gebhart/patrepeval huggingface dataset:
Human-engineered monoclonal antibodies retain full specific binding activity by preserving non-CDR complementarity-modulating residues (1994)

Humanization of murine monoclonal antibodies for human therapy has commonly been achieved by complementarity-determining region (CDR) grafting, in which murine CDR loops are grafted onto human framework regions. Difficulties with that method have revealed the importance of certain framework residues in determining both the 3-D structure of CDR loops and the overall affinity of the molecule for its specific ligand. In the general model of structure-function relationships presented here, each amino acid position in the variable region is classified according to the benefit of achieving a more human-like antibody versus the risk of decreasing or abolishing specific binding affinity. Substitutions of human residues at low-risk positions (exposed to solvent but not contributing to antigen binding or antibody structure) are likely to decrease immunogenicity with little or no effect on binding affinity. Changes at high-risk positions (directly involved in antigen binding, CDR stabilization or internal packing) are avoided to preserve the biological activity of the antibody. Moderate-risk changes are made with caution. This model has been tested experimentally using H65, an anti-CD5 murine monoclonal antibody, whose binding activity had been greatly reduced by two previous attempts at humanization by conventional CDR grafting. The new 'human-engineered' H65 antibody containing 20 low-risk human consensus substitutions (expressed as either IgG or Fab) retains the full binding avidity of parental murine and chimeric H65 antibodies. A human-engineered antibody with an additional 14 moderate-risk substitutions has unexpectedly enhanced avidity (3- to 7-fold). This method is generally applicable to the design of other human-engineered antibodies with therapeutic potential.
A Theoretical Study on C−COOH Homolytic Bond Dissociation Enthalpies (2010)

The knowledge of C-COOH homolytic bond dissociation enthalpies (BDEs) is of great importance in understanding various chemical and biochemical processes involving the decarboxylation reaction. In the present study, the density functional theory (DFT method), B3P86/6-311++G(2df,2p)//B3LYP/6-31+G(d), is found to be reliable to predict the C-COOH BDE of various structurally unrelated carboxylic acids. The mean absolute deviation (MAD) and root-mean-square deviation (rmsd) of this optimal method are equal to 2.0 and 2.5 kcal/mol, respectively. With the authorized theoretical protocol in hand, an extensive C-COOH BDE scale containing over 100 carboxylic acids has been established. The availability of this body of data enabled a detailed investigation of remote substituent effect on four types of carboxylic acids, including para-substituted benzoic acid, beta-substituted cis-propenoic acid, beta-substituted trans-propenoic acid, and substituted propiolic acid. Also with the C-COOH BDE data obtained in this work, an excellent linear relationship has been found between the C-COOH BDE of carboxylic acids and the C-H BDE of their hydrocarbon analogues. After comparing the energy barrier of the Pd-catalyzed decarboxylation reaction (DeltaG(decarboxylation)++) with the related C-COOH BDE, a negative correlation between the DeltaG(decarboxylation)++ and the C-COOH BDE was found.
Etiology and pathophysiology of chronic transplant dysfunction (2000)

Chronic transplant dysfunction (CTD) is the predominant cause of late graft failure. The common histopathological feature in all transplanted organs is intimal hyperplasia accompanied by organ specific lesions. The knowledge about CTD is incomplete, and there is no therapy to prevent or treat it. This review describes the current knowledge on the etiology of CTD, with emphasis on kidney transplants, and postulates a pathophysiologic route through which CTD may develop.
A late B lymphocyte action in dysfunctional tissue repair following kidney injury and transplantation (2019)

