gebhart/patrepeval huggingface dataset:
Ig Constant Region Effects on Variable Region Structure and Function (2016)

The adaptive humoral immune response is responsible for the generation of antimicrobial proteins known as immunoglobulin molecules or antibodies. Immunoglobulins provide a defense system against pathogenic microbes and toxins by targeting them for removal and/or destruction. Historically, antibodies have been thought to be composed of distinct structural domains known as the variable and constant regions that are responsible for antigen binding and mediating effector functions such as opsonization and complement activation, respectively. These domains were thought to be structurally and functionally independent. Recent work has revealed however, that in some families of antibodies, the two regions can influence each other. We will discuss the body of work that led to these observations, as well as the mechanisms that have been proposed to explain how these two different antibody regions may interact in the function of antigen binding.
Computer program for the analysis and the management of DNA sequences (1982)

A program package is described for the management and the analysis of DNA sequence data. The programs - with the exception of a few Fortran routines - are written in the programming language APL. They are best used interactively although batch processing is possible. The package has been in constant use for about 3 years and contains programs for most of the routine problems presently found in a DNA sequencing laboratory.
Hormonotoxins: abrogation of ribosome inactivating property of gelonin in the disulfide linked ovine luteinizing hormone-gelonin conjugates. (1991)

In order to synthesize a bioeffective hormonotoxin for selective targeting to specific cells in the gonads, gelonin, a single chain ribosome-inactivating protein obtained from an Indian plant called Gelonium multiflorum was covalently linked to ovine luteinizing hormone (oLH) by a disulfide bond. Ovine LH-S-S-gelonin conjugates of different molar ratios were subjected to determine the ribosome-inactivating property in a cell-free translation assay using rabbit reticulocyte lysate system. A single amino group modification with N-succinimidyl-3-(2-pyridyldithio)propionate resulted in a loss of 90% protein synthesis inhibition activity. Upon conjugation of gelonin to oLH, the activity was further inhibited ranging from 2.5-6.4%. A 1:1 to 1:1.5 molar ratio (oLH-S-S-gelonin) conjugates showed 2.5-4.6% activity while 1:2.8 to 1:2.2 molar ratio exhibited 5.5-6.4% inhibition ability.
Evidence of eosinophil granule major basic protein in human placenta. (1989)

A protein immunochemically related to the eosinophil granule major basic protein (gMBP) is found in increased concentration in the plasma of pregnant women and has been localized to placental trophoblasts by immunofluorescence. Pregnancy MBP (pMBP) is indistinguishable from gMBP in its reactivity with polyclonal antisera and a panel of 14 mouse mAbs. We report the purification of pMBP from human placenta by: (a) affinity chromatography over mAb immobilized on Sepharose, (b) gel filtration in 6 M guanidine.HCl buffer, and (c) reversed-phase HPLC. Purified pMBP and gMBP are biochemically indistinguishable in that both: (a) bind to DNA, (b) polymerize and bind to carrier proteins via disulfide linkages, (c) have a molecular weight of 14,000, (d) have isoelectric points greater than 10.6, (e) comigrate in two-dimensional gels, (f) coelute during reversed-phase HPLC on C18 columns, (g) have identical peptide maps after three different digestions, and (h) have partial amino acid sequence identity. This physicochemical identity has important implications as to the role of pMBP in human placentation.
Conjugate Vaccines against Group BStreptococcusTypes IV and VII (2002)

Although rarely encountered, group B Streptococcus (GBS) types IV and VII have been isolated from infants and adults with invasive disease. This study was designed to determine the immunogenicity and efficacy in animals of conjugate vaccines prepared with GBS types IV and VII capsular polysaccharide (CPS). Despite the striking similarities in structure of these 2 carbohydrate antigens, high-titer rabbit antiserum to each conjugate vaccine was serotype specific. Active vaccination of female mice with the conjugate vaccines induced type-specific IgG and resulted in survival of >90% of newborn pups challenged with viable GBS of homologous serotype. If needed, types IV and VII CPS conjugate vaccines of the design described can be added to the formulation of a multivalent GBS vaccine.
Structural requirements for differentiation-induction and growth-inhibition of mouse erythroleukemia cells by isoflavones. (1995)

