gebhart/patrepeval huggingface dataset:
Construction and expression of plasmids containing mutated diphtheria toxin A-chain-coding sequences (1991)

We previously demonstrated that cells can be killed through transfection of an expression plasmid that encodes the diphtheria toxin A-chain fragment (DT-A). This report describes the construction of expression plasmids containing three mutant DT-A-coding sequences substituting glutamic acid 148 with aspartic acid, serine, or glutamine which are known to have 100- to 300-fold-reduced ADP-ribosylation activity measured in vitro. The toxicity of these constructs was determined in cotransfection experiments using HeLa and 293 cells with a luciferase expression plasmid as the reporter. Dose responses were compared for the three new DT-A mutant plasmids and for the corresponding plasmids containing wild-type DT-A and the previously characterized tox 176 mutant. The dose required to produce 50% inhibition of control luciferase expression in 293 embryonic kidney cells for the five plasmids ranged from 0.01 micrograms for wild-type DT-A to 1.2 micrograms for the least toxic plasmid, which replaces glutamic acid 148 with glutamine. In conclusion, a wide range of DT-A toxicity can be achieved by using plasmid expression vectors that encode different DT-A mutations.
REVIEWS (1992)

Journal Article REVIEWS Get access Milton Studies XXV. Edited by JAMES D. SIMMONDS. Pp. vi+284. Pittsburgh: University of Pittsburgh Press, 1990. $32.95. TOM BLACKBURN TOM BLACKBURN Swarthmore Collge Search for other works by this author on: Oxford Academic Google Scholar The Review of English Studies, Volume XLIII, Issue 172, November 1992, Pages 557–559, https://doi.org/10.1093/res/XLIII.172.557 Published: 01 November 1992
Oncogene amplification during tumorigenesis of established rat fibroblasts reversibly transformed by activated human ras oncogenes. (1986)

Normal rat fibroblasts of the established cell line Rat 4 were cotransformed with activated human ras oncogenes and with a cloned chicken thymidine kinase (tk) gene. Linkage between tk and ras genes allowed the isolation of oncogene deletion revertants and of cell clones showing varying degrees of malignant phenotype. Southern and Northern experiments in concert with tumorigenicity assays show that the malignant transformation of these cells by mutant ras oncogenes is a gradual but reversible process that depends on the relative abundance of oncogene sequences and their corresponding transcripts. We also show that moderate amplification of a c-K-ras oncogene in these cells results in a clear increase in their tumorigenicity and that the mutant gene present in low copy numbers in cultured cells undergoes amplification in the corresponding in vivo induced tumors.
Analysis of biomarker data: logs, odds ratios, and receiver operating characteristic curves (2010)

The appropriate analysis of biomarkers depends on the research question. Odds ratios obtained from logistic regression describe associations of biomarkers with clinical events; failure to accurately transform the markers, however, may result in misleading estimates. Although the C-statistic is often used to assess the ability of new biomarkers to improve the prediction of event risk, other measures may be more suitable.
Transcriptional regulation of the liver beta-galactoside alpha 2,6-sialyltransferase by glucocorticoids. (1990)

Hepatic expression of the beta-galactoside alpha 2,6-sialyltransferase is at least in part specified by circulatory glucocorticoids. In this report we use the glucocorticoid agonist, RU362, and the antagonist, RU486, to demonstrate the participation of the glucocorticoid receptor pathway in beta-galactoside alpha 2,6-sialyltransferase regulation. The existing pool of sialyltransferase mRNA is turned over with an approximate half-life of 13 h, and presence of dexamethasone does not alter this rate of degradation. By means of nuclear run-off assays and measurement of nuclear unprocessed transcripts we demonstrate that dexamethasone induction of beta-galactoside alpha 2,6-sialyltransferase mRNA in rat Reuber H35 cells is mediated by a transcriptional enhancement mechanism. The same initiation site is utilized for sialyltransferase transcription in both basal- and hormone-stimulated synthesis. Sialyltransferase sequences residing upstream of this transcriptional initiation point are used to control chloramphenicol acetyltransferase expression in fusion constructs following transient transfection into H35 cells to demonstrate the presence of a functional promoter. Although no element with similarity to the known GRE consensus sequence resides within this promoter region, chloramphenicol acetyltransferase expression under the control of the sialyltransferase promoter is subject to a low (1.6-fold) but reproducible induction in response to dexamethasone. Implications of this observation to glucocorticoid regulation are discussed.
Neural memory of the genioglossus muscle during sleep is stage‐dependent in healthy subjects and obstructive sleep apnoea patients (2018)

