gebhart/patrepeval huggingface dataset:
Short report: Monitoring ESR1 mutations by circulating tumor DNA in aromatase inhibitor resistant metastatic breast cancer (2015)

Acquired estrogen receptor gene (ESR1) mutations have been recently reported as a marker of resistance to aromatase inhibitors in hormone receptor positive metastatic breast cancer. We retrospectively considered seven patients treated for metastatic breast cancer with available samples from the primary tumor before any treatment, cryopreserved metastasis removed during progression and concomitant plasmas. All these seven patients were in disease progression after previous exposure to aromatase inhibitors for at least 6 months, and were assessed for ESR1 mutations detection in tumor and circulating DNA. For these patients, Sanger sequencing identified four metastases with clear ESR1 mutation and one possible, whereas digital PCR identified six mutated metastases. Then, under blind conditions and using digital PCR, corresponding circulating ESR1 mutations were successfully detected in four of these six metastatic breast cancer patients. Moreover, in two patients with serial blood samples following treatments exposure, the monitoring of circulating ESR1 mutations clearly predicted disease evolution. In the context of high interest for ESR1 mutations, our results highlight that these acquired recurrent mutations may be tracked in circulating tumor DNA and may be of clinical relevance for metastatic breast cancer patient monitoring.
Proteolytic cleavage of synthetic fragments of vesicle‐associated membrane protein, isoform‐2 by botulinum type B neurotoxin (1993)

Recent data suggest that botulinum type-B neurotoxin is a protease which acts on vesicle-associated membrane protein, isoform 2 (VAMP-2). In this report, botulinum type-B neurotoxin is shown to cleave a synthetic fragment (HV62) of VAMP-2, corresponding to the bulk of the hydrophilic domain (amino acids 33-94). The neurotoxin acts at a single site between Gln76 and Phe77. Little or no proteolytic activity by botulinum type-B neurotoxin was observed with peptides containing 7, 10 or 20 amino acids spanning the site of cleavage. The proteolytic action of neurotoxin was strongly inhibited by EDTA and o-phenanthroline whereas captopril and phosphoramidon were ineffective. A series of model peptide substrates were synthesised in order to define the smallest VAMP-2 fragment to be cleaved by botulinum type-B neurotoxin. Data obtained from these substrates suggest that the neurotoxin belongs to a novel class of zinc-endoprotease; more than 12 amino acid residues are required on both the NH2- and COOH-terminal side of the cleavage site for optimal proteolytic activity. The results demonstrate that no other components of cellular vesicles are required for the specific action of the neurotoxin on VAMP-2. The data further show that the highly specific action of the neurotoxin is not dictated solely by the properties of the amino acid residues at the cleavage site but is also dependent on amino acid sequences distal to its site of action.
Isolation and Expression of the Full-Length cDNA Encoding CD59 Antigen of Human Lymphocytes (1990)

To identify the primary structure of CD59 antigen and to elucidate its function, a full-length cDNA clone of CD59 was isolated. The cDNA sequence contained an open reading frame that encodes an 128-amino-acid peptide. The amino-terminal 25 amino acids represented a typical signal peptide sequence and the carboxy-terminal hydrophobic amino acids were characteristic for phosphatidylinositol-anchored proteins. The predicted mature protein sequence showed 35% homology with murine Ly-6C.1 and 31% with Ly-6A.2. The number and the distribution of cysteine residues were conserved, implying that the CD59 represented a human homologue of murine Ly-6. RNA blot hybridization analysis revealed the expression of CD59 mRNA in placental, lung, and pancreatic tissues. The mRNA was not only expressed in T-cell lines but in some of monocytic, myeloid, and B-cell lines. In all of these tissues and cell lines, at least four mRNA species were detected. DNA blot hybridization analysis revealed a rather simple genomic structure, which suggested a single gene as compared with the complex multigene family of murine Ly-6.
THE ROLE OF CD28/B7 COSTIMULATORY PATHWAY ON RECURRENT AUTOIMMUNITY AFTER ISLET TRANSPLANTATION IN AUTOIMMUNE NOD MICE (1999)

