gebhart/patrepeval huggingface dataset:
Characterization of Mechanisms Involved in Transrepression of NF-κB by Activated Glucocorticoid Receptors (1995)

Glucocorticoids are potent immunosuppressants which work in part by inhibiting cytokine gene transcription. We show here that NF-kappa B, an important regulator of numerous cytokine genes, is functionally inhibited by the synthetic glucocorticoid dexamethasone (DEX). In transfection experiments, DEX treatment in the presence of cotransfected glucocorticoid receptor (GR) inhibits NF-kappa B p65-mediated gene expression and p65 inhibits GR activation of a glucocorticoid response element. Evidence is presented for a direct interaction between GR and the NF-kappa B subunits p65 and p50. In addition, we demonstrate that the ability of p65, p50, and c-rel subunits to bind DNA is inhibited by DEX and GR. In HeLa cells, DEX activation of endogenous GR is sufficient to block tumor necrosis factor alpha or interleukin 1 activation of NF-kappa B at the levels of both DNA binding and transcriptional activation. DEX treatment of HeLa cells also results in a significant loss of nuclear p65 and a slight increase in cytoplasmic p65. These data reveal a second mechanism by which NF-kappa B activity may be regulated by DEX. We also report that RU486 treatment of wild-type GR and DEX treatment of a transactivation mutant of GR each can significantly inhibit p65 activity. In addition, we found that the zinc finger domain of GR is necessary for the inhibition of p65. This domain is also required for GR repression of AP-1. Surprisingly, while both AP-1 and NF-kappa B can be inhibited by activated GR, synergistic NF-kappa B/AP-1 activity is largely unaffected. These data suggest that NF-kappa B, AP-1, and GR interact in a complex regulatory network to modulate gene expression and that cross-coupling of NF-kappa B and GR plays an important role in glucocorticoid-mediated repression of cytokine transcription.
The sequential maximum angle convex cone (SMACC) endmember model (2004)

A new endmember extraction method has been developed that is based on a convex cone model for representing vector data. The endmembers are selected directly from the data set. The algorithm for finding the endmembers is sequential: the convex cone model starts with a single endmember and increases incrementally in dimension. Abundance maps are simultaneously generated and updated at each step. A new endmember is identified based on the angle it makes with the existing cone. The data vector making the maximum angle with the existing cone is chosen as the next endmember to add to enlarge the endmember set. The algorithm updates the abundances of previous endmembers and ensures that the abundances of previous and current endmembers remain positive or zero. The algorithm terminates when all of the data vectors are within the convex cone, to some tolerance. The method offers advantages for hyperspectral data sets where high correlation among channels and pixels can impair un-mixing by standard techniques. The method can also be applied as a band-selection tool, finding end-images that are unique and forming a convex cone for modeling the remaining hyperspectral channels. The method is described and applied to hyperspectral data sets.
Searching for the prototypic eye genetic network: Sine oculis is essential for eye regeneration in planarians (2000)

We have identified a sine oculis gene in the planarian Girardia tigrina (Platyhelminthes; Turbellaria; Tricladida). The planarian sine oculis gene (Gtso) encodes a protein with a sine oculis (Six) domain and a homeodomain that shares significant sequence similarity with so proteins assigned to the Six-2 gene family. Gtso is expressed as a single transcript in both regenerating and fully developed eyes. Whole-mount in situ hybridization studies show exclusive expression in photoreceptor cells. Loss of function of Gtso by RNA interference during planarian regeneration inhibits eye regeneration completely. Gtso is also essential for maintenance of the differentiated state of photoreceptor cells. These results, combined with the previously demonstrated expression of Pax-6 in planarian eyes, suggest that the same basic gene regulatory circuit required for eye development in Drosophila and mouse is used in the prototypic eye spots of platyhelminthes and, therefore, is truly conserved during evolution.
Synthetic Nucleosides and Nucleotides. XX1. Synthesis of Various 1-β-

D

-Xylofuranosyl-5-Alkyluracils and Related Nucleosides (1982)

