gebhart/patrepeval huggingface dataset:
Hypermethylation-associated inactivation of p14(ARF) is independent of p16(INK4a) methylation and p53 mutational status. (2000)

The INK4a/ARF locus encodes two cell cycle-regulatory proteins, p16INK4a andp14ARF, which share an exon using different reading frames. p14ARF antagonizes MDM2-dependent p53 degradation. However, no point mutations in p14ARF not altering p16INK4a have been described in primary tumors. We report that p14ARF is epigenetically inactivated in several colorectal cell lines, and its expression is restored by treatment with demethylating agents. In primary colorectal carcinomas, p14ARF promoter hypermethylation was found in 31 of 110 (28%) of the tumors and observed in 13 of 41 (32%) colorectal adenomas but was not present in any normal tissues. p14ARF methylation appears in the context of an adjacent unmethylated p16INK4a promoter in 16 of 31 (52%) of the carcinomas methylated at p14ARF. Although p14ARF hypermethylation was slightly overrepresented in tumors with wild-type p53 compared to tumors harboring p53 mutations [19 of 55 (34%) versus 12 of 55 (22%)], this difference did not reach statistical significance. p14ARF aberrant methylation was not related to the presence of K-ras mutations. Our results demonstrate that p14ARF promoter hypermethylation is frequent in colorectal cancer and occurs independently of the p16INK4a methylation status and only marginally in relation to the p53 mutational status.
Immunotherapy for head and neck cancer: latest developments and clinical potential (2016)

Head and neck squamous cell cancer (HNSCC) is a malignancy with a rapidly changing demographic profile, given the recent epidemic of human papilloma virus related cancers. Most patients present with locally advanced disease and receive combination therapeutic approaches with curative potential, albeit with significant toxicity. Up to a third of patients, however, will eventually develop recurrent or metastatic disease. The prognosis of such patients is dismal, as palliative treatment options remain limited. Immune-directed therapies offer a novel therapeutic strategy beyond cytotoxic chemotherapy and are currently being evaluated in a wide variety of malignancies. HNSCC is a particularly favorable disease for immunotherapy, as immune evasion and dysregulation have been shown to play a key role in the initiation and progression of HNSCC. This review focuses on the latest developments in immunotherapy in HNSCC, with a particular focus on checkpoint inhibitors, adoptive cellular therapies, and vaccines.
Stereoselective catalytic hydrogenation of sorbic acid and sorbic alcohol with new Cp*Ru complexes (2000)

The new Cp*Ru complexes [Cp*Ru(η4-MeCHCHCHCHCO2H)]+ X− (X− = CF3SO3− or [B{C6H3(CF3)2-3,5} 4]−) are very effective catalysts for the hydrogenation of sorbic acid to cis-hex-3-enoic acid and of sorbic alcohol to cis-hex-3-en-1-ol (leaf alcohol) under mild conditions in liquid two-phase systems.
Deep learning for tissue microarray image-based outcome prediction in patients with colorectal cancer (2016)

Recent advances in computer vision enable increasingly accurate automated pattern classification. In the current study we evaluate whether a convolutional neural network (CNN) can be trained to predict disease outcome in patients with colorectal cancer based on images of tumor tissue microarray samples. We compare the prognostic accuracy of CNN features extracted from the whole, unsegmented tissue microarray spot image, with that of CNN features extracted from the epithelial and non-epithelial compartments, respectively. The prognostic accuracy of visually assessed histologic grade is used as a reference. The image data set consists of digitized hematoxylin-eosin (H and E) stained tissue microarray samples obtained from 180 patients with colorectal cancer. The patient samples represent a variety of histological grades, have data available on a series of clinicopathological variables including long-term outcome and ground truth annotations performed by experts. The CNN features extracted from images of the epithelial tissue compartment significantly predicted outcome (hazard ratio (HR) 2.08; CI95% 1.04-4.16; area under the curve (AUC) 0.66) in a test set of 60 patients, as compared to the CNN features extracted from unsegmented images (HR 1.67; CI95% 0.84-3.31, AUC 0.57) and visually assessed histologic grade (HR 1.96; CI95% 0.99-3.88, AUC 0.61). As a conclusion, a deep-learning classifier can be trained to predict outcome of colorectal cancer based on images of H and E stained tissue microarray samples and the CNN features extracted from the epithelial compartment only resulted in a prognostic discrimination comparable to that of visually determined histologic grade.
Does Nitric Oxide Mediate Autoimmune Destruction of β-Cells?: Possible Therapeutic Interventions in IDDM (1992)