The mechanisms initiating late immune responses to an allograft are poorly understood. Here we show, via transcriptome analysis of serial protocol biopsies from kidney transplants, that the initial responses to kidney injury correlate with a late B lymphocyte signature relating to renal dysfunction and fibrosis. With a potential link between dysfunctional repair and immunoreactivity, we investigate the immunological consequences of dysfunctional repair examining chronic disease in mouse kidneys 18 months after a bilateral ischemia/reperfusion injury event. In the absence of foreign antigens, a sustained immune response involving both innate and adaptive immune systems accompanies a transition to chronic kidney damage. At late stages, B lymphocytes exhibite an antigen-driven proliferation, selection and maturation into broadly-reacting antibody-secreting cells. These findings reveal a previously unappreciated role for dysfunctional tissue repair in local immunomodulation that may have particular relevance to transplant-associated immunobiology.
Metabolism of toluene and xylenes by Pseudomonas (putida (arvilla) mt-2: evidence for a new function of the TOL plasmid (1975)

Pseudomonas putida (arvilla) mt-2 carries genes for the catabolism of toluene, m-xylene, and p-xylene on a transmissible plasmid, TOL. These compounds are degraded by oxidation of one of the methyl substituents via the corresponding alcohols and aldehydes to benzoate and m- and p-toluates, respectively, which are then further metabolised by the meta pathway, also coded for by the TOL plasmid. The specificities of the benzyl alcohol dehydrogenase and the benzaldehyde dehydrogenase for their three respective substrates are independent of the carbon source used for growth, suggesting that a single set of nonspecific enzymes is responsible for the dissimilation of the breakdown products of toluene and m- and p-xylene. Benzyl alcohol dehydrogenase and benzaldehyde dehydrogenase are coincidently and possible coordinately induced by toluene and the xylenes, and by the corresponding alcohols and aldehydes. They are not induced in cells grown on m-toluate but catechol 2,3-oxygenase can be induced by m-xylene.
Human Colon Carcinoma Ki- ras 2 Oncogene and Its Corresponding Proto-Oncogene (1984)

We isolated cDNA clones corresponding to the normal human Ki-ras2 gene and to the transforming allele of the Ki-ras2 gene present in the human colon carcinoma cell line SW480. These two cDNAs encode p21 proteins which differ only at the amino acid at position 12. The normal cDNA encodes a glycine at this position, and the transforming allele encodes a valine. Expression of these cDNAs indicates that this amino acid 12 alteration confers oncogenic activity on the mutated gene. Analysis of the relationship of the cDNAs and Kirsten sarcoma virus ras gene to a genomic clone allowed us to identify two alternative 3' coding exons for the Ki-ras2 gene, suggesting that the Ki-ras2 gene encodes two p21 proteins which differ at their carboxy termini. Our data also show that only one of the p21s is necessary to convert cells to a tumorigenic phenotype.
Inhibition of cardiac guanylate cyclase by doxorubicin and some of its analogs: possible relationship to cardiotoxicity. (1982)

The anthracycline antibiotic doxorubicin induces a variety of cardiotoxic effects. We have recently demonstrated that this drug also causes a selective inhibition of rat and human cardiac guanylate cyclase activity in vitro. In the present study, we examined the effect of 30 analogs of doxorubicin on cardiac guanylate cyclase activity. Structural modifications of these anthracycline antibiotics were found to alter their effect on rat cardiac guanylate cyclase activity, N-Substitutions on the sugar moiety eliminated the inhibitory action observed with the parent compound. Long-chain hydrocarbon substitutions in place of the methylketone side chain had a similar effect. Removal or substitution of the C-4 methoxy group had little or no effect on the ability of these compounds to modify guanylate cyclase activity. Substitutions of the C-9 side chain by a hydrazone derivative resulted in compounds that stimulated the enzyme. All of the anthracenedione derivatives were inhibitory. A comparison of the inhibitory effect of some of these anthracycline derivatives on in vitro cardiac guanylate cyclase activity with their cardiotoxic potency suggests a possible relationship between these two parameters.
Molecules and structures involved in the adhesion of natural killer cells to vascular endothelium. (1991)