Several studies have shown that obstructive sleep apnoea (OSA) improves during slow wave sleep (SWS) for reasons that remain unclear. Recent studies have identified forms of neural memory such as short-term potentiation or after-discharge that can occur in response to upper airway obstruction. Neural memory may play a role in the development of stable breathing during SWS by increasing upper airway muscles activity in this sleep stage. We hypothesize that the after-discharge of the genioglossus muscle following upper airway obstruction is enhanced during SWS compared to non-rapid eye movement stage 2 (N2). During sleep, we performed five-breath drops in continuous positive airway pressure (CPAP-drop) to simulate obstructive events and reflexively activate the genioglossus. Immediately afterwards, CPAP was returned to an optimal level. Once the post-drop ventilation returned to eupnoea, the genioglossus after-discharge was measured as the time it took for genioglossus activity to return to baseline levels. In total, 171 CPAP-drops were analysed from a group of 16 healthy subjects and 19 OSA patients. A mixed-model analysis showed that after-discharge duration during SWS was 208% (95% confidence interval = 112% to 387%, P = 0.022) greater than during N2 after adjusting for covariates (ventilatory drive, CPAP levels). There was also a non-significant trend for a -35% reduction in after-discharge duration following an arousal vs. no-arousal from sleep (95% confidence interval = -59.5% to 5%, P = 0.08). Genioglossus after-discharge is two-fold greater in SWS vs. N2, which could partly explain the breathing stabilization described in OSA patients during this sleep stage.
Cerebrospinal fluid F2‐isoprostane levels are increased in Alzheimer's disease (1998)

Postmortem studies have associated Alzheimer's disease (AD) with regionally increased oxidative damage to brain. Lacking, however, is a specific marker of oxidative damage to brain that may be measured during life. We tested the hypothesis that cerebrospinal fluid (CSF) concentrations of F2-isoprostanes (F2-IsoPs), stable products of arachidonate peroxidation, are increased in CSF of AD patients. CSF from lateral ventricles (VF) was analyzed from 11 AD patients and 11 control subjects who participated in a rapid autopsy program. VF F2-IsoP concentrations were significantly elevated in AD patients compared with control subjects (72 +/- 7 vs 46 +/- 4 pg/ml) and were significantly linearly correlated with brain weight (-0.3 pg/ml/g, r2 = 0.32). These results suggest that quantification of CSF F2-IsoP concentrations may provide a useful biomarker of central nervous system oxidative damage in AD.
Gender Differences in Genetic Risk Profiles for Cardiovascular Disease (2008)

A false discovery rate analysis suggests that we may expect half of the reported findings for combined gender analysis to be true positives, while at least third of the reported genotype-gender interaction results are true positives. The asymmetry in positive findings between the genders could imply that genetic risk loci for CVD are more readily detectable in women, while for men they are more confounded by environmental/lifestyle risk factors. The possible differences in genetic risk profiles between the genders should be addressed in more detail in genetic studies of CVD, and more focus on female CVD risk is also warranted in genome-wide association studies.
Formation of protein kinase recognition sites by covalent modification of the substrate. Molecular mechanism for the synergistic action of casein kinase II and glycogen synthase kinase 3. (1987)