497 CD28/B7 pathway is a major costimulatory signal for T cell activation and differentiation. Although it has been shown that blockade of CD28/B7 pathway can prevent graft rejection and induce tolerance, whether the same strategy can be used to prevent recurrence of autoimmune diabetes after islet transplantation in spontaneously diabetic NOD mice has not been explored. In this study, we investigate the effect of CTLA4Ig or anti-B7.1 (CD80) and anti-B7.2 (CD86) monoclonal antibodies on recurrence of autoimmune diabetes in NOD mice. Islets from NOR which is MHC matched control strain for NOD mouse were prepared by collagenase digestion and Euro-Ficoll purification. Five hundred islets were transplanted under the left kidney capsule of each diabetic NOD mouse. Islet graft survival was monitored by blood glucose measurement. CTLA4Ig at 200 μg or anti-B7.1 and anti-B7.2 antibodies at 100 μg each were given i.p. on days-1, 0 and then once every two days until return of hyperglycemia, respectively. The mean survival of NOR islet grafts in untreated diabetic NOD mice was 8.4±2.0 days. CTLA4Ig could not prevent recurrence of autoimmune diabetes although it slightly prolonged NOR islet graft survival in NOD mice. The mean islet graft survival in NOD mice under treatment with CTLA4Ig was 12.5±2.5 days. Anti-B7.1 and anti-B7.2 antibodies also could not prevent recurrence of autoimmune diabetes. Hyperglycemia was returned in anti-B7.1 and anti-B7.2 antibodies treated NOD mice after 12.0±4.3 days. Pathological examination revealed a massive lymphocytes infiltration in the damaged islet grafts. Immunostaining for insulin and lymphocyte subsets showed only a few insulin granules present in islet grafts and the major infiltrated cells in all damaged islet grafts were CD3+, CD4+ and CD8+ lymphocytes. These results demonstrated that blockade of CD28/B7 costimulatory pathway can not prevent recurrence of autoimmune diabetes after islet transplantation in autoimmune diabetic NOD mice. Our data also indicated other approaches are needed to prevent recurrent autoimmune attack on the transplanted islets for successful clinical islet transplantation although targeting CD28/B7 signals is a feasible strategy for induction of tolerance.
Epigenetic Alterations in Cholangiocarcinoma-Sustained IL-6/STAT3 Signaling in Cholangio- carcinoma due to SOCS3 Epigenetic Silencing (2009)

Cholangiocarcinoma (CCA) is a highly lethal malignant tumor arising from the biliary tract epithelium, characterized by its typically late clinical presentation and lack of effective therapeutic modalities. Chronic inflammatory conditions, including primary sclerosing cholangitis, liver fluke infestation and hepatolithiasis, are listed in the risk factors, but for most cases of CCA the cause is unknown. Recent advances in molecular pathogenesis have highlighted the importance of epigenetic alterations including promoter hypermethylation and histone deacetylation in addition to genetic changes in the process of cholangiocarcinogenesis. This review provides a comprehensive overview of the genes hypermethylated in CCA to date and their putative roles in cholangiocarcinogenesis. Among genes hypermethylated, we found the CpG island hypermethylation in suppressor of cytokine signaling 3 (SOCS3) gene promoter in CCA. Interleukin-6 (IL-6)-mediated signal transducers and activators of transcription 3 (STAT3) activation are aberrantly sustained in CCA cells, resulting in resistance to apoptosis. SOCS3 controls the IL-6/STAT3 signaling pathway by a classic feedback loop. Indeed, SOCS3 epigenetic silencing is responsible for sustained IL-6/STAT3 signaling in CCA. These findings provide new perspectives for epigenetic therapy to restore SOCS3 in this cancer.
Occurrence of Genetic Drift and Founder Effect during Quasispecies Evolution of the VP2 and NS3/NS3A Genes of Bluetongue Virus upon Passage between Sheep, Cattle, and Culicoides sonorensis (2001)

Bluetongue virus (BTV) is the cause of an insect-transmitted virus infection of ruminants that occurs throughout much of the world. Individual gene segments differ between field strains of BTV; thus, we hypothesized that key viral genes undergo genetic drift during alternating passage of BTV in its ruminant and insect hosts. To test this hypothesis, variation in the consensus sequence and quasispecies heterogeneity of the VP2 and NS3/NS3A genes of a plaque-purified strain of BTV serotype 10 was determined during alternating infection of vector Culicoides sonorensis and a sheep and calf. Consensus sequences were determined after reverse transcriptase-nested PCR amplification of viral RNA directly from ruminant blood and homogenized insects, and quasispecies heterogeneity was determined by the sequencing of clones derived from directly amplified viral RNA. Comparison of these sequences to those of the original BTV inoculum used to initiate the cycle of BTV infection demonstrated, for the first time, that individual BTV gene segments evolve independently of one another by genetic drift in a host-specific fashion, generating quasispecies populations in both ruminant and insect hosts. Furthermore, a unique viral variant was randomly ingested by C. sonorensis insects that fed on a sheep with low-titer viremia, thereby fixing a novel genotype by founder effect. Thus, we conclude that genetic drift and founder effect contribute to diversification of individual gene segments of field strains of BTV.
Alteration of tight junctional permeability in the rat parotid gland after isoproterenol stimulation (1984)

