gebhart/patrepeval huggingface dataset:
BRAF inhibition is associated with increased clonality in tumor-infiltrating lymphocytes (2013)

There have been significant advances with regard to BRAF-targeted therapies against metastatic melanoma. However, the majority of patients receiving BRAF inhibitors (BRAFi) manifest disease progression within a year. We have recently shown that melanoma patients treated with BRAFi exhibit an increase in melanoma-associated antigens and in CD8+ tumor-infiltrating lymphocytes in response to therapy. To characterize such a T-cell infiltrate, we analyzed the complementarity-determining region 3 (CDR3) of rearranged T-cell receptor (TCR) β chain-coding genes in tumor biopsies obtained before the initiation of BRAFi and 10-14 d later. We observed an increase in the clonality of tumor-infiltrating lymphocytes in 7 of 8 patients receiving BRAFi, with a statistically significant 21% aggregate increase in clonality. Over 80% of individual T-cell clones detected after initiation of BRAFi treatment were new clones. Interestingly, the comparison of tumor infiltrates with clinical responses revealed that patients who had a high proportion of pre-existing dominant clones after the administration of BRAFi responded better to therapy than patients who had a low proportion of such pre-existing dominant clones following BRAFi. These data suggest that although the inhibition of BRAF in melanoma patients results in tumor infiltration by new lymphocytes, the response to treatment appears to be related to the presence of a pre-existing population of tumor-infiltrating T-cell clones.
Engagement of Glucocorticoid-Induced TNFR Family-Related Receptor on Effector T Cells by its Ligand Mediates Resistance to Suppression by CD4+CD25+ T Cells (2004)

Nonactivated CD4+CD25+ regulatory T cells constitutively express glucocorticoid-induced TNFR family-related receptor (GITR), a TNFR family member whose engagement was presumed to abrogate regulatory T cell-mediated suppression. Using GITR-/- mice, we report that GITR engagement on CD25-, not CD25+ T cells abrogates T cell-mediated suppression. Mouse APCs constitutively express GITR ligand (GITR-L), which is down-regulated following TLR signaling in vivo. Although GITR-/-CD25- T cells were capable of mounting proliferative responses, they were incapable of proliferation in the presence of physiological numbers of CD25+ T cells. Thus, GITR-L provides an important signal for CD25- T cells, rendering them resistant to CD25+ -mediated regulation at the initiation of the immune response. The down-regulation of GITR-L by inflammatory stimuli may enhance the susceptibility of effector T cells to suppressor activity during the course of an infectious insult.
Cannabinoid CB2 receptors are expressed by perivascular microglial cells in the human brain: An immunohistochemical study (2004)

Two types of cannabinoid receptors have been characterized so far, CB1 and CB2. While CB1 receptors are present both in the CNS and in the periphery, CB2 receptors showed an almost exclusive distribution within the immune system. We now report that CB2 receptors are present in a specific microglial cell type of the human cerebellum. Thus, we have performed immunohistochemical analysis of tissue sections of white matter areas of the human cerebellum and detected the presence of CB2 receptors in perivascular microglial cells. These findings match with the well-known immunomodulatory role of CB2 receptors and open new perspectives on the possible role that these receptors may play in pathophysiological events.
Solution structure determination of oligoureas using methylene spin state selective NMR at 13C natural abundance (2008)

Ability of N,N'-linked oligoureas containing proteinogenic side chains to adopt a stable helix conformation in solution has been described recently. NMR as well as circular dichroism (CD) spectroscopies were employed to gain insight into their specific fold. It is herein proposed to extend the structural information available on these peptidomimetics by an advantageous use of a methylene spin state selective NMR experiment. Homodecoupling provided by the pulse scheme made it possible to readily measure conformation-dependent (3)J(HH) constants that are difficult if not impossible to obtain with standard NMR experiments. Adding those couplings to the NMR restraints improved the quality of the structure calculations significantly, as judged by a ca 30% decrease of the root mean square deviation (RMSD) obtained over an ensemble of 20 structures. Moreover, accurate determination of individual (1)J(CH) couplings within each methylene group revealed uniform values throughout the oligourea sequence, with (1)J(CH) systematically slightly larger for the pro-S hydrogen than for the pro-R. As shown in this study, the methylene spin state selective NMR experiment displays a good intrinsic sensitivity and could therefore provide valuable structural information at (13)C natural abundance for peptidomimetic molecules and foldamers bearing diastereotopic methylene protons.
The Construction and Use of a Human-Mouse Myeloma Analogue Suitable for the Routine Production of Hybridomas Secreting Human Monoclonal Antibodies (1987)