Cytokines have been implicated as immunological effector molecules that induce dysfunction and destruction of the pancreatic beta-cell. The mechanisms of cytokine action on the beta-cell are unknown; however, nitric oxide, resulting from cytokine-induced expression of nitric oxide synthase, has been implicated as the cellular effector molecule mediating beta-cell dysfunction. Nitric oxide is a free radical that targets intracellular iron-containing enzymes, which results in the loss of their function. The cytokine IL-1 beta induces the formation of nitric oxide in isolated rat islets and the insulinoma cell line, Rin-m5F. NMMA and NAME, both inhibitors of nitric oxide synthase, completely protect islets from the deleterious effects of IL-1 beta. These inhibitors are competitive in nature and inhibit both the cytokine-inducible and constitutive isoforms of nitric oxide synthase with nearly identical kinetics. This may preclude their use as therapeutic agents because of increases in blood pressure which result from the inhibition of constitutive nitric oxide synthase activity. Aminoguanidine, an inhibitor of nonenzymatic glycosylation of cellular and extracellular constituents associated with diabetic complications, recently has been reported to inhibit nitric oxide synthase. Aminoguanidine is approximately 40-fold more effective in inhibiting the inducible isoform of nitric oxide synthase, suggesting that aminoguanidine or analogues may serve as potential therapeutic agents to block diseases associated with nitric oxide production by the inducible isoform of nitric oxide synthase. In vivo administration of TNF IL-1 has been shown to induce anti-diabetogenic effects in the NOD mouse. This anti-diabetogenic effect of cytokines appears to conflict with evidence suggesting that cytokines mediate beta-cell dysfunction.(ABSTRACT TRUNCATED AT 250 WORDS)
Similar specificity of membrane transport for folate analogues and their metabolites by murine and human tumor cells: a clinically directed laboratory study. (1984)

Mediated transport of folate compounds exhibited similar kinetic characteristics and structural specificity in a series of cultured murine and human tumor cells examined in a parallel fashion. In each case, influx was characterized by a single saturable component with an approach to steady-state conforming to a single exponential, while efflux was first order (poorly saturable). Both mediated fluxes exhibited high temperature dependence (Q10 27-37 degrees = 6 to 8). During competition studies with various analogues, it was found that positions 4, 5, 7, and 10 and the gamma-carboxyl position of the folate molecule were specified for influx in tumor cells from each species. Also, short-chain alkyl substitution at position 10 was specified in the case of N10, but not in the case of C10. None of the modifications at position 10 affected mediated efflux in either cell type. The linkage of additional glutamyl residues at the gamma-carboxyl-position resulted in reduced saturability (increased value for Ki) of influx in both murine and human tumor cells in a manner proportional to the number of glutamyl residues. Mediated influx in human ovarian carcinoma cells obtained from malignant effusions in several patients and in an established cell line derived from one of these patients showed similar kinetics for folate analogue transport and specificity for modification at position 10 of the 4-amino-folate molecule. Mediated entry of 10-deazaaminopterin and its 10-ethyl derivative compared to entry of methotrexate was 4- to 11-fold greater in murine tumor cells and 4- to 9-fold greater in human tumor cells in culture or when clinically derived. Mediated efflux was not specified for position 10 on the 4-amino folate structure in any tumor cell type. These findings appear to provide some basis for concluding that the results of studies of this type in model murine systems or with tumor cell lines established in culture have relevance to clinical cancer.
Essential Functional Interactions of SAGA, a Saccharomyces cerevisiae Complex of Spt, Ada, and Gcn5 Proteins, With the Snf/Swi and Srb/Mediator Complexes (1997)

The Saccharomyces cerevisiae transcription factor Spt20/Ada5 was originally identified by mutations that suppress Ty insertion alleles and by mutations that suppress the toxicity caused by Gal4-VP16 overexpression. Here we present evidence for physical associations between Spt20/Ada5 and three other Spt proteins, suggesting that they exist in a complex. A related study demonstrates that this complex also contains the histone acetyltransferase, Gcn5, and Ada2. This complex has been named SAGA (Spt/Ada/Gcn5 acetyltransferase). To identify functions that genetically interact with SAGA, we have screened for mutations that cause lethality in an spt20 delta/ada5 delta mutant. Our screen identified mutations in SNF2, SIN4, and GAL11. These mutations affect two known transcription complexes: Snf/Swi, which functions in nucleosome remodeling, and Srb/mediator, which is required for regulated transcription by RNA polymerase II. Systematic analysis has demonstrated that spt20 delta/ada5 delta and spt7 delta mutations cause lethality with every snf/swi and srb/mediator mutation tested. Furthermore, a gcn5 delta mutation causes severe sickness with snf/swi mutations, but not with srb/mediator mutations. These findings suggest that SAGA has multiple activities and plays critical roles in transcription by RNA polymerase II.
Functional Differences between Subpopulations of Mobilized Peripheral Blood‐Derived CD34+Cells Expressing Different Levels of HLA‐DR, CD33, CD38 and c‐kit Antigens (1997)