The permeability of junctional complexes to ultrastructural tracers of different molecular weight and the freeze-fracture appearance of junctional structure were investigated in the resting and stimulated rat parotid gland. Tracers were administered retrogradely via the main excretory duct, and allowed to flow by gravity (16 mmHg) into the gland for 15-60 min. Secretion was induced in some animals by intraperitoneal injection of isoproterenol. In resting glands, the tracers microperoxidase , cytochrome c, myoglobin, tyrosinase (subunits), and hemoglobin were restricted to the luminal space of the acini and ducts. In glands stimulated 1-4 h before tracer administration, reaction product for microperoxidase , cytochrome c, myoglobin, and tyrosinase was found in the intercellular and interstitial spaces, whereas hemoglobin was usually retained in the lumina. In contrast, horseradish peroxidase and lactoperoxidase appeared to penetrate the tight junctions and reaction product was localized in the extracellular spaces in both resting and stimulated glands. Diffuse cytoplasmic staining for horseradish peroxidase and lactoperoxidase was frequently observed in acinar and duct cells. The distribution of horseradish peroxidase was similar in both Sprague-Dawley and Wistar-Furth rats, and at concentrations of 0.1-10 mg/ml in the tracer solution. Freeze-fracture replicas of stimulated acinar cells revealed an increased irregularity of the tight junction meshwork, but no obvious gaps or discontinuities were observed. These findings indicate that (a) tight junctions in the resting rat parotid gland are impermeable to tracers of molecular weight greater than or equal to 1,900; (b) stimulation with isoproterenol results in a transient increase in junctional permeability allowing passage of tracers of molecular weight less than or equal to 34,500; (c) junctional permeability cannot be directly correlated with junctional structure; and (d) the behavior of horseradish peroxidase and lactoperoxidase in the rat parotid gland is inconsistent with their molecular weights. Cell membrane damage due to the enzymatic activity or binding of these two tracers may account for the observed distribution.
Studies of nitrogen mustard transport by mouse myeloma and hemopoietic precursor cells. (1973)

We studied the transport of nitrogen mustard (HN2) by mouse hemopoietic and transplantable myeloma (Adj. PC-5 and MOPC 460D) stem cells, using gradients of temperature and choline chloride. Bone marrow and myeloma cells were exposed to HN2 in culture at various temperatures, washed, and tested for colony-forming efficiency. The protective effect of lowered temperatures was similar for normal marrow colony-forming units and both lines of myeloma cells. When cells were exposed to HN2 in the presence of choline chloride, the survival of colony-forming units increased, and the dose response curves were similar among the three classes of cells. We were unable to demonstrate a qualitative difference in the transport of HN2 by mouse hemopoietic precursor cells and the stem cells of two myelomas with different sensitivities to HN2.
The Effect of Science Journal Writings on the cognitive and affective features of the science gifted students (2004)

The purpose of this study is to find out the effect of science journal writings on the cognitive and affective features of the science gifted students. In this research, the tasks of on-line science journal writings were assigned for 6 months and the subjects in this study were 21 students of Chemistry Division of the Center for Science Gifted Education, Seoul National University. Consequently in science journals, science concepts are found in various aspects according to the writing formats, and psychological and behavioral characteristics of the science-gifted are revealed in positive or negative aspects. In cognitive prospect, science journal writing equips students with better understanding about science concepts and scientific research. In affective prospect, science journal writing help students improve observation and attitude toward science as wren as writing skills. Accordingly, science journal writing has positive effect on cognitive and affective characteristics of the science-gifted. In conclusion, acknowledged by most of science-gifted students as both beneficial and appropriate in their education program, science journal writing should be emphasized in education for science-gifted students.
Total Synthesis of Epothilone B, Epothilone D, andcis- andtrans-9,10-Dehydroepothilone D (2001)