A human-mouse myeloma analogue termed HMMA2.11TG/O was constructed by fusion of the mouse myeloma cell line P3x63Ag8.653, a mutant derivative of MOPC21, with bone marrow mononuclear cells from a patients with IgA myeloma. The HMMA2.11TG/O cell line is resistant to 6-thioguanine and ouabain and sensitive to HAT. The cell line secretes no detectable immunoglobulin and has a hybrid karyotype and cell surface phenotype. An average fusion efficiency for growth of hybridomas of 1/17,000 fused cells was obtained in fusions with human peripheral blood mononuclear cells (PBM), Pokeweed Mitogen (PWM) stimulated PBM, and Epstein-Barr Virus (EBV) transformed polyclonal B cell lines. Over 75% of hybrids secrete detectable immunoglobulin and the cloning efficiency of the hybrids at 1 cell/well averages 25%. Antibody secreting cloned hybridoma cell lines were obtained by fusion directly with PBM from an immunized volunteer and by fusion with in vitro, secondarily immunized, EBV transformed polyclonal cell lines. Five hybridomas secreting human monoclonal IgM anti-tetanus antibodies and 2 secreting human monoclonal IgG anti-tetanus antibodies were selected and cloned from 6 fusions performed specifically for anti-tetanus antibody. Immunoglobulin and antibody secretion by cloned hybrids has been stable for 5-10 months at present. Immunoglobulin and antibody secretion in routine cultures passaged every 3-4 days has been 8-42 micrograms/ml. This human-mouse myeloma analogue should prove useful for the routine production of human monoclonal antibodies.
Distributed-protocol authentication scheme (1987)

The purpose of this RFC is to focus discussion on authentication
problems in the Internet and possible methods of solution. The
proposed solutions this document are not intended as standards for the
Internet at this time. Rather, it is hoped that a general consensus
will emerge as to the appropriate solution to authentication problems,
leading eventually to the adoption of standards. This document
suggests mediated access-control and authentication procedures
suitable for those cases when an association is to be set up between
users belonging to different trust environments.
The Crystal Structure of a Self-Activating G Protein α Subunit Reveals Its Distinct Mechanism of Signal Initiation (2011)

In animals, heterotrimeric guanine nucleotide-binding protein (G protein) signaling is initiated by G protein-coupled receptors (GPCRs), which activate G protein α subunits; however, the plant Arabidopsis thaliana lacks canonical GPCRs, and its G protein α subunit (AtGPA1) is self-activating. To investigate how AtGPA1 becomes activated, we determined its crystal structure. AtGPA1 is structurally similar to animal G protein α subunits, but our crystallographic and biophysical studies revealed that it had distinct properties. Notably, the helical domain of AtGPA1 displayed pronounced intrinsic disorder and a tendency to disengage from the Ras domain of the protein. Domain substitution experiments showed that the helical domain of AtGPA1 was necessary for self-activation and sufficient to confer self-activation to an animal G protein α subunit. These findings reveal the structural basis for a mechanism for G protein activation in Arabidopsis that is distinct from the well-established mechanism found in animals.
Synthesis, Anion Exchange, and Delamination of Co−Al Layered Double Hydroxide:  Assembly of the Exfoliated Nanosheet/Polyanion Composite Films and Magneto-Optical Studies (2006)