Abstract Treatment of D-xylose (1) with 0.5% methanolic hydrogen chloride under controlled conditions followed by benzoylation and acetolysis afforded crystalline 1-O-acetyl-2, 3, 5-tri-O-benzoyl-α-D-xylofuranose (4) in good yield. Coupling of 4 with 2, 4-bis-trimethylsilyl derivatives of 5-alkyluracils (methyl, ethyl, propyl and butyl) (5a-5d), 5-fluorouracil (5e) and uracil (5f) in acetonitrile in the presence of stannic chloride gave 1-(2,3,5-tri-O-benzoyl-β-D-xylofuranosyl)-nucleosides (6a-6f). Saponification of 6 with sodium methoxide afforded 1-β-D-xylofuranosyl-5-substituted uracils (7a-7f). Condensation of 4 with free adenine in similar fashion and deblocking gave carcinostatic 9-β-D-xylofuranosyladenine (7g).
An evaluation of oligonucleotide-based therapeutic strategies for polyQ diseases (2012)

Using three cellular models of polyQ diseases and the same experimental setup we directly compared the performance of different oligonucleotide-based treatment strategies that are currently under development. Based on the results obtained by us and others we discussed the advantages and drawbacks of these strategies considering them from several different perspectives. The strategy aimed at nonallele-selective inhibiting of causative gene expression by targeting specific sequence of the implicated gene is the easiest to implement but relevant benefits are still uncertain. The gene replacement strategy that combines the nonallele-selective gene silencing with the expression of the exogenous normal allele is a logical extension of the former and it deserves to be explored further. Both allele-selective RNAi approaches challenge cellular RNA interference machinery to show its ability to discriminate between similar sequences differing in either single base substitutions or repeated sequence length. Although both approaches perform well in allele discrimination most of our efforts are focused on repeat targeting due to its potentially higher universality.
The Escherichia coli relBE genes belong to a new toxin–antitoxin gene family (1998)

Toxin-antitoxin systems are defined as a group of plasmid- and chromosome-encoded loci that specify a cell toxin and a protein antitoxin. Plasmid-encoded toxin-antitoxin systems stabilize their replicons by killing plasmid-free cells. Here, we show that the relBE genes of Escherichia coli K-12 have all the basic features previously connected with toxin-antitoxin systems: (i) relE encodes a cytotoxin lethal or inhibitory to host cells; (ii) relB encodes an antitoxin that prevents the lethal action of the relE-encoded toxin; (iii) the relBE genes stabilize a mini-R1 test plasmid; and (iv) the RelB antitoxin autoregulates the relBEF operon at the level of transcription. Using database searching, we found relBE homologues on the chromosomes of E. coli K-12, Haemophilus influenzae and Vibrio cholerae. A fifth relBE homologue was identified on the enterotoxin encoding E. coli plasmid P307. Indirect evidence suggests that the toxicity of RelE may be related to the inhibition of protein synthesis. Based on these observations, we propose a model that explains the delayed relaxed phenotype associated with mutations in relB.
Clinical and EEG Features of Complex Partial Seizures of Extratemporal Origin (1986)

Complex partial seizures (CPSs) of extratemporal origin are frequently misdiagnosed. Common reasons for diagnostic errors are failure to recognize the epileptic cause of the attacks or to appreciate localizing clinical seizure characteristics and nonspecific or misleading scalp EEG findings. This report describes clinical characteristics of two types of extratemporal CPSs, frontal and occipital. Frontal lobe CPSs are brief, frequent attacks that begin and end suddenly. They are dominated by complex, semi-purposeful motor automatisms, and vocalization and sexual automatisms are common. Their often bizarre appearance frequently leads to a misdiagnosis of hysteria. Occipital lobe CPSs are characterized primarily by their spread pattern, which can follow various paths. They may mimic temporal lobe CPSs, sensorimotor partial seizures, or supplementary motor partial seizures. Scalp EEGs are frequently misleading. The initial clinical symptoms are the most important clue to correct diagnosis and include elemental visual symptoms, visual loss, eye pulling or movement sensations in the absence of detectable movement, rapid forced blinking or eye flutter, and contralateral eye deviation.
Colony-stimulating factors as promoters of ameboid microglia (1988)