The phosphonium salt 35, representing one of the two principal subunits of the epothilones, was prepared from propargyl alcohol via heptenone 22. A Wittig reaction of the phosphorane from 35 with aldehyde 33, obtained from aldol condensation of ketone 27 with aldehyde 28, afforded 37. Seco acid 42 derived from 37 underwent lactonization to give cis-9,10-dehydroepothilone D (43) which was selectively reduced with diimide to yield epothilone D (4) and, after epoxidation, epothilone B (2). An alternative route to epothilone D employed alkyne 39, obtained from 33, in a Castro-Stephens reaction with allylic bromide 34 to furnish enyne 40. The latter was semi-hydrogenated to provide 37. Alkyne 46, prepared from alcohol 45, was converted to trans-vinylstannane 47 which, in a Stille coupling with allylic chloride 50, gave 51. Seco acid 52 derived from 51 underwent lactonization to give trans-9,10-dehydroepothilone D (54). Bioassay data comparing the antiproliferative activity and tubulin polymerization of 43 and 54 with epothilone B (2), epothilone D (4), and paclitaxel (7) showed that the synthetic analogues were less potent than their natural counterparts, although both retain full antiproliferative activity against a paclitaxel-resistant cell line. No significant difference in potency was noted between cis analogue 43 and its trans isomer 54.
Fasting plasma homocysteine as a sensitive parameter of antifolate effect: A study of psoriasis patients receiving low-dose methotrexate treatment (1989)

We have investigated the effect of low-dose methotrexate (25 mg weekly) on plasma homocysteine in 13 patients who had psoriasis. Total, free, and protein-bound homocysteine were determined both during fasting and after methionine loading. Psoriasis patients had significantly higher basal plasma homocysteine levels than age-matched control subjects. In addition, the methionine loading test was abnormal in four of the patients, but this was not significant. Psoriasis patients, although not folate deficient, did have lower serum folate levels than control subjects. There was a significant and transient increase in fasting plasma homocysteine levels within 48 hours after administration of low-dose methotrexate. This response was repeated after each administration and was observed eight to 20 times in three patients whose progress was monitored for 2 to 6 months. Notably, methotrexate did not affect the plasma profile for homocysteine after methionine loading. This study showed the level of fasting plasma homocysteine to be a sensitive and responsive parameter of antifolate drug treatment.
Discovering naturally processed antigenic determinants that confer protective T cell immunity (2013)

CD8+ T cells (TCD8) confer protective immunity against many infectious diseases, suggesting that microbial TCD8 determinants are promising vaccine targets. Nevertheless, current T cell antigen identification approaches do not discern which epitopes drive protective immunity during active infection - information that is critical for the rational design of TCD8-targeted vaccines. We employed a proteomics-based approach for large-scale discovery of naturally processed determinants derived from a complex pathogen, vaccinia virus (VACV), that are presented by the most frequent representatives of four major HLA class I supertypes. Immunologic characterization revealed that many previously unidentified VACV determinants were recognized by smallpox-vaccinated human peripheral blood cells in a variegated manner. Many such determinants were recognized by HLA class I-transgenic mouse immune TCD8 too and elicited protective TCD8 immunity against lethal intranasal VACV infection. Notably, efficient processing and stable presentation of immune determinants as well as the availability of naive TCD8 precursors were sufficient to drive a multifunctional, protective TCD8 response. Our approach uses fundamental insights into T cell epitope processing and presentation to define targets of protective TCD8 immunity within human pathogens that have complex proteomes, suggesting that this approach has general applicability in vaccine sciences.
Production of γ‐Linolenic Acid and Stearidonic Acid in Seeds of Marker‐Free Transgenic Soybean1 (2004)

Through a single desaturation step, the Borago officinalis L. Δ 6 desaturase can convert linoleic acid and α‐linolenic acid to γ‐linolenic acid (GLA) and stearidonic acid (STA), respectively. Both GLA and STA are of interest to the pharmaceutical and nutraceutical industries. Production of these fatty acids is costly. One potential strategy to reduce production cost would be to generate them in a major oilseed crop. To this end, a cDNA of the B. officinalis Δ 6 ‐desaturase gene was cloned downstream of the embryo‐specific promoter β‐conglycinin. The resultant cassette was assembled into a two T‐DNA binary vector, in which the second T‐DNA element harbored a selectable marker cassette. The final plasmid was subsequently used to transform soybean [ Glycine max (L.) Merr.]. The simultaneous delivery of two T‐DNA elements was used as a strategy to derive soybean progeny transgenic for the Δ 6 desaturase T‐DNA and free of the marker gene T‐DNA. Twenty‐nine transgenic soybean lines were recovered that harbored both T‐DNA elements, of which 17 produced GLA and STA in the seed storage lipids. Average GLA levels ranged from 3.4 up to 28.7%, while STA levels varied from just under 0.6 to 4.2% in the T 1 generation. Among the 17 lines that produced GLA and STA, four lines were identified that were free of the selectable marker T‐DNA element.
Effect of solvent on enantioselective esterification of naproxen by lipase with trimethylsilyl methanol (1994)