This paper describes a systematic study on the synthesis, anion exchange, and delamination of Co-Al layered double hydroxide (LDH), with the aim of achieving fabrication and clarifying the properties of LDH nanosheet/polyanion composite films. Co-Al-CO3 LDH hexagonal platelets of 4 mum in lateral size were synthesized by the urea method under optimized reaction conditions. The as-prepared CO3(2-)-LDH was converted to Cl- -LDH by treating with a NaCl-HCl mixed solution, retaining its high crystallinity and hexagonal platelike morphology. LDHs intercalated with a variety of anions (such as NO3-, ClO4-, acetate, lactate, dodecyl sulfate, and oleate) were further prepared from Cl- -LDH via an anion-exchange process employing corresponding salts. Exchanged products in various anion forms were found to show different delamination behaviors in formamide. Among them, best results were observed for NO3- -LDH in terms of the exfoliating degree and the quality of the exfoliated nanosheets. The delamination gave a pink transparent suspension containing well-defined nanosheets with lateral sizes of up to 2 microm. The resulting nanosheets were assembled layer-by-layer with an anionic polymer, poly(sodium styrene 4-sulfonate) (PSS), onto quartz glass substrates to produce composite films. Magnetic circular dichroism (MCD) measurements revealed that the assembled multilayer films exhibited an interesting magneto-optical response.
Mechanism of activation of triciribine phosphate (TCN-P) as a prodrug form of TCN. (1986)

The tricyclic nucleotide triciribine phosphate (TCN-P) was synthesized as a water-soluble derivative of the tricyclic nucleoside TCN (L. B. Townsend et al, INSERM 81:37, 1978). Growth of L1210 cells in vitro was inhibited equally by TCN and TCN-P. A requirement for adenosine kinase activity for activation of both TCN and TCN-P was established by the observation that growth inhibition by either compound was decreased 200-fold by the adenosine kinase inhibitor 5-iodotubercidin and greater than 5000-fold in L1210/T, an adenosine kinase-deficient subline. The TCN/TCN-P resistance of L1210/T cells was correlated with lack of formation of intracellular TCN-P from either TCN or TCN-P. Thus, it appeared that TCN-P was hydrolyzed to TCN and then rephosphorylated intracellularly. Both the horse serum-containing culture medium and the intact cells possessed nucleotide phosphatase activity, which may contribute to the hydrolysis of TCN-P to TCN in the L1210 cell cultures. The requirement for hydrolysis of TCN-P to TCN for formation of intracellular TCN-P from exogenous TCN-P was also shown directly by the observation that human erythrocytes, which lack ectophosphatases, readily formed intracellular TCN-P from TCN but not from TCN-P when incubated in buffer.
The Evolution of Modern Agriculture and Its Future with Biotechnology (2002)

Since the dawn of agriculture, humans have been manipulating crops to enhance their quality and yield. Via conventional breeding, seed producers have developed the modern corn hybrids and wheat commonly grown today. Newer techniques, such as radiation breeding, enhanced the seed producers' ability to develop new traits in crops. Then in the 1980's-1990's, scientists began applying genetic engineering techniques to improve crop quality and yield. In contrast to earlier breeding methods, these techniques raised questions about their safety to consumers and the environment. This paper provides an overview of the kinds of genetically modified crops developed and marketed to date and the value they provide farmers and consumers. The safety assessment process required for these crops is contrasted with the lack of a formal process required for traditionally bred crops. While European consumers have expressed concern about foods and animal feeds containing ingredients from genetically modified crops, Americans have largely been unconcerned or unaware of the presence of genetically modified foods on the market. This difference in attitude is reflected in Europe's decision to label foods containing genetically modified ingredients while no such labeling is required in the U.S. In the future, genetic modification will produce a variety of new products with enhanced nutritional or quality attributes.
Extracellular MUC3 mucin secretion follows adherence of Lactobacillus strains to intestinal epithelial cells in vitro (2003)

Probiotic microbes induce MUC3 mucin transcription and translation with extracellular secretion of the MUC3 mucins. Epithelial cell adherence enhances the effects of probiotics on eukaryotic mucin expression.
Polybenzimidazole‐based block copolymers: From monomers to membrane electrode assemblies for high temperature polymer electrolyte membrane fuel cells (2017)

ABSTRACT In this study, PBI‐based block copolymers were developed and their performance as membranes in high temperature polymer electrolyte membrane fuel cells was evaluated. This type of block copolymer consists of “phosphophilic” PBI and “phosphophobic” non‐PBI segments. The final properties of such block copolymers strongly depended on the length of the individual blocks and their chemical structures. In a systematic approach, a series of various block copolymers was synthesized and characterized both in terms of ex situ properties (e.g., proton conductivity, phosphoric acid uptake, swelling behavior) and in situ fuel cell tests. A very poor membrane‐electrode interface limited the performance of the membrane electrode assemblies, but was remarkably improved in power output, stability, and long‐term durability by treating the electrode interface with a fluorinated PBI derivative. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55 , 1831–1843
Role of the alveolar type II cell in the development and progression of pulmonary tumors induced by 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone in the A/J mouse. (1992)