Isoflavones are natural plant phytoestrogens which have been shown to have anticancer proliferation, differentiation and chemopreventive effects. In order to determine structure-function requirements, we compared the effects of several isoflavone derivatives and one flavone on mouse erythroleukemia (MEL) cell growth and differentiation. All chemicals tested are closely related in structure to genistein (4',5,7-trihydroxyisoflavone), a known differentiation inducer and tyrosine protein kinase inhibitor. Genistein, daidzein (4',7-dihydroxyisoflavone) and genistin (7-glucoside of genistein) induced differentiation of MEL cells based on benzidine staining. Biochanin A (5,7-dihydroxy-4'-metho-xyisoflavone) and apigenin (4',5,7-trihydroxyflavone) had no differentiation inducing effect. The potency of these chemicals on cell growth inhibition was apigenin > genistein > genistin > biochanin A > daidzein. These results suggest that the isoflavone structure and 4'-hydroxyl group are essential for the differentiation induction effect, whereas trihydroxyl derivatives are good growth inhibitors. Daidzein is a potent differentiation inducer with the least cytotoxic effect.
Comparative Effectiveness and Cost-Effectiveness of Screening Colonoscopy vs. Sigmoidoscopy and Alternative Strategies (2012)

Screening colonoscopy may be cost-effective compared with FIT and sigmoidoscopy, depending on the relative rates of screening uptake and adherence and the protective benefit of colonoscopy in the proximal colon. Colonoscopy's cost-effectiveness compared with sigmoidoscopy is contingent on the ability to deliver ~50% protection against CRC in the proximal colon.
Antifungal Protein PAF Severely Affects the Integrity of the Plasma Membrane ofAspergillus nidulansand Induces an Apoptosis-Like Phenotype (2005)

The small, basic, and cysteine-rich antifungal protein PAF is abundantly secreted into the supernatant by the beta-lactam producer Penicillium chrysogenum. PAF inhibits the growth of various important plant and zoopathogenic filamentous fungi. Previous studies revealed the active internalization of the antifungal protein and the induction of multifactorial detrimental effects, which finally resulted in morphological changes and growth inhibition in target fungi. In the present study, we offer detailed insights into the mechanism of action of PAF and give evidence for the induction of a programmed cell death-like phenotype. We proved the hyperpolarization of the plasma membrane in PAF-treated Aspergillus nidulans hyphae by using the aminonaphtylethenylpyridinium dye di-8-ANEPPS. The exposure of phosphatidylserine on the surface of A. nidulans protoplasts by Annexin V staining and the detection of DNA strand breaks by TUNEL (terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling) gave evidence for a PAF-induced apoptotic-like mechanism in A. nidulans. The localization of reactive oxygen species (ROS) by dichlorodihydrofluorescein diacetate and the abnormal cellular ultrastructure analyzed by transmission electron microscopy suggested that ROS-elicited membrane damage and the disintegration of mitochondria played a major role in the cytotoxicity of PAF. Finally, the reduced PAF sensitivity of A. nidulans strain FGSC1053, which carries a dominant-interfering mutation in fadA, supported our assumption that G-protein signaling was involved in PAF-mediated toxicity.
Regulatory B cell production of IL-10 inhibits lymphoma depletion during CD20 immunotherapy in mice (2011)