The mechanism for synergistic phosphorylation by glycogen synthase kinase 3 (GSK-3) and casein kinase II was studied using a synthetic peptide which contains the sequence of a potentially important proline/serine-rich regulatory region of rabbit muscle glycogen synthase. The peptide, Ac-PRPAS(3a)VPPS(3b)PSLS(3c)RHSS(4)PHQS(5) EDEEEP-amide, has five known phosphorylation sites of the native enzyme designated sites 3a, 3b, 3c, 4, and 5, which are spaced every fourth residue. The peptide was phosphorylated specifically at site 5 by casein kinase II with an apparent Km of 23 microM, but it was not phosphorylated by GSK-3. However, after initial phosphorylation of site 5 by casein kinase II, the peptide became an effective substrate for GSK-3 with an apparent Km of 2 microM. GSK-3 introduced up to four phosphates and appeared to catalyze the sequential modification of sites 4, 3c, 3b, and 3a, respectively. The results can be explained if GSK-3 recognizes the sequence -SXXXS(P). Phosphorylation of site 5 by casein kinase II creates this recognition site. Thereafter, each successive phosphorylation introduced by GSK-3 generates a new recognition site. The results provide a molecular basis to explain the synergistic action of casein kinase II and GSK-3 that is also observed with native glycogen synthase. In addition, this investigation emphasizes how protein recognition sites in some cellular targets may have to be formed post-translationally.
No Survival Benefit From Postoperative Adjuvant Chemotherapy After D2 Radical Resection for the Patients With Stage II Gastric Cancer (2010)

Postoperative adjuvant chemotherapy did not produce survival benefits for the patients with stage II gastric cancer. Randomized controlled clinical trials are demanded to confirm the finding from this study.
Neuropathological Findings in the Brain of Karen Ann Quinlan -- The Role of the Thalamus in the Persistent Vegetative State (1994)

Although the neuropathological findings in the case of Karen Ann Quinlan were complex, the disproportionately severe damage in the thalamus as compared with the cerebral cortex supports the hypothesis that the thalamus is critical for cognition and awareness and may be less essential for arousal.
Single-Chain Variable Fragment-Based Bispecific Antibodies: Hitting Two Targets with One Sophisticated Arrow (2019)

Despite the success of monoclonal antibodies (mAbs) to treat some disorders, the monospecific molecular entity of mAbs as well as the presence of multiple factors and pathways involved in the pathogenesis of disorders, such as various malignancies, infectious diseases, and autoimmune disorders, and resistance to therapy have restricted the therapeutic efficacy of mAbs in clinical use. Bispecific antibodies (bsAbs), by concurrently recognizing two targets, can partly circumvent these problems. Serial killing of tumor cells by bsAb-redirected T cells, simultaneous blocking of two antigens involved in the HIV-1 infection, and concurrent targeting of the activating and inhibitory receptors on B cells to modulate autoimmunity are part of the capabilities of bsAbs. After designing and developing a large number of bsAbs for years, catumaxomab, a full-length bsAb targeting EpCAM and CD3, was approved in 2009 to treat EpCAM-positive carcinomas besides blinatumomab, a bispecific T cell engager antibody targeting CD19 and CD3, which was approved in 2014 to treat relapsed or refractory acute lymphoblastic leukemia. Furthermore, approximately 60 bsAbs are under investigation in clinical trials. The current review aims at portraying different formats of the single-chain variable fragment (scFv)-based bsAbs and shedding light on the scFv-based bsAbs in preclinical development, different phases of clinical trials, and the market.
DNA methylation and gene expression differences in children conceived in vitro or in vivo (2009)

