gebhart/patrepeval huggingface dataset:
Pharmacological enhancement of in vivo foreign gene expression in muscle. (1994)

Intramuscular injection of naked plasmid DNA provides a means for gene transfer and expression in striated muscle. In this study, the effects of treating muscle with normal saline, etidocaine, mepivacaine, acetic anhydride, sodium bicarbonate, Notechis scutatus venom, cardiotoxin and bupivacaine before plasmid DNA injection on foreign gene expression were evaluated. Dose dependence, strain and species specificity, the time interval between pharmacological agent and plasmid DNA injection, the stability of gene expression and the fate of the injected plasmid DNA were studied using reporter gene expression, by histological examination and semi-quantitative polymerase chain reaction. Of the various agents tested, the best enhancement of foreign gene expression occurred in muscle treated with 0.75% bupivacaine five to seven days before plasmid DNA injection. Rat and mouse quadriceps muscle treated with 0.75% bupivacaine had levels of luciferase activity four- to 40-times greater than non-bupivacaine-treated muscle. Also, beta-galactosidase expressing myofibers were observed throughout the length of the muscle in samples treated with 0.75% bupivacaine before reporter gene injection. Muscle treated with 0.75% bupivacaine fully recovered from the degeneration caused by its injection with no long-term effects histologically. The heightened level of reporter gene expression persisted in 0.75% bupivacaine-treated muscle for one month, but decreased to that of non-bupivacaine-treated muscle by two months after plasmid DNA injection. Enhancement of foreign gene expression may be particularly advantageous in vaccination protocols employing intramuscular plasmid injection.
In Vivo Microbial Stimulation Induces Rapid CD40 Ligand–independent Production of Interleukin 12 by Dendritic Cells and their Redistribution to T Cell Areas (1997)

The early induction of interleukin (IL)-12 is a critical event in determining the development of both innate resistance and adaptive immunity to many intracellular pathogens. Previous in vitro studies have suggested that the macrophage (MPhi) is a major source of the initial IL-12 produced upon microbial stimulation and that this response promotes the differentiation of protective T helper cell 1 (Th1) CD4+ lymphocytes from precursors that are primed on antigen-bearing dendritic cells (DC). Here, we demonstrate by immunolocalization experiments and flow cytometric analysis that, contrary to expectation, DC and not MPhi are the initial cells to synthesize IL-12 in the spleens of mice exposed in vivo to an extract of Toxoplasma gondii or to lipopolysaccharide, two well characterized microbial stimulants of the cytokine. Importantly, this production of IL-12 occurs very rapidly and is independent of interferon gamma priming or of signals from T cells, such as CD40 ligand. IL-12 production by splenic DC is accompanied by an increase in number of DCs, as well as a redistribution to the T cell areas and the acquisition of markers characteristic of interdigitating dendritic cells. The capacity of splenic DC but not MPhi to synthesize de novo high levels of IL-12 within hours of exposure to microbial products in vivo, as well as the ability of the same stimuli to induce migration of DC to the T cell areas, argues that DC function simultaneously as both antigen-presenting cells and IL-12 producing accessory cells in the initiation of cell-mediated immunity to intracellular pathogens. This model avoids the need to invoke a three-cell interaction for Th1 differentiation and points to the DC as both a sentinel for innate recognition and the dictator of class selection in the subsequent adaptive response.
The Importance of Drug Scheduling in Cancer Chemotherapy: Etoposide as an Example (1996)

Abstract Etoposide is a drug whose antineoplastic activity is dependent on the schedule of drug administration. This article reviews the rationale for a prolonged schedule of etoposide administration and the therapeutic results of use of such a schedule in the treatment of cancer. The pharmacology of etoposide is also reviewed, with particular attention paid to the pharmacokinetics of oral etoposide and etoposide plasma concentrations associated with cytotoxicity.
Clofazimine-an effective treatment for Melkersson-Rosenthal syndrome or Miescher's cheilitis (1986)

Three cases of histological proven Miescher's granulomatous cheilitis and one case of Melkersson‐Rosenthal syndrome were treated over a 4‐month period. All cases showed histological improvement with clearance of granulomata but persistence of oedema. No side‐effects were reported. Biopsy changes in all four cases are presented.
Sexual Differentiation of the Central Nervous System (1981)