Current therapies for non-Hodgkin lymphoma commonly include CD20 mAb to deplete tumor cells. However, the response is not durable in a substantial proportion of patients. Herein, we report our studies in mice testing the hypothesis that heterogeneity in endogenous tissue CD20+ B cell depletion influences in vivo lymphoma therapy. Using highly effective CD20 mAbs that efficiently deplete endogenous mature B cells and homologous CD20+ primary lymphoma cells through monocyte- and antibody-dependent mechanisms, we found that lymphoma depletion and survival were reduced when endogenous host B cells were not depleted, particularly a rare IL-10-producing B cell subset (B10 cells) known to regulate inflammation and autoimmunity. Even small numbers of adoptively transferred B10 cells dramatically suppressed CD20 mAb-mediated lymphoma depletion by inhibiting mAb-mediated monocyte activation and effector function through IL-10-dependent mechanisms. However, the activation of innate effector cells using a TLR3 agonist that did not activate B10 cells overcame the negative regulatory effects of endogenous B10 cells and enhanced lymphoma depletion during CD20 immunotherapy in vivo. Thus, we conclude that endogenous B10 cells are potent negative regulators of innate immunity, with even small numbers of residual B10 cells able to inhibit lymphoma depletion by CD20 mAbs. Consequently, B10 cell removal could provide a way to optimize CD20 mAb-mediated clearance of malignant B cells in patients with non-Hodgkin lymphoma.
Cloning, sequencing, and expression of RecA proteins from three distantly related thermophilic eubacteria. (1994)

Sequences of the recA genes of the highly divergent thermopholic eubacteria Thermus aquaticus (and Thermus thermophilus), Thermotoga maritima, and Aquifex pyrophilus were determined from fragments derived by polymerase chain reaction (PCR) with degenerate primers and from inverse PCR products obtained using unique primers based on the fragment sequences. The source of the PCR products was verified by Southern hybridization. Complete PCR-derived recA genes were cloned into an expression vector regulated by a temperature-sensitive lambda-repressor, and independently derived clones expressing thermostable recA were selected. DNA sequences were verified to be authentic by direct cycle-sequencing of PCR products and/or sequencing of several clones. In contrast to Escherichia coli RecA protein, all the purified thermophilic RecA proteins exhibited single-stranded DNA-dependent ATPase activity optima above 70 degrees C. Phylogenetic analysis of RecA sequences suggested that the thermophilic RecA proteins were at least as different from one another as were Gram-positive organisms, mesophilic Gram-negative organisms, and cyanobacteria. In spite of substantial sequence divergence, interesting characteristics of the thermostable RecA proteins included increased valine content, common amino acid replacements at two highly conserved sites, and an increase in the calculated isoelectric point of approximately a full pH unit.
Centromeric Retroelements and Satellites Interact with Maize Kinetochore Protein CENH3 (2002)

Maize centromeres are composed of CentC tandem repeat arrays, centromeric retrotransposons (CRs), and a variety of other repeats. One particularly well-conserved CR element, CRM, occurs primarily as complete and uninterrupted elements and is interspersed thoroughly with CentC at the light microscopic level. To determine if these major centromeric DNAs are part of the functional centromere/kinetochore complex, we generated antiserum to maize centromeric histone H3 (CENH3). CENH3, a highly conserved protein that replaces histone H3 in centromeres, is thought to recruit many of the proteins required for chromosome movement. CENH3 is present throughout the cell cycle and colocalizes with the kinetochore protein CENPC in meiotic cells. Chromatin immunoprecipitation demonstrates that CentC and CRM interact specifically with CENH3, whereas knob repeats and Tekay retroelements do not. Approximately 38 and 33% of CentC and CRM are precipitated in the chromatin immunoprecipitation assay, consistent with data showing that much, but not all, of CENH3 colocalizes with CentC.
Evidence for the presence of a protease-activated receptor distinct from the thrombin receptor in human keratinocytes. (1995)