The present study was designed to define molecules and structures involved in the interaction of natural killer (NK) cells with the vascular endothelium in vitro. Resting and interleukin 2 (IL-2)-activated NK cells were studied for their capacity to adhere to resting and IL-1-treated human umbilical vein endothelial cells (EC). In the absence of stimuli, NK cells showed appreciable adhesion to EC, with levels of binding intermediate between polymorphs and monocytes. The binding ability was increased by pretreatment of NK cells with IL-2. Using the appropriate monoclonal antibody, the beta 2 leukocyte integrin CD18/CD11a was identified as the major adhesion pathway of NK cells to unstimulated EC. Activation of EC with IL-1 increased the binding of NK cells. In addition to the CD18-CD11a/intercellular adhesion molecule pathway, the interaction of resting or IL-2-activated NK cells to IL-1-activated EC involved the VLA-4 (alpha 4 beta 1)-vascular cell adhesion molecule 1 receptor/counter-receptor pair. No evidence for appreciable involvement of endothelial-leukocyte adhesion molecule was obtained. Often, NK cells interacted either with the culture substrate or with the EC surface via dot-shaped adhesion structures (podosomes) protruding from the ventral surface and consisting of a core of F-actin surrounded by a ring of vinculin and talin. The identification of molecules and microanatomical structures involved in the interaction of NK cells with EC may provide a better understanding of the regulation of NK cell recruitment from blood, their extravasation, and their migration to tissues.
Comprehensive Cell Surface Protein Profiling Identifies Specific Markers of Human Naive and Primed Pluripotent States (2017)

Human pluripotent stem cells (PSCs) exist in naive and primed states and provide important models to investigate the earliest stages of human development. Naive cells can be obtained through primed-to-naive resetting, but there are no reliable methods to prospectively isolate unmodified naive cells during this process. Here we report comprehensive profiling of cell surface proteins by flow cytometry in naive and primed human PSCs. Several naive-specific, but not primed-specific, proteins were also expressed by pluripotent cells in the human preimplantation embryo. The upregulation of naive-specific cell surface proteins during primed-to-naive resetting enabled the isolation and characterization of live naive cells and intermediate cell populations. This analysis revealed distinct transcriptional and X chromosome inactivation changes associated with the early and late stages of naive cell formation. Thus, identification of state-specific proteins provides a robust set of molecular markers to define the human PSC state and allows new insights into the molecular events leading to naive cell resetting.
Cutting Edge: Proinflammatory and Th2 Cytokines Synergize to Induce Thymic Stromal Lymphopoietin Production by Human Skin Keratinocytes (2007)

Thymic stromal lymphopoietin (TSLP) is an epithelial cell-derived cytokine that strongly activates dendritic cells (DC) and can initiate allergic inflammation. The factors inducing the production of human TSLP are not known. In this study, we show that proinflammatory (TNF-alpha or IL-1alpha) and Th2 (IL-4 or IL-13) cytokines synergized to induce the production of TSLP in human skin explants. TSLP production in situ was restricted to epidermal keratinocytes of the suprabasal layer. TSLP production could not be inhibited by factors regulating Th2 inflammation, such as IL-10, TGF-beta, or IFN-gamma. Cytokine-treated skin culture supernatants induced the maturation of blood CD11c(+) DC in a TSLP-dependent manner. Our data provide the first evidence of TSLP induction and subsequent DC activation in human skin. Blocking TSLP-inducing cytokines could represent a novel strategy for the treatment of allergic diseases.
Bit rates in audio source coding (1992)

The goal is to introduce and solve the audio coding optimization problem. Psychoacoustic results such as masking and excitation pattern models are combined with results from rate distortion theory to formulate the audio coding optimization problem. The solution of the audio optimization problem is a masked error spectrum, prescribing how quantization noise must be distributed over the audio spectrum to obtain a minimal bit rate and an inaudible coding errors. This result cannot only be used to estimate performance bounds, but can also be directly applied in audio coding systems. Subband coding applications to magnetic recording and transmission are discussed in some detail. Performance bounds for this type of subband coding system are derived.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Interleukin-13 in asthma (2003)