Immunomodulators were tested for their ability to stimulate proliferation and biologic activity of ameboid microglia. Only the colony-stimulating factors (CSFs), multipotential-CSF (multi-CSF) and granulocyte/macrophage-CSF (GM-CSF), were potent mitogens for microglia. Other immunomodulators, including interleukin-1, interleukin-2, interferon gamma, tumor necrosis factor, or granulocyte-CSF (G-CSF), had no effect upon microglial growth in vitro. Multi-CSF or GM-CSF were also observed to induce more rapid phagocytosis of polystyrene microspheres by cultured ameboid cells. In order to determine which immunomodulators alter brain inflammatory responses in vivo, we infused recombinant forms of GM-CSF, multi-CSF, macrophage-CSF, or G-CSF into the cerebral cortex of rats. Within 48 hr after infusion multi-CSF or GM-CSF stimulated the appearance of large numbers of mononuclear phagocytes at the site of injection. These same factors also accelerated the clearance of polystyrene microspheres from the brain. Our observations indicate that certain classes of immunomodulators which are mitogens and activators of ameboid microglia in vitro amplify the inflammatory response of the CNS in vivo by action upon intrinsic brain mononuclear phagocytes.
Fluorescence Quenching of 1‐Pyrenemethanol by Methylviologen in Polystyrene Latex Dispersions (1996)

Abstract Fluorescence quenching of 1‐pyrenemethanol by methylviologen through photoinduced electron transfer is investigated in polystyrene (PS) latex dispersions as well as in aqueous homogeneous solutions. In aqueous homogeneous solutions, the Stern‐Volmer plot for the intensity is linear and close to that for the lifetime, indicating a dynamic quenching mechanism. In PS latex dispersions, however, the Stern‐Volmer plots for the intensity are downward curving and the decay curves are not so much affected by the quencher as those for aqueous solutions, implying a significant contribution of static quenching. The downward‐curving Stern‐Volmer plots are well described by a two‐site model that assumes accessible and inaccessible sites to the acceptor on latex particles. The Stern‐Volmer constants obtained indicate that in the latex dispersions the fluorescence quenching occurs several hundreds times more efficiently than that in an aqueous homogeneous solution. This drastic enhancement of the quenching in latex dispersions is attributed to the increase in the local concentrations of the reactants on the latex surface. We have demonstrated the usefulness of latex surfaces as a new type of reaction field for photoinduced electron transfer.
Insomnia, depression and aging. Assessing sleep and mood interactions in older adults. (2004)

Insomnia and depression are related to each other on the level of epidemiology, clinical presentation, neurobiology, and treatment implications. The changes in sleep seen in older adults make these relationships particularly strong. Epidemiological studies show that depression is one of the strongest risk factors for current insomnia, but recent evidence indicates that this relationship is bi-directional: current insomnia is a risk factor for future depression. Changes in objective measures of sleep in depression mirror the changes seen in the aging process. Treating sleep disturbances may improve outcomes in patients with depression. Physicians should routinely question their older patients about sleep problems and depression.
Validation of a Gas Chromatographic Method for Determination of Fatty Alcohols in 10 mg Film-Coated Tablets of Policosanol (2002)

A gas chromatographic method using a packed column and 1-eicosanol as an internal standard was validated for the determination of the fatty alcohols that compose policosanol in 10 mg film-coated tablets. The alcohols were determined as trimethylsilyl derivatives, prepared with N-methyl-N-trimethylsilyltrifluoroacetamide. The method can detect degradation products with high retention times, without interfering with the peaks of the active principle. Good linearity (correlation coefficient = 0.9992) and accuracy (mean recovery -100.27 +/- 1.66%) were proven over a range of 25-200% of the nominal concentration. Within- and between-day precision at the nominal 100% value met the acceptance criteria (<2%). Ruggedness was examined through an intralaboratory experimental study in which 6 operational changes were made; the changes were found to have no effect on quantitation, repeatability, resolution, and relative retention time. The method is suitable for the quality control process and stability studies of these tablets.
Environmental Regulation of Lateral Root Emergence inMedicago truncatulaRequires the HD-Zip I Transcription Factor HB1 (2010)