Thrombin receptor activation was explored in human epidermal keratinocytes and human dermal fibroblasts, cells that are actively involved in skin tissue repair. The effects of thrombin, trypsin, and the receptor agonist peptides SFLLRN and TFRIFD were assessed in inositolphospholipid hydrolysis and calcium mobilization studies. Thrombin and SFLLRN stimulated fibroblasts in both assays to a similar extent, whereas TFRIFD was less potent. Trypsin demonstrated weak efficacy in these assays in comparison with thrombin. Results in fibroblasts were consistent with human platelet thrombin receptor activation. Keratinocytes, however, exhibited a distinct profile, with trypsin being a far better activator of inositolphospholipid hydrolysis and calcium mobilization than thrombin. Furthermore, SFLLRN was more efficacious than thrombin, whereas no response was observed with TFRIFD. Since our data indicated that keratinocytes possess a trypsin-sensitive receptor, we addressed the possibility that these cells express the human homologue of the newly described murine protease-activated receptor, PAR-2 [Nystedt, S., Emilsson, K., Wahlestedt, C. & Sundelin, J. (1994) Proc. Natl. Acad. Sci. USA 91, 9208-9212]. PAR-2 is activated by nanomolar concentrations of trypsin and possesses the tethered ligand sequence SLIGRL. SLIGRL was found to be equipotent with SFLLRN in activating keratinocyte inositolphospholipid hydrolysis and calcium mobilization. Desensitization studies indicated that SFLLRN, SLIGRL, and trypsin activate a common receptor, PAR-2. Northern blot analyses detected a transcript of PAR-2 in total RNA from keratinocytes but not fibroblasts. Levels of thrombin receptor message were equivalent in the two cell types. Our results indicate that human keratinocytes possess PAR-2, suggesting a potential role for this receptor in tissue repair and/or skin-related disorders.
A novel approach to the identification of T-cell epitopes in Mycobacterium tuberculosis using human T-lymphocyte clones. (1987)

Current approaches to the analysis of antigens involved in the cellular immune response to mycobacterial infection rely on the initial identification and isolation of molecular components using monoclonal antibodies. In order to overcome the constraints of this approach, we have utilized a procedure involving T-cell recognition of antigens fractionated by polyacrylamide gel electrophoresis (SDS-PAGE) and added to proliferation assays after blotting onto nitrocellulose membranes. Analysis of human T-cell responses to Mycobacterium tuberculosis and Mycobacterium bovis BCG by this procedure revealed distinctive patterns of reactivity to different molecular weight components indicative of the selective recognition of immunodominant and species-specific determinants. Human T-cell clones were subsequently derived, and SDS-PAGE immunoblotting was used to identify the antigen recognized by each clone. Three epitopes defined by individual T-cell clones were identified on separate polypeptides with molecular weights 16,000-18,000 (clone P53), 18,000-20,000 (clone P57) and 52,000-55,000 (clone P35). This study demonstrates the potential application of T-cell cloning in conjunction with SDS-PAGE immunoblotting for the dissection and analysis of the cellular immune response to pathogenic agents during human infection.
Microdosimetry and radiocurability: modelling targeted therapy with -emitters (1996)

Tumour control probability (TCP) is a more relevant quantity than the dose distribution in the target volume for estimating the likely efficacy of any type of radiation therapy, be it external beam or targeted using radionuclides. This paper concentrates on a TCP modelling study, for tumour spheres of different radii assuming a uniform uptake of six different emitters (ranging from to or 0.58 to 2.3 MeV in endpoint energy). The dose at varying radii, expressed as a fraction of the equilibrium dose, , was computed by numerical integration of the point-dose kernel over the sphere volume, and shows clearly the effect of electron disequilibrium for small radii and also at the edges of the spheres. These were converted into volume - dose distributions V(D) and then into clonogenic cell numbers, n(D), from which the TCPs for spheres of different radii were computed, for different cumulated activities per unit mass, in megabecquerel hours per gram assuming a clonogenic cell density of and a tumour-cell radiosensitivity of . Using V(D) rather than simply the mean dose decreases the TCP at both large and small tumour radii for a given number of megabecquerel hour per gram. Curves of iso-TCP go through a shallow minimum in megabecquerel hour per gram at a tumour radius approximately equal to the maximum -particle range. The fall in dose at small radii outweighs the reduction in cell number, making it improbable that micrometastases can be eliminated solely by -emitters targeted to the tumour cells. An explicit comparison with external-beam therapy for a fixed number of tumour cells divided into different numbers of spheres further emphasizes the difficulties caused by small tumours in -particle targeted therapy. Alternative strategies to overcome these limitations are briefly discussed.
General Roles of Abscisic and Jasmonic Acids in Gene Activation as a Result of Mechanical Wounding (1992)