Some time ago, the Th2 cytokine, interleukin (IL)-13, was identified as a critical regulator of the allergic response. Initial studies in animal models of disease provided compelling evidence that IL-13, independent from other Th2 cytokines, was necessary and sufficient to induce all features of allergic asthma. This contention was supported in human disease when strong associations between IL-13 levels and genetic polymorphisms in the IL-13 gene and disease correlates were found. With the preponderance of evidence continuing to support the importance of IL-13 in allergic disorders, attention is now turned towards understanding the mechanisms by which this cytokine may mediate the pathophysiologic features of allergic disease. The emerging paradigm is that IL-13 induces features of the allergic response via its actions on epithelial and smooth muscle cells not through traditional effector pathways involving eosinophils and IgE-mediated events. In light of recent developments, this review will explore our current understanding of the role of IL-13 in the pathogenesis of allergy and asthma with a particular focus on new insights into the mechanisms by which IL-13 induces the features of asthma.
Human recombinant soluble guanylyl cyclase: Expression, purification, and regulation (2000)

The alpha1- and beta1-subunits of human soluble guanylate cyclase (sGC) were coexpressed in the Sf9 cells/baculovirus system. In addition to the native enzyme, constructs with hexahistidine tag at the amino and carboxyl termini of each subunit were coexpressed. This permitted the rapid and efficient purification of active recombinant enzyme on a nickel-affinity column. The enzyme has one heme per heterodimer and was readily activated with the NO donor sodium nitroprusside or 3-(5'-hydroxymethyl-2'furyl)-1-benzyl-indazole (YC-1). Sodium nitroprusside and YC-1 treatment potentiated each other in combination and demonstrated a remarkable 2,200-fold stimulation of the human recombinant sGC. The effects were inhibited with 1H-(1,2, 4)oxadiazole(4,3-a)quinoxalin-1one (ODQ). The kinetics of the recombinant enzyme with respect to GTP was examined. The products of the reaction, cGMP and pyrophosphate, inhibited the enzyme. The extent of inhibition by cGMP depended on the activation state of the enzyme, whereas inhibition by pyrophosphate was not affected by the enzyme state. Both reaction products displayed independent binding and cooperativity with respect to enzyme inhibition. The expression of large quantities of active enzyme will facilitate structural characterization of the protein.
Autoinducer 2 Controls Biofilm Formation in Escherichia coli through a Novel Motility Quorum-Sensing Regulator (MqsR, B3022) (2005)

The cross-species bacterial communication signal autoinducer 2 (AI-2), produced by the purified enzymes Pfs (nucleosidase) and LuxS (terminal synthase) from S-adenosylhomocysteine, directly increased Escherichia coli biofilm mass 30-fold. Continuous-flow cells coupled with confocal microscopy corroborated these results by showing the addition of AI-2 significantly increased both biofilm mass and thickness and reduced the interstitial space between microcolonies. As expected, the addition of AI-2 to cells which lack the ability to transport AI-2 (lsr null mutant) failed to stimulate biofilm formation. Since the addition of AI-2 increased cell motility through enhanced transcription of five motility genes, we propose that AI-2 stimulates biofilm formation and alters its architecture by stimulating flagellar motion and motility. It was also found that the uncharacterized protein B3022 regulates this AI-2-mediated motility and biofilm phenotype through the two-component motility regulatory system QseBC. Deletion of b3022 abolished motility, which was restored by expressing b3022 in trans. Deletion of b3022 also decreased biofilm formation significantly, relative to the wild-type strain in three media (46 to 74%) in 96-well plates, as well as decreased biomass (8-fold) and substratum coverage (19-fold) in continuous-flow cells with minimal medium (growth rate not altered and biofilm restored by expressing b3022 in trans). Deleting b3022 changed the wild-type biofilm architecture from a thick (54-mum) complex structure to one that contained only a few microcolonies. B3022 positively regulates expression of qseBC, flhD, fliA, and motA, since deleting b3022 decreased their transcription by 61-, 25-, 2.4-, and 18-fold, respectively. Transcriptome analysis also revealed that B3022 induces crl (26-fold) and flhCD (8- to 27-fold). Adding AI-2 (6.4 muM) increased biofilm formation of wild-type K-12 MG1655 but not that of the isogenic b3022, qseBC, fliA, and motA mutants. Adding AI-2 also increased motA transcription for the wild-type strain but did not stimulate motA transcription for the b3022 and qseB mutants. Together, these results indicate AI-2 induces biofilm formation in E. coli through B3022, which then regulates QseBC and motility; hence, b3022 has been renamed the motility quorum-sensing regulator gene (the mqsR gene).
Schwann cell grafting into the retina of the dystrophic RCS rat limits functional deterioration. Royal College of Surgeons. (2000)

Schwann cells injected into the subretinal space limit functional deterioration and prolong photoreceptor survival. It is suggested that they act by local release of growth factors that either support photoreceptors directly and/or stimulate phagocytosis in RPE cells.
Preface (2007)

After ten years of regular journal fare, this issue of LT is special. To commemorate the journal's decennial, it collects the responses to an invitation (or, in some cases, request) from LT 's Editorial Board to reflect on where typology stands and where it is, or ought to be, going. These were the questions we asked two dozen or so prospective reflectors – ALT members all, and connected with LT in one way or another, but sampled for expected diversity rather than unity in how they would be answering our questions (and free rein was given anyhow as regards style): Has headway been made in linguistic typology or have we been going round in circles? What has most memorably been found out in typology, and what is there yet to discover (the lexicon, semantics, phonology, …)? What state is typology in now, intellectually and academically, and where will it go in future? What indeed is typology and what is not? What is, or ought to be, special about the aims, methods, and results of typology, in relation to other types of linguistic pursuits – such as: grammar and dictionary writing; field linguistics; historical linguistics, deep and shallow time; sociolinguistics; psycho- and neurolinguistics; language acquisition/learning and teaching; computational linguistics; well, “theoretical” linguistics; … ? How does, or should, typology interact with the world at large, inhabited among others by cognitive/social/physical/evolutionary anthropologists, population scientists, archaeologists, cognitive neuroscientists, statisticians, language learners, school children, the reading and/or viewing public? How well is LT serving the field as a forum? Is LT 's remit well- or ill-defined, cogent or futile? Is LT a faithful or distorting mirror of scholarly goings-on in typology? Does LT breed complacency and stagnation or provoke thought and stir into action? Published in LT , does work have the resonance it ought to be getting?
Thymine dimers bend DNA. (1988)

A 32-base-pair DNA fragment containing a thymine photodimer was constructed and ligated head-to-tail to obtain multimers of this sequence in which thymine dimers were in phase with the helix screw axis (approximately equal to 3 turns apart). The ligation products were analyzed by one- and two-dimensional gel electrophoresis and quantitative electron microscopy. These analyses show that the thymine photodimer introduces a bend of approximately equal to 30 degrees in DNA, which causes anomalously slow migration of DNA fragments in polyacrylamide gels and facilitates the formation of small covalent circles. Repair of thymine dimers by DNA photolyase abolishes the anomalous migration.
New Sedative and Hypotensive Phenylpiperazine Amides (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew Sedative and Hypotensive Phenylpiperazine AmidesSHIN HAYAO and R. N. SCHUTCite this: J. Org. Chem. 1961, 26, 9, 3414–3419Publication Date (Print):September 1, 1961Publication History Published online1 May 2002Published inissue 1 September 1961https://pubs.acs.org/doi/10.1021/jo01067a095https://doi.org/10.1021/jo01067a095research-articleACS PublicationsRequest reuse permissionsArticle Views97Altmetric-Citations8LEARN 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