The adaptation of root architecture to environmental constraints is a major agricultural trait, notably in legumes, the third main crop worldwide. This root developmental plasticity depends on the formation of lateral roots (LRs) emerging from primary roots. In the model legume Medicago truncatula, the HD-Zip I transcription factor HB1 is expressed in primary and lateral root meristems and induced by salt stress. Constitutive expression of HB1 in M. truncatula roots alters their architecture, whereas hb1 TILLING mutants showed increased lateral root emergence. Electrophoretic mobility shift assay, promoter mutagenesis, and chromatin immunoprecipitation-PCR assays revealed that HB1 directly recognizes a CAATAATTG cis-element present in the promoter of a LOB-like (for Lateral Organ Boundaries) gene, LBD1, transcriptionally regulated by auxin. Expression of these genes in response to abscisic acid and auxin and their behavior in hb1 mutants revealed an HB1-mediated repression of LBD1 acting during LR emergence. M. truncatula HB1 regulates an adaptive developmental response to minimize the root surface exposed to adverse environmental stresses.
Carisbamate as adjunctive treatment of partial onset seizures in adults in two randomized, placebo‐controlled trials (2009)

Carisbamate 400 mg/day was effective in patients with refractory partial-onset seizures in one of these global studies. More than 200 mg/day of carisbamate is required for efficacy. Carisbamate was well-tolerated in both studies.
Implementation and evaluation of patient-specific three-dimensional internal dosimetry. (1997)

The dose-volume histogram representation of absorbed dose to a target volume provides valuable information in assessing tumor control probability and normal tissue toxicity.
Tumor Metabolism of Malignant Gliomas (2013)

Constitutively activated oncogenic signaling via genetic mutations such as in the EGFR/PI3K/Akt and Ras/RAF/MEK pathways has been recognized as a major driver for tumorigenesis in most cancers. Recent insights into tumor metabolism have further revealed that oncogenic signaling pathways directly promote metabolic reprogramming to upregulate biosynthesis of lipids, carbohydrates, protein, DNA and RNA, leading to enhanced growth of human tumors. Therefore, targeting cell metabolism has become a novel direction for drug development in oncology. In malignant gliomas, metabolism pathways of glucose, glutamine and lipid are significantly reprogrammed. Moreover, molecular mechanisms causing these metabolic changes are just starting to be unraveled. In this review, we will summarize recent studies revealing critical gene alterations that lead to metabolic changes in malignant gliomas, and also discuss promising therapeutic strategies via targeting the key players in metabolic regulation.
Application of differential display, with in situ hybridization verification, to microscopic samples of breast cancer tissue (2003)

The technique of differential display (DD) has been used widely to identify potentially interesting overexpressed or repressed genes in a variety of compared samples. When used in studying tissue samples, it inevitably confronts problems of limited amount of input material and cell-type heterogeneity. We report here the application of in situ hybridization as a method of confirmatory test for DD as well as definition of cell type expressing differential cDNA. This procedure employed material derived from a single case of human mammary, grade III, infiltrating ductal carcinoma, using free-hand microdissection, where we have compared gene expression profiles in invasive tumour with those in adjacent normal tissue. A total of 21 cDNAs were found to be differentially expressed between the two tissue types; 11 upregulated in the tumour sample and 10 upregulated in the normal sample. Six cDNAs were utilized as probes for in situ hybridization analysis of a further five cases of comparably staged breast cancer. One of these clones, 11AT1, which was found to be homologous to Hsc70, was shown to be overexpressed in tumour cells relative to adjacent normal stroma and to benign glandular epithelium in all five cases; an increase in expression was further confirmed at protein level by immunohistochemistry. The study demonstrated the applicability of in situ hybridization as a screening test in DD strategy for studying tissue material and a reasonable technique combination of identifying changes in gene expression associated with tumour development.
Tumor protein p53-induced nuclear protein 1 (TP53INP1) in spontaneous chronic pancreatitis in the WBN/Kob rat: drug effects on its expression in the pancreas. (2004)

TP53INP1 expression may reflect the acute-phase response and apoptosis of acinar cells in the course of chronic pancreatitis.
Systemic Interleukin-2 Modulates the Anti-Idiotypic Response to Chimeric Anti-GD2 Antibody in Patients with Melanoma (1996)