Epidemiological data indicate that children conceived in vitro have a greater relative risk of low birth-weight, major and minor birth defects, and rare disorders involving imprinted genes, suggesting that epigenetic changes may be associated with assisted reproduction. We examined DNA methylation at more than 700 genes (1536 CpG sites) in placenta and cord blood and measured gene expression levels of a subset of genes that differed in methylation levels between children conceived in vitro versus in vivo. Our results suggest that in vitro conception is associated with lower mean methylation at CpG sites in placenta and higher mean methylation at CpG sites in cord blood. We also find that in vitro conception-associated DNA methylation differences are associated with gene expression differences at both imprinted and non-imprinted genes. The range of inter-individual variation in gene expression of the in vitro and in vivo groups overlaps substantially but some individuals from the in vitro group differ from the in vivo group mean by more than two standard deviations. Several of the genes whose expression differs between the two groups have been implicated in chronic metabolic disorders, such as obesity and type II diabetes. These findings suggest that there may be epigenetic differences in the gametes or early embryos derived from couples undergoing treatment for infertility. Alternatively, assisted reproduction technology may have an effect on global patterns of DNA methylation and gene expression. In either case, these differences or changes may affect long-term patterns of gene expression.
Immunohistochemical study of substance P-like immunoreactivity in human thyroid and medullary carcinoma of the thyroid. (1983)

Substance P-like immunoreactivity (SPL-IR) was identified by the indirect peroxidase anti-peroxidase (PAP) method in normal thyroid glands as well as in medullary thyroid carcinoma. The SPL-IR cells were visualized intrafollicularly in the thyroid, within cells which resembled the parafollicular C cells which contain calcitonin immunoreactivity. The SPL-IR cells distributed differently in the normal thyroid and in thyroid with secondary C cell hyperplasia.
Stimulation of the Calcitonin Gene-Related Peptide Enhancer by Mitogen-Activated Protein Kinases and Repression by an Antimigraine Drug in Trigeminal Ganglia Neurons (2003)

Calcitonin gene-related peptide (CGRP) is involved in the underlying pathophysiology of all vascular headaches, including migraines. Elevated levels of CGRP during migraine are restored to normal coincident with headache relief after treatment with the antimigraine drug sumatriptan. We have used primary cultures of trigeminal neurons under conditions simulating migraine pathology and therapy to study the mechanisms controlling the CGRP promoter. Using reporter genes in transient transfection assays, we demonstrate that an 18 bp enhancer containing a helix-loop-helix element is both necessary and sufficient for full promoter activity. NGF treatment and cotransfection with an upstream activator of the extracellular signal-regulated MAP kinases (MAPKs) activated the enhancer. Treatment with sumatriptan repressed NGF- and MAPK-stimulated CGRP promoter activity. Repression was also observed using a synthetic MAPK-responsive reporter gene. Sumatriptan regulation of CGRP gene expression did not couple to a G(i)/G(o) pathway, but rather caused a prolonged increase in intracellular calcium. The importance of the prolonged calcium signal in repression of MAPK activity was demonstrated by using the ionophore ionomycin to mimic sumatriptan action. We propose that activation of MAPK pathways may increase CGRP gene expression during migraine, and that sumatriptan can diametrically oppose that activation via a prolonged elevation of intracellular calcium.
[Androstenedione, DHEA sulfate, cortisol, aldosterone and testosterone in bronchial asthma patients]. (1990)

The basic level and the 24 h rhythm of secretion of cortisol, aldosterone, androstanedion, DHEA-sulfate and testosterone were determined in 26 men with bronchial asthma, 19 up to 50 years of age, in a free from attacks period. 20 of the patients had never been treated with corticosteroids and 6 patients had used corticosteroid drugs. In 26.32% of the patients who had not been treated with corticosteroids the basic cortisole level was either decreased or on the lower normal limit. At the same time in 55% of these patients a different degree increase of the basic DHEA-sulfate level was found and in 30% of the patients the androstanedione basic level was increased. The changes in the 24 h rhythm of androstanedione and DHEA-sulfate secretion were similar to those of cortisol. Normal rhythm of secretion of cortisol, aldosterone and testosterone was established mainly in patients with preserved basic hormonal secretion. In contrast to these, normal rhythm of androstanedione and DHEA-sulfate secretion was found more frequently in patients with increased basic secretion of these hormones.
A rapid quantitative assay for the detection of mammalian heparanase activity (1997)