We have investigated the functional characteristics of peripheral blood-derived CD34+ cells mobilized by a combination of chemotherapy and G-CSF (mobilized peripheral blood-derived [MPB] CD34+ cells). In this study, subpopulations of MPB CD34+ cells have been directly compared in clonal cultures, long-term cultures with bone marrow (BM) stromal cells, and single-cell cultures. MPB CD34+ cells could be subdivided by expression levels of HLA-DR (DR), CD38, CD33 and c-kit antigens. The majority of MPB CD34+ cells expressed DR and CD38 antigens. In contrast, approximately 60% and 20% of the MPB CD34+ cells expressed CD33 and c-kit antigens, respectively. Interestingly, MPB CD34+ cells can be subdivided into three fractions which express high, low or negative levels of c-kit receptor. All types of committed progenitors were observed in populations of CD34+DR+, CD34+DR-, CD34+CD33-, CD34+CD38+ and CD34+ c-kit(low) cells. Colony forming unit-granulocyte/macrophage was highly enriched in the population of CD34+CD33+ cells, whereas BFU-E was highly enriched in the population of CD34+ c-kit(high) cells. In the population of CD34+CD38- cells, however, a few myeloid progenitors were detected. In addition, limiting dilution analyses clearly showed that the long-term culture-initiating cell (LTC-IC) is enriched in the populations of CD34+DR-, CD34+CD33- and CD34+c-kit-(or low) cells, but very few in CD34+ c-kit(high) cells, and that CD38 antigen is not a useful marker for the enrichment of LTC-IC derived from MPB CD34+ cells. Moreover, single cell clone sorting experiments clearly demonstrated the functional differences between CD34+CD38+ and CD34+CD38- cells as well as CD34+ cells expressing different levels of c-kit receptor. Our results suggest that an immunophenotype of LTC-IC is different between BM-, cord blood- and MPB-derived CD34+ cells and that primitive and committed progenitors existing in these sources may be functionally different.
Usual choline and betaine dietary intake and incident coronary heart disease: the Atherosclerosis Risk in Communities (ARIC) Study (2007)

Higher intakes of choline and betaine were not protective for incident CHD. Similar investigations in other populations are of interest.
Drosophila in cancer research: the first fifty tumor suppressor genes (1994)

In Drosophila, over 50 genes have been identified in which loss-of-function mutations lead to excess cell proliferation in the embryo, in the central nervous system, imaginal discs or hematopoietic organs of the larva, or in the adult gonads. Twenty-two of these genes have been cloned and characterized at the molecular level, and nine of them show clear homology to mammalian genes. Most of these mammalian genes had not been previously implicated in cell proliferation control. Overgrowth in some of the mutants involves conversion to a cell type that, in normal development, shows more cell proliferation than the original cell type. Thus the neurogenic mutants, including Notch, show conversion of epidermal cells to neuroblasts, leading to the 'neurogenic' phenotype of excess nervous tissue. The ovarian tumor mutants show conversion of the female germ line to a cell type resembling the male germ line, which undergoes more proliferation than the female germ line. Mutations of the fat locus cause hyperplastic overgrowth of imaginal discs, in which the epithelial structure is largely intact. The predicted fat protein product is a giant relative of cadherins, supporting indications from human cancer that cadherins play an important role in tumor suppression. Mutations in the lethal(2)giant larvae and lethal(1)discs large genes cause neoplastic overgrowth of imaginal discs as well as the larval brain. The dlg gene encodes a membrane-associated guanylate kinase homolog that is localized at septate junctions between epithelial cells. This protein is a member of a family of homologs that also includes two proteins found at mammalian tight junctions (ZO-1 and ZO-2) and a protein found at mammalian synaptic junctions (PSD-95/SAP90). Genes in which mutations cause blood cell overproduction include aberrant immune response-8, which encodes the RpS6 ribosomal protein and hopscotch, which encodes a putative non-receptor protein tyrosine kinase. The gene products identified by ovarian tumor mutants do not show clear amino acid sequence homology to known proteins. Drosophila provides an opportunity to rapidly identify and characterize tumor suppressor genes, many of which have mammalian homologs that might also be involved in cell proliferation control and tumor suppression.
Circulation and homing of melanoma‐reactive T cells to both cutaneous and visceral metastases after vaccination with monocyte‐derived dendritic cells (2004)

Anticancer immune therapies aim at the induction of tumor-specific T cells, which ultimately should kill tumor cells. The effector cells should, therefore, not only exert cytotoxic activity but also home to and infiltrate the tumor site. Hence, monitoring of immune modulating therapies should not be restricted to the circulating pool of peripheral blood mononuclear cells (PBMC) but also include tumor-infiltrating lymphocytes (TIL), as well as the correlation of these findings to the clinical course. We report here on the longitudinal immunologic workup of a melanoma patient who developed remarkably potent ex vivo detectable antimelