. J. Croxall, F. J. Sowa, and J. A. NieuwlandCite this: J. Am. Chem. Soc. 1935, 57, 9, 1549–1551Publication Date (Print):September 1, 1935Publication History Published online1 May 2002Published inissue 1 September 1935https://pubs.acs.org/doi/10.1021/ja01312a012https://doi.org/10.1021/ja01312a012research-articleACS PublicationsRequest reuse permissionsArticle Views86Altmetric-Citations6LEARN 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
Identificación microbiológica de marchitez vascular en col china (Brassica campestris L. var pekinensis) en Cogua, Colombia (2010)

La col china (Brassica campestris L. var pekinensis) es una hortaliza de origen asiático apreciada en todos los continentes por su valor nutricional y propiedades medicinales. Reportes de productores de todo el país han manifestado que hay pérdidas económicas en este cultivo al parecer originadas por enfermedades bacterianas; una de ellas es la marchitez bacteriana, que disminuye el tiempo de viabilidad del producto, también su continuidad en el mercado y, en consecuencia, la no utilización del mismo por parte del consumidor. Cultivadores en Cogua, Colombia reportan pérdidas de un 80% en su producción a causa de esta patología. La principal manifestación es la presencia de lesiones húmedas y marchitez en los bordes externos de las hojas.El objetivo de este proyecto fue la identificación microbiológica de los posibles patógenos de la marchitez bacteriana en un cultivo de col china en Cogua, Colombia. La metodología utilizada incluyó el análisis de los microorganismos presentes en plantas sanas y enfermas, el aislamiento de bacterias de las lesiones vasculares, la elaboración de pruebas de patogenicidad y la identificación fenotípica del patógeno. Los resultados permitieron concluir que el microorganismo patógeno que ocasionaba marchitez bacteriana en los cultivos de col china en Cogua, Colombia era Xanthomonas axonopodis. La identificación de patógenos en plantas de interés económico permite tomar medidas más eficientes referentes a las buenas prácticas agrícolas para manejar enfermedades en plantas y disminuir las pérdidas de producción.
A Soluble Receptor Decoy Protects Rats against Anthrax Lethal Toxin Challenge (2005)

Successful postexposure treatment for inhalation anthrax is thought to include neutralization of anthrax toxin. The soluble anthrax toxin receptor/tumor endothelial marker 8 and capillary morphogenesis protein 2 (sATR/TEM8 and sCMG2, respectively) receptor decoys bind to anthrax toxin protective antigen (PA) and compete with cellular receptors for binding. Here, we show that, in a tissue-culture model of intoxication, sCMG2 is a 11.4-fold more potent antitoxin than sATR/TEM8 and that this increased activity corresponds to an approximately 1000-fold higher PA-binding affinity. Stoichiometric concentrations of sCMG2 protect rats against lethal toxin challenge, making sCMG2 one of the most effective anthrax antitoxins described to date.
Centralized path planning for multiple robots: Optimal decoupling into sequential plans (2009)

We develop an algorithm to decouple a multi-robot path planning problem into subproblems whose solutions can be executed sequentially. Given an external path planner for general configuration spaces, our algorithm finds an execution sequence that minimizes the dimension of the highest-dimensional subproblem over all possible execution sequences. If the external planner is complete (at least up to this minimum dimension), then our algorithm is complete because it invokes the external planner only for spaces of dimension at most this minimum. Our algorithm can decouple and solve path planning problems with many robots, even with incomplete external planners. We show scenarios involving 16 to 65 robots, where our algorithm solves planning problems of dimension 32 to 130 using a PRM planner for at most eight dimensions. 1
Liver transplantation: Issues for the next 20 years (2009)

The growing numbers of potential transplant recipients on waiting lists is increasingly disproportionate to the supply of cadaveric donor organs. The hope for the next 20 years is that supply will satisfy demand. This requires both a reduction in indications for the procedure and an increase in the transplants performed. A multi-pronged approach is needed to increase cadaveric organ donation, generating enthusiasm for donation among both the general public and hospital staff. Accurate assessment of marginal grafts with stringent criteria known to predict graft function will diminish wastage of organs. Methods of rehabilitating marginal grafts during extracorporeal perfusion will increase organ availability. Supply of non-heart beating donors can be greatly expanded and protocols developed with ethical consent to optimize their initial function despite warm ischemia. Splitting livers that fulfill selection criteria, thus providing for two recipients, should be universally applied with acceptable incentives to those units who do not directly benefit. A proportion of recipients, though not those transplanted for autoimmune disease, will be spared the side-effects of immunosuppression thanks to immune tolerance. Protocols for close monitoring of those patients for rejection during treatment withdrawal must be carefully observed. In addition to gene therapy, it is highly likely that hepatocyte transplantation will replace orthotopic grafting in patients without cirrhosis, especially for inherited metabolic diseases. It is much more difficult to envisage that heterologous stem cell transplantation or xenotransplantation will have clinical impact in the next 20 years, although research in those areas has obvious long-term potential.
Giant voltage modulation of magnetic anisotropy in strained heavy metal/magnet/insulator heterostructures (2015)

Ab initio electronic structure calculations reveal that epitaxial strain has a dramatic effect on the voltage-controlled magnetic anisotropy (VCMA) in Ta/FeCo/MgO junctions. Strain can give rise to a wide range of novel VCMA behaviors where the MA can change from a $\ensuremath{\vee}$- to a $\ensuremath{\wedge}$-shape electric-field dependence with giant VCMA coefficients which are asymmetric under voltage reversal. The underlying mechanism is the interplay of the strain- and electric-field-induced changes in the spin-orbit coupled $d$ states at the interfaces and the strain-induced modification of the dielectric constant of MgO. These findings demonstrate the feasibility of highly sensitive VCMA through strain engineering, which may provide a viable avenue for tailoring magnetoelectric properties for spintronic applications.