The role of the type II cell in the development of pulmonary tumors induced in the adult A/J mouse (6 weeks of age) by treatment with a single dose (100 mg/kg, i.p.) of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) was investigated. Twenty-four h following treatment with NNK, the concentration of O6-methylguanine was similar in Clara and type II cells. However, hyperplasias were detected only along the alveolar septa in lungs 14 weeks after carcinogen treatment. Examination of the ultrastructure of several hyperplasias revealed that the proliferating cells resembled type II pneumocytes. The proliferating cells were cuboidal in shape, with centrally localized ovoid nuclei characterized by minor indentations. Lamellar bodies, one of the major hallmarks of the type II cell, were present in the cytoplasm. The progression of pulmonary lesions was followed by sacrificing mice at 4-week intervals from 14 to 54 weeks after treatment with NNK. From 34 to 42 weeks after treatment, progression to neoplasia was demonstrated by a decline in the frequency of hyperplasias and an increase in the frequency of adenomas. Approximately 50% of the adenomas were observed arising within hyperplasias. Carcinomas appeared to increase in frequency 34 weeks after carcinogen treatment and comprised greater than 50% of the pulmonary lesions by 54 weeks. Approximately 30% of the carcinomas were observed arising within adenomas. The growth pattern of carcinomas began to change from solid to mixed (solid and papillary) 42 weeks after NNK. Moreover, electron micrographic analysis demonstrated that, within a hyperplasia, proliferating type II cells could change from cuboidal to columnar in shape and could also exhibit nuclear indentations, both characteristics displayed by the Clara cell. Thus, this divergence of the type II cell from its well characterized morphological features indicates that the selective growth advantage which these initiated cells possess can result in changes to the normal ultrastructure of this cell as it progresses toward malignancy. DNA was isolated from 20 hyperplasias and screened for the presence of an activated K-ras gene. This gene was activated in 17 of 20 lesions, with 85% of the mutations involving a GC to AT transition within codon 12 (GGT to GAT), a mutation consistent with base mispairing produced by the formation of the O6-methylguanine adduct. This specificity for activation of the K-ras gene was identical to that observed previously in adenocarcinomas induced by NNK.(ABSTRACT TRUNCATED AT 400 WORDS)
OsMOGS is required for N‐glycan formation and auxin‐mediated root development in rice (Oryza sativa L.) (2014)

N-glycosylation is a major modification of glycoproteins in eukaryotic cells. In Arabidopsis, great progress has been made in functional analysis of N-glycan production, however there are few studies in monocotyledons. Here, we characterized a rice (Oryza sativa L.) osmogs mutant with shortened roots and isolated a gene that coded a putative mannosyl-oligosaccharide glucosidase (OsMOGS), an ortholog of α-glucosidase I in Arabidopsis, which trims the terminal glucosyl residue of the oligosaccharide chain of nascent peptides in the endoplasmic reticulum (ER). OsMOGS is strongly expressed in rapidly cell-dividing tissues and OsMOGS protein is localized in the ER. Mutation of OsMOGS entirely blocked N-glycan maturation and inhibited high-mannose N-glycan formation. The osmogs mutant exhibited severe defects in root cell division and elongation, resulting in a short-root phenotype. In addition, osmogs plants had impaired root hair formation and elongation, and reduced root epidemic cell wall thickness due to decreased cellulose synthesis. Further analysis showed that auxin content and polar transport in osmogs roots were reduced due to incomplete N-glycosylation of the B subfamily of ATP-binding cassette transporter proteins (ABCBs). Our results demonstrate that involvement of OsMOGS in N-glycan formation is required for auxin-mediated root development in rice.
MicroRNAs Induced During Adipogenesis that Accelerate Fat Cell Development Are Downregulated in Obesity (2009)