Thomas Hildmann, Marcus Ebneth, , , Lothar Willmitzer, , General Roles of Abscisic and Jasmonic Acids in Gene Activation as a Result of Mechanical Wounding, The Plant Cell, Vol. 4, No. 9 (Sep., 1992), pp. 1157-1170
Human poliovirus receptor gene expression and poliovirus tissue tropism in transgenic mice (1992)

Expression of the human poliovirus receptor (PVR) in transgenic mice results in susceptibility to poliovirus infection. In the primate host, poliovirus infection is characterized by restricted tissue tropism. To determine the pattern of poliovirus tissue tropism in PVR transgenic mice, PVR gene expression and susceptibility to poliovirus infection were examined by in situ hybridization. PVR RNA is expressed in transgenic mice at high levels in neurons of the central and peripheral nervous system, developing T lymphocytes in the thymus, epithelial cells of Bowman's capsule and tubules in the kidney, alveolar cells in the lung, and endocrine cells in the adrenal cortex, and it is expressed at low levels in intestine, spleen, and skeletal muscle. After infection, poliovirus replication was detected only in neurons of the brain and spinal cord and in skeletal muscle. These results demonstrated that poliovirus tissue tropism is not governed solely by expression of the PVR gene nor by accessibility of cells to virus. Although transgenic mouse kidney tissue expressed poliovirus binding sites and was not a site of poliovirus replication, when cultivated in vitro, kidney cells developed susceptibility to infection. Identification of the changes in cultured kidney cells that permit poliovirus infection may provide information on the mechanism of poliovirus tissue tropism.
Engineering an Anion-Binding Cavity in Antichymotrypsin Modulates the “Spring-Loaded” Serpin−Protease Interaction (1998)

Expressed in a kinetically trapped folding state, a serpin couples the thermodynamic driving force of a massive beta-sheet rearrangement to the inhibition of a target protease. Hence, the serpin-protease interaction is the premier example of a "spring-loaded" protein-protein interaction. Amino acid substitutions in the hinge region of a serpin reactive loop can weaken the molecular spring, which converts the serpin from an inhibitor into a substrate. To probe the molecular basis of this conversion, we report the crystal structure of A349R antichymotrypsin in the reactive loop cleaved state at 2.1 A resolution. This amino acid substitution does not block the beta-sheet rearrangement despite the burial of R349 in the hydrophobic core of the cleaved serpin along with a salt-linked acetate ion. The inhibitory activity of this serpin variant is not obliterated; remarkably, its inhibitory properties are anion-dependent due to the creation of an anion-binding cavity in the cleaved serpin.
Triglyceride accumulation protects against fatty acid-induced lipotoxicity (2003)

Excess lipid accumulation in non-adipose tissues is associated with insulin resistance, pancreatic beta-cell apoptosis and heart failure. Here, we demonstrate in cultured cells that the relative toxicity of two common dietary long chain fatty acids is related to channeling of these lipids to distinct cellular metabolic fates. Oleic acid supplementation leads to triglyceride accumulation and is well tolerated, whereas excess palmitic acid is poorly incorporated into triglyceride and causes apoptosis. Unsaturated fatty acids rescue palmitate-induced apoptosis by channeling palmitate into triglyceride pools and away from pathways leading to apoptosis. Moreover, in the setting of impaired triglyceride synthesis, oleate induces lipotoxicity. Our findings support a model of cellular lipid metabolism in which unsaturated fatty acids serve a protective function against lipotoxicity though promotion of triglyceride accumulation.
Intramolecular 1,3-diyl trapping reactions. A formal total synthesis of (.+-.)-coriolin (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIntramolecular 1,3-diyl trapping reactions. A formal total synthesis of (.+-.)-coriolinLuc Van Hijfte and R. Daniel LittleCite this: J. Org. Chem. 1985, 50, 20, 3940–3942Publication Date (Print):October 1, 1985Publication History Published online1 May 2002Published inissue 1 October 1985https://pubs.acs.org/doi/10.1021/jo00220a058https://doi.org/10.1021/jo00220a058research-articleACS PublicationsRequest reuse permissionsArticle Views2397Altmetric-Citations54LEARN 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