Sexual differentiation of reproductive and behavior patterns is largely effected by hormones produced by the gonads. In many higher vertebrates, an integral part of this process is the induction of permanent and essentially irreversible sex differences in central nervous function, in response to gonadal hormones secreted early in development.
Inflammation and autoantibody markers identify rheumatoid arthritis patients with enhanced clinical benefit following rituximab treatment (2011)

The presence of any RF isotype and/or IgG anti-CCP autoantibodies together with an elevated CRP level identifies a subgroup of patients with RA in whom the benefit of rituximab treatment may be enhanced. Although the clinical benefit of rituximab was greater in the biomarker-positive population compared with the biomarker-negative population, the clinical benefit of rituximab compared with placebo was also clinically meaningful in the biomarker-negative population.
Sugar composition of dietary fibre and short-chain fatty acid production during in vitro fermentation by human bacteria (1993)

The aim of the present study was to assess the relationship between the disappearance of dietary fibre sugars and the production of individual short-chain fatty acids (SCFA). The bacterial degradation of five dietary fibres whose sugars were quantified was investigated in vitro using a human faecal inoculum. Involvement of the main fibre sugars in SCFA production was evaluated by a stepwise multiple linear regression. The results show first that the nature and chiefly the associations between the fibre sugars were key variables in the fermentability. Second, the nature and the amounts of SCFA produced were closely related to the in vitro fermentation of the main sugars available: uronic acids seemed to be principally involved in the production of acetic acid whereas the production of propionic acid could be promoted by the fermentation of glucose and, to a lesser extent, by that of xylose and arabinose. Xylose tended to have a greater impact than uronic acids and glucose on the production of butyric acid. Thus, it would be possible to predict which SCFA could be specifically produced during the fermentation of a fibre, as far as the chemical composition and structure of this fibre are known.
Granulocyte-colony stimulating factor mobilizes T helper 2-inducing dendritic cells (2000)

Abstract Peripheral blood stem cells (PBSC) obtained from granulocyte-colony stimulating factor (G-CSF)-mobilized donors are increasingly used for allogeneic transplantation. Despite a 10-fold higher dose of transplanted T cells, acute graft-versus-host disease (GVHD) does not develop in higher proportion in recipients of PBSC than in recipients of marrow. T cells from G-CSF-treated experimental animals preferentially produce IL-4 and IL-10, cytokines characteristic of Th2 responses, which are associated with diminished GVHD-inducing ability. We hypothesized that G-CSF-mobilized PBSC contain antigen-presenting cells, which prime T-lymphocytes to produce Th2 cytokines. Two distinct lineages of dendritic cells (DC) have been described in humans, DC1 and DC2, according to their ability to induce naive T-cell differentiation to Th1 and Th2 effector cells, respectively. We have used multicolor microfluorometry to enumerate DC1 and DC2 in the peripheral blood of normal donors. G-CSF treatment with 10 to 16 μg/kg per day for 5 days increased peripheral blood DC2 counts from a median of 4.9 × 106/L to 24.8 × 106/L (P = .0009), whereas DC1 counts did not change. Purified DC1, from either untreated or G-CSF treated donors, induced the proliferation of allogeneic naive T cells, but fresh DC2 were poor stimulators. Tumor necrosis factor- (TNF-)-activated DC1 induced allogeneic naive T cells to produce IFN-γ, which is typical of Th1 responses, whereas TNF--activated DC2 induced allogeneic naive T cells to produce IL-4 and IL-10, which are typical of Th2 responses. PBSC transplants contained higher doses of DC2 than marrow transplants (median, 2.4 × 106/kg versus 0.5 × 106/kg) (P = .006), whereas the dose of DC1 was comparable. Thus, it is conceivable that transplantation of G-CSF-stimulated PBSC does not result in overwhelming acute GVHD because the graft contains predominantly Th2-inducing DC. Adoptive transfer of purified DC2 may be exploited to induce immune deviation after transplantation of hematopoietic stem cells or organ allografts.
Preparation and optical properties of Ga1−xInxN thin films (1975)

By the use of the electron beam plasma technique, it has been found that the solid solutions of Ga1−xInxN can be synthesized over the entire composition region. From the optical measurements, the direct energy gap at 78 °K was determined to be 3.46 eV for GaN and 2.11 eV for InN. Also its composition dependence was found to deviate downward from linearity. From the infrared reflectivity measurement and the resultant K-K dispersion analysis, the transverse optical frequencies for long-wavelength phonons of GaN and InN were 563 and 478 cm−1, respectively. The optical phonons in this quasibinary system were concluded to exhibit a one-mode–type behavior. The Brout sum rule was discussed for a large number of the diatomic crystals of ANB8−N type and its relation with respect to the reduced mass was derived as Σiω2i(k=0) =A μ−1.5. According to this relation, the longitudinal optical frequency of InN was deduced to be 694 cm−1. On the other hand, from the result of the annealing treatment for the solid-solution alloys and the theoretical consideration, it was pointed out that this quasibinary system has a solid-phase misibility gap in chemical equilibrium.
A dual-luciferase reporter system for studying recoding signals. (1998)

A new reporter system has been developed for measuring translation coupling efficiency of recoding mechanisms such as frameshifting or readthrough. A recoding test sequence is cloned in between the renilla and firefly luciferase reporter genes and the two luciferase activities are subsequently measured in the same tube. The normalized ratio of the two activities is proportional to the efficiency with which the ribosome "reads" the recoding signal making the transition from one open reading frame to the next. The internal control from measuring both activities provides a convenient and reliable assay of efficiency. This is the first enzymatic dual reporter assay suitable for in vitro translation. Translation signals can be tested in vivo and in vitro from a single construct, which allows an intimate comparison between the two systems. The assay is applicable for high throughput screening procedures. The dual-luciferase reporter system has been applied to in vivo and in vitro recoding of HIV-1 gag-pol, MMTV gag-pro, MuLV gag-pol, and human antizyme.
SILICON IN THE QUANTUM LIMIT: QUANTUM COMPUTING AND DECOHERENCE IN SILICON ARCHITECTURES (2005)

Semiconductor architectures hold promise for quantum information processing (QIP) applications due to their large industrial base and perceived scalability potential. Electron spins in silicon in particular may be an excellent architecture for QIP and also for spin electronics (spintronics) applications. While the charge of an electron is easily manipulated by charged gates, the spin degree of freedom is well isolated from charge fluctuations. Inherently small spin-orbit coupling and the existence of a spin-zero Si isotope facilitate long single spin qubit coherence times. Here we consider the relaxation properties of localized electronic states in silicon due to donors, quantum wells, and quantum dots, including effects due to phonons and Rashba spin-orbit coupling. Our analysis is impeded by the complicated, many-valley band structure of silicon and previously unaddressed physics in silicon quantum wells. We find that electron spins in silicon and especially strained silicon have excellent decoherence properties. Where possible we compare with experiment to test our theories. We go beyond issues of coherence in a quantum computer to problems of control and measurement. Precisely what makes spin relaxation so long in semiconductor architectures makes spin measurement so difficult. To address this, we propose a new scheme for spin readout which has the added benefit of automatic spin initialization, a vital component of quantum computing and quantum error correction. Our results represent important practical milestones on the way to the design and construction of a silicon-based quantum computer.
Regulatory features of the epidermal growth factor receptor (1987)

The role of EGF receptor concentration in tumor growth was investigated in athymic mice by measuring the rate of growth of clonal human epidermoid carcinoma A431 cells containing different extents of EGF receptor gene amplification and protein expression. A direct correlation-between the rate of tumor growth and EFG receptor concentration was found, supporting previous cell culture studies that quantitated the relationship between activated EGF receptors and cell proliferation. Holo EGF receptor is activated by ligand binding to the extracellular domain to activate cytoplasmic tyrosine protein kinase activity. A model of single molecule transmembrane signaling is proposed. The function of two phosphorylation sites on the EGF receptor has been analyzed by use of site-directed mutagenesis. Comparison of normal and mutant hEGF receptors expressed in rodent cells lacking endogenous EGF receptors indicates that: 1) Thr654, located 10 amino acids carboxyl terminal to the inner membrane boundary, is a major site of heterologous regulation via protein kinase C catalyzed phosphorylation, and 2) Tyr1173, the major site of self-phosphorylation, located at the carboxyl terminus, provides a secondary level of regulation of receptor function by acting as a competitive inhibitor with exogenous substrates.
Development of wearable optical topography system for mapping the prefrontal cortex activation (2009)

Optical topography (OT) based on near infrared spectroscopy is effective for measuring changes in the concentrations of oxygenated hemoglobin (oxy-Hb) and deoxygenated hemoglobin (deoxy-Hb) in the brain. It can be used to investigate brain functions of subjects of all ages because it is noninvasive and less constraining for subjects. Conventional OT systems use optical fibers to irradiate the scalp and detect light transmitted through the tissue in the human head, but optical fibers limit the subject's head position, so some small systems have been developed without using optical fibers. These systems, however, have a small number of measurement channels. We developed a prototype of a small, light, and wearable OT system that covers the entire forehead. We measured changes in the concentrations of oxy-Hb and deoxy-Hb in the prefrontal cortex while a subject performed a word fluency task. The results show typical changes in oxy-Hb and deoxy-Hb during the task and suggest that the prototype of our system can be used to investigate functions in the prefrontal cortex.
Mass and fatty acid composition of the 3-phosphorylated phosphatidylinositol bisphosphate isomer in stimulated human platelets (1993)

By high pressure liquid chromatography (HPLC) analysis, the occurrence of radiolabeled 3-phosphorylated phosphoinositides has been well documented in several cell systems, including agonist-stimulated platelets. The actual mass amounts and fatty acid composition of these unique lipids, however, have not been reported to date. In the present study, we report the mass and fatty acid composition of phosphatidylinositol (PI) 3,4-P2 from U46619-stimulated platelets using a thin-layer chromatographic system for the separation of PI 3,4-P2 from PI 4,5-P2. The mass of PI 3,4-P2 in the stimulated platelet was 180 +/- 9.7 pmol/1 x 10(9) platelets (mean +/- S.E., n = 4), representing 9.3% of total phosphatidylinositol bisphosphate (PIP2). Based on HPLC analysis, PI 3,4-P2 in unstimulated platelets represented < 0.5% of total PIP2 (which corresponds to < 7.0 pmol/1 x 10(9) platelets). Fatty acid analysis of this lipid revealed a composition very similar to the conventional polyphosphoinositides (stearic and arachidonic acids accounting for 44.2 and 40.4 mol %, respectively, of the fatty acids). Since PI 3,4-P2 also did not appear to be distinct from the other polyphosphoinositides, in regard to radiolabeling properties, it was concluded that this lipid is unlikely to originate from a unique precursor pool. This conclusion validates the use of HPLC analysis of radiolabeled phosphoinositides for the estimation of PI 3,4-P2 mass in agonist-stimulated platelets. The chromatographic procedure described should prove useful for the mass and fatty acid analysis of PI 3,4-P2 from other cell systems.
Monitoring the T-Cell Receptor Repertoire at Single-Clone Resolution (2006)

The adaptive immune system recognizes billions of unique antigens using highly variable T-cell receptors. The alphabeta T-cell receptor repertoire includes an estimated 10(6) different rearranged beta chains per individual. This paper describes a novel micro-array based method that monitors the beta chain repertoire with a resolution of a single T-cell clone. These T-arrays are quantitative and detect T-cell clones at a frequency of less than one T cell in a million, which is 2 logs more sensitive than spectratyping (immunoscope), the current standard in repertoire analysis. Using T-arrays we detected CMV-specific CD4+ and CD8+ T-cell clones that expanded early after viral antigen stimulation in vitro and in vivo. This approach will be useful in monitoring individual T-cell clones in diverse experimental settings, and in identification of T-cell clones associated with infectious disease, autoimmune disease and cancer.
Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes (2009)

Our microarray platform targeting the complementary strand of annotated genes successfully identified novel NATs that could not be identified by publically available cDNA data, and as such could not be detected by the usual "sense-targeting" microarray approach. Differentially expressed NATs monitored by this platform may provide candidates for investigations of gene function. An advantage of our microarray platform is that it can be applied to any genes and target samples of interest.
rbcS genes in Solanum tuberosum: conservation of transit peptide and exon shuffling during evolution. (1988)

Five genes of the rbcS gene family of Solanum tuberosum (potato) were studied. One of these is a cDNA clone; the other four are located on two genomic clones representing two different chromosomal loci containing one (locus 1) and three genes (locus 2), respectively. The intron/exon structure of the three genes in locus 2 is highly conserved with respect to size and position. These genes contain two introns, whereas the gene from locus 1 contains three introns. Although in most cases the amino acid sequences in the transit peptide part of different rbcS genes from the same species varied considerably more than the corresponding mature amino acid sequences, one exception found in tomato and potato indicates that the transit peptide of rbcS could have a special function. A comparison of the rbcS genes of higher plants with those of prokaryotes offers suggestive evidence that introns first served as spacer material in the process of exon shuffling and then were removed stepwise during the evolution of higher plants.
Hepatoma-Derived Growth Factor Is a Novel Prognostic Factor for Patients with Pancreatic Cancer (2006)

These findings suggest that HDGF could be a novel prognostic factor for pancreatic ductal carcinoma.
Taxol and embryonic development in the chick (1994)

Taxol, an inhibitor of microtubule disassembly, is currently under investigation in the therapy of several human cancers. The current investigation was undertaken to characterize potential taxol developmental toxicity in chicks. On one of days 1-4 of incubation, taxol was administered in dimethylsulfoxide (DMSO) or olive oil in a range of doses, the highest of which produced a high incidence of early embryo death. Production of gross structural malformations was sporadic and occurred in vehicle-treated as well as taxol-treated embryos. A more common manifestation of taxol toxicity was a syndrome of visceral abnormalities, including regression of the vitelline circulation, dilatation of the atria, and hemorrhage in the left side of the head and thorax, often with decreased eye pigmentation. Regardless of the day of treatment, this syndrome occurred at 4.5-5 days. To investigate the possibility that taxol induced its effect through disruption of angiogenesis in the vitelline circulation, filters soaked in taxol were applied to the margin of the germ disc. No inhibition of vessel development was demonstrated. We conclude that taxol decreases the viability of embryos and that this impairment of survival precludes the development of birth defects. Solvent toxicity is an important confounder in the investigation of taxol embryotoxicity.
Shape and Radius of Posterior Corneal Surface (1993)

The average asphericity values are below 1, hence the posterior corneal surface is described as a flattening ellipse. The rate of flattening of this surface is greater than the rate of flattening along the averaged anterior corneal surface.
Mutations in the Cytoplasmic Tail of Murine Leukemia Virus Envelope Protein Suppress Fusion Inhibition by R Peptide (2001)

During viral maturation, the cytoplasmic tail of the murine leukemia virus (MuLV) envelope (Env) protein undergoes proteolytic cleavage by the viral protease to release the 16-amino-acid R peptide, and this cleavage event activates the Env protein's fusion activity. We introduced Gly and/or Ser residues at different positions upstream of the R peptide in the cytoplasmic tail of the Friend MuLV Env protein and investigated their effects on fusion activity. Expression in HeLa T4 cells of a mutant Env protein with a single Gly insertion after I619, five amino acids upstream from the R peptide, induced syncytium formation with overlaid XC cells. Env proteins containing single or double Gly-Ser insertions after F614, 10 amino acids upstream from the R peptide, induced syncytium formation, and mutant proteins with multiple Gly insertions induced various levels of syncytium formation between HeLa T4 and XC cells. Immunoprecipitation and surface biotinylation assays showed that most of the mutants had surface expression levels comparable to those of the wild-type or R peptide-truncated Env proteins. Fluorescence dye redistribution assays also showed no hemifusion in the Env proteins which did not induce fusion. Our results indicate that insertion mutations in the cytoplasmic tail of the MuLV Env protein can suppress the inhibitory effect of the R peptide on membrane fusion and that there are differences in the effects of insertions in two regions in the cytoplasmic tail upstream of the R peptide.