Our results provide the first experimental evidence for miR-103 function in adipose biology. The remarkable inverse regulatory pattern for many miRNAs during adipogenesis and obesity has important implications for understanding adipose tissue dysfunction in obese mice and humans and the link between chronic inflammation and obesity with insulin resistance.
Inhibition of experimental autoimmune encephalomyelitis by inhalation but not oral administration of the encephalitogenic peptide: influence of MHC binding affinity (1993)

This study explores antigen administration via mucosal surfaces as a potential means of inducing antigen-specific non-responsiveness in experimental autoimmune encephalomyelitis (EAE). In the H-2u mouse model of EAE, the acetylated N-terminal peptide of myelin basic protein represents a dominant T cell epitope which on its own is sufficient to induce disease. Oral administration of the encephalitogenic peptide over a wide range of doses failed to induce oral tolerance to EAE. In marked contrast, a single intranasal dose of this peptide (Ac1-9 or Ac1-11) profoundly inhibited EAE when administered prior to disease induction. We investigated this phenomenon further by using two analogues of Ac1-11 with alanine or tyrosine at position 4 which display higher affinity binding to the I-Au molecule than the original peptide with lysine at this position. There was a positive correlation between the degree of protection from EAE and the affinity of individual peptides for class II MHC. Peptide inhalation inhibited not only EAE induced by subcutaneous injection of the encephalitogenic peptide but also disease induced by a complex mixture of potential auto-antigens such as spinal cord homogenate. Thus, in contrast to oral tolerance, nonresponsiveness by peptide inhalation is inducible with the encephalitogenic peptide in the absence of additional regulatory epitopes. The finding that a single epitope may protect against EAE induced with whole spinal cord homogenate implies, however, that regulatory mechanisms affecting additional potential self-epitopes may play a significant role.
Endocrine events prior to puberty in heifers: role of somatotropin, insulin-like growth factor-I and insulin-like growth factor binding proteins. (1992)

We have utilized active immunization against growth hormone releasing factor (GRF) to investigate relationships among somatotropin (ST), insulin-like growth factor-I (IGF-I), IGF binding proteins (IGFBP) and ovarian function in heifers. Active immunization against GRF (GRFi) has been demonstrated to abolish episodic release of ST and decrease serum concentrations of IGF-I. In initial experiments investigating onset of puberty, breeds of heifers differing in growth rate and reproductive traits (Angus, Charolais and Simmental) were immunized against GRF or served as controls (immunized against carrier protein, human serum albumin, HSAi). GRFi decreased rate of muscle and skeletal growth, but increased deposition of adipose tissue. In Angus and Charolais, but not Simmental heifers, GRFi at 6 mo of age significantly delayed onset of puberty beyond 18 mo of age. Retrospective analyses of serum IGF-I revealed that GRFi heifers reaching puberty at a normal age had greater pre-treatment (6 mo of age) IGF-I than GRFi heifers in which puberty was delayed. Collectively, these results strongly indicate that the bovine hypothalamic-hypophyseal-ovarian axis is particularly sensitive to changes in metabolism at or near 6 mo of age. Another series of experiments tested the hypothesis that lowering serum IGF-I via GRFi initially at 3 mo of age would increase the percentage of Angus and Simmental heifers not reaching puberty. Three mo old Angus and Simmental heifers were assigned to GRFi (n = 18), HSAi (n = 14) or received no treatment (controls, n = 16). HSAi and GRFi heifers were unilaterally ovariectomized (ULO) at 6 mo of age. As anticipated, GRFi at a younger age increased percentage of heifers not reaching puberty; over 75% of control and HSAi heifers reached puberty by 14 mo of age compared to 22% of GRFi heifers. Serum and follicular fluid (FFL; follicles < or = 4 mm) concentrations of IGF-I were suppressed by GRFi. Serum, but not FFL concentrations of IGF binding protein-2 (IGFBP-2) were greater in GRFi than in HSAi heifers. GRFi delayed puberty apparently by suppressing follicular growth because number of follicles < or = 7 mm was significantly lower in GRFi than in HSAi heifers. In conclusion, active immunization against GRF at 3 or 6 months of age delays puberty in beef heifers. Delayed puberty was preceded by suppression of follicular growth, and decreased concentrations of IGF-I in serum and follicular fluid.(ABSTRACT TRUNCATED AT 400 WORDS)