Improvement of stereoselective resolution of racemic Naproxen, 2-(6-methoxy-2-naphthyl)propionic acid, was attempted with esterifcation reaction by Candida cylindracea lipase. By carefully selecting the organic medium, a 72-time enhancement of yield of the desired S-ester was achieved. The optimal reaction temperature was approximately 53 degrees C, and an alcohol concentration between 20 mM and 40 mM in an 80% (v/v) isooctane and 20% (v/v) toluene mixture was found. (c) 1994 John Wiley & Sons, Inc.
IL-18-deficient mice are resistant to endotoxin-induced liver injury but highly susceptible to endotoxin shock (1999)

IL-18 is an IL-1-related cytokine which shares biological functions with IL-12. These include the activation of NK cells, induction of IFN-gamma production and Th1 cell differentiation. In this study we analyzed the effect of IL-18 deficiency on lipopolysaccharide (LPS)-induced liver injury and endotoxin shock in Propionibacterium acnes-primed mice. P. acnes-primed IL-18-deficient (IL-18KO) mice showed resistance to LPS-induced liver injury. Unexpectedly, P. acnes-primed IL-18KO mice were highly susceptible to LPS-induced endotoxin shock. Serum level of tumor necrosis factor (TNF)-alpha were markedly elevated (approximately 10-fold higher) within 1.5 h after LPS challenge in IL-18KO mice as compared with wild-type mice. Anti-TNF-alpha antibody administration to IL-18KO mice was significantly protective against endotoxin-induced lethality. P. acnes-primed IL-18KO macrophages produced approximately 6-fold more TNF-alpha protein than did P. acnes-primed wild-type control macrophages. Taken together, these findings demonstrate that IL-18 is responsible for the progression of endotoxin-induced liver injury as well as down-regulation of endotoxin-induced TNF-alpha production in P. acnes-primed mice.
Tumor Delivery and In Vivo Processing of Disulfide-Linked and Thioether-Linked Antibody−Maytansinoid Conjugates (2009)

Antibody-drug conjugates (ADCs) are designed to eradicate cancer cells that express the target antigen on their cell surface. A key component of an ADC is the linker that covalently connects the cytotoxic agent to the antibody. Several antibody-maytansinoid conjugates prepared with disulfide-based linkers such as those targeting the CanAg antigen have been shown to display more activity in preclinical mouse xenograft models than corresponding conjugates prepared with uncleavable thioether-based linkers. To investigate how the linker influences delivery and activation of antibody-maytansinoid conjugates, we isolated and characterized the [(3)H]maytansinoids from CanAg-positive tumor tissues following a single intravenous administration of 300 microg/kg (based on maytansinoid dose) of anti-CanAg antibody (huC242)-(3)H-maytansinoid conjugates prepared with cleavable disulfide linkers and an uncleavable thioether linker. We identified three target-dependent tumor metabolites of the disulfide-linked huC242-SPDB-DM4, namely, lysine-N(epsilon)-SPDB-DM4, DM4, and S-methyl-DM4. We found similar metabolites for the less hindered disulfide-linked huC242-SPP-DM1 conjugate with the exception that no S-methyl-DM1 was detected. The sole metabolite of the uncleavable thioether-linked huC242-SMCC-DM1 was lysine-N(epsilon)-SMCC-DM1. The AUC for the metabolites of huC242-SMCC-DM1 at the tumor over 7 d was about 2-fold greater than the corresponding AUC for the metabolites of the disulfide-linked conjugates. The lipophilic metabolites of the disulfide-linked conjugates were found to be nearly 1000 times more cytotoxic than the more hydrophilic lysine-N(epsilon)-linker-maytansinoids in cell-based viability assays when added extracellularly. The cell killing properties associated with the lipophilic metabolites of the disulfide-linked conjugates (DM4 and S-methyl-DM4, and DM1) provide an explanation for the superior in vivo efficacy that is often observed with antibody-maytansinoid conjugates prepared with disulfide-based linkers in xenograft mouse models.