The induction of human antimouse antibodies (HAMA) and human anti-idiotypic (anti-Id) responses in cancer patients receiving therapeutic monoclonal antibody (mAb) may limit the effectiveness of the administered mAb. This report evaluates the influence of systemic interleukin-2 (IL-2) on the anti-Id response to anti-disialoganglioside (anti-GD2) antibody given as treatment for patients with melanoma. Twenty-eight patients with melanoma received combined immunotherapy with anti-GD2 antibody and IL-2 at 1.5 x 10(6) U/m2/day given 4 days/week. The anti-GD2 antibody [murine 14.G2a mAb; dose levels of 2-5 mg/m2/day (4 patients); or human-mouse chimeric 14.18 (ch14.18) antibody; dose levels of 2-10 mg/m2/day (24 patients)] was scheduled to be given for 5 days either before, during, or after initial systemic IL-2 treatment. All four patients who received murine 14.G2a developed HAMA anti-isotype antibodies (660-1,000 ng/ml) as well as measurable anti-Id antibodies. All three patients who received initial treatment with ch14.18 alone developed a strong anti-Id antibody response after IL-2 was started 1 week later. The serum level of anti-Id antibody decreased during subsequent ch14.18 infusions, suggesting that the anti-Id antibody may be binding the administered ch14.18. In contrast, measurable anti-Id antibody was detected in only 3 of 14 patients who received IL-2 before, during, and after initial ch14.18 administration. Two of four patients receiving systemic IL-2 before and during initial ch14.18 infusions, and two of three patients receiving systemic IL-2 concurrent with initial ch14.18 infusions developed anti-Id antibodies. These data suggest that the anti-Id response to chimeric anti-GD2 antibody is influenced by the timing of systemic IL-2 in relation to antibody administration and can be suppressed by systemic treatment with IL-2 given before, during, and after the antibody administration.
Leucine alters the interaction of the leucine‐responsive regulatory protein (Lrp) with the fim switch to stimulate site‐specific recombination in Escherichia coli (1998)

The leucine-responsive regulatory protein (Lrp) is a global regulator that controls the expression of numerous operons in Escherichia coli. Lrp can act as a repressor or as an activator of transcription with its effects being potentiated, repressed or unaffected by the presence of exogenous leucine. The phase variation of type 1 fimbria in E. coli provides a unique system in which to investigate the effects of leucine on Lrp, as it is the only known example in which Lrp is a positive regulator and leucine potentiates this effect. Previous studies determined that Lrp binds with high affinity to two sites within the fim switch (fim sites 1 and 2), and binding to these sites stimulates recombination. Here, it is shown that, even though leucine stimulates the fim switch in vivo, it nevertheless causes a slight decrease in Lrp binding to the fim switch in vitro. These contradictory results are explicable by the finding that Lrp binding to a third region adjacent to fim sites 1 and 2 inhibits recombination. According to this model, leucine stimulates recombination by selectively disrupting Lrp binding to this newly characterized region, while having little or no effect on Lrp binding to fim sites 1 and 2.
Allele-specific copy number profiling by next-generation DNA sequencing (2014)

The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in the characterization of tumor genomes and the inference of their clonal history. We describe a new method, falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normals. falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases. By using the Binomial distribution rather than a normal approximation, falcon more effectively pools evidence from sites with low coverage. A modified Bayesian information criterion is used to guide model selection for determining the number of copy number events. Falcon is evaluated on in silico spike-in data and applied to the analysis of a pre-malignant colon tumor sample and late-stage colorectal adenocarcinoma from the same individual. The allele-specific copy number estimates obtained by falcon allows us to draw detailed conclusions regarding the clonal history of the individual's colon cancer.
Liposomal doxorubicin: antitumor activity and unique toxicities during two complementary phase I studies. (1995)

The toxicity profile of DOX-SL differs prominently from that of the free drug administered by bolus or rapid infusion and with some differences, resembles that of prolonged continuous infusion. This finding, as well as the antitumor activity observed, supports wide phase II testing of DOX-SL in solid tumors.