Heparan sulphate (HS) is an important component of the extracellular matrix and the vasculature basal laminar which functions as a barrier to the extravasation of metastatic and inflammatory cells. Cleavage of HS by endoglycosidase or heparanase activity produced by invading cells may assist in the disassembly of the extracellular matrix and basal laminar, and thereby facilitate cell migration. Heparanase activity has previously been shown to be related to the metastatic potential of murine and human melanoma cell lines [Nakajima, Irimura and Nicolson (1988) J. Cell. Biochem. 36, 157-167]. To determine heparanase activity, porcine mucosal HS was partially de-N-acetylated and re-N-acetylated with [3H]acetic anhydride to yield a radiolabelled substrate. This procedure prevented the masking of, or possible formation of, new heparanase-sensitive cleavage sites as has been observed with previous methods of radiolabelling. Heparanase activity in a variety of tissues and cell homogenates including human platelets, colonic carcinoma cells, umbilical vein endothelial cells and rat mammary adenocarcinoma cells (both metastatic and non-metastatic variants) and liver homogenates all degraded the substrate in a stepwise fashion from 18.5 to approximately 13, 8 and finally to 4.5 kDa fragments, as assessed by gel-filtration analysis, confirming the substrate as suitable for the detection of heparanase activity present in a variety of cells and tissues. A rapid quantitative assay was developed with the HS substrate using a novel method for separating degradation products from the substrate by taking advantage of the decreased affinity of the heparanase-cleaved products for the HS-binding plasma protein chicken histidine-rich glycoprotein (cHRG). Incubation mixtures were applied to cHRG-Sepharose columns, with unbound material corresponding to heparanase-degradation products. Heparanase activity was determined for a variety of human, rat and murine cell and tissue homogenates. The highly metastatic rat mammary adenocarcinoma and murine lung carcinoma cell lines had four to ten times the heparanase activity of non-metastatic variants, confirming the correlation of heparanase activity with metastatic potential. Human cancer patients had twice the serum heparanase levels of normal healthy adults. The assay will be valuable for the determination of heparanase activity from a variety of tissue and cell sources, as a diagnostic tool for the determination of heparanase potential, and for the development of specific inhibitors of heparanase activity and metastasis.
Advanced CMOS transistors with a novel HfSiON gate dielectric (2003)

We report for the first time on short channel transistors fabricated using HfSiON, a new high-k gate dielectric material. HfSiON has superior electrical characteristics such as low leakage current relative to SiO/sub 2/, low interfacial trap density, electron and hole carrier mobilities /spl sim/80% of the universal curve at E/sub eff/>0.8 MV/cm and scalability to equivalent oxide thicknesses of less than 10 /spl Aring/. This material is also thermally stable up to 1100/spl deg/C in contact with poly Si, and exhibits boron blocking significantly better than SiO/sub 2/ and SiON. The results indicate that this material is a promising high-k gate dielectric with good transistor characteristics.
Preclinical trials using an immunoconjugate of T101 and methotrexate in an athymic mouse/human T-cell tumor model. (1988)

We made an immunoconjugate (IC) using the anti-CD5 monoclonal antibody T101 and the chemotherapeutic drug methotrexate. Methotrexate was conjugated to T101 using an active ester intermediate, yielding a drug: antibody molar ratio of 12.4. Although T101 immunoreactivity was not significantly altered by conjugation, the IC did not demonstrate antigen-specific cytotoxicity in vitro. Methotrexate activity, assayed in vitro, decreased approximately 100-fold following conjugation. The IC was tested for in vivo efficacy in athymic mice bearing human T-cell (MOLT 4) xenografts. Experimental arms used in the study included i.p. injections of saline, T101, methotrexate, the IC, and a mixture of T101 and methotrexate. Doses ranged from 500 micrograms T101 (17.5 micrograms methotrexate) to 2 mg T101 (70 micrograms methotrexate). Injections were administered only after palpable tumors were established. In experiments at all doses, totaling 66 animals per arm, injection of the IC significantly inhibited tumor growth, and resulted in more tumor regressions and fewer animal deaths than the other four experimental arms. These data demonstrate that the IC promotes a potential advantage over the use of methotrexate through an increase in the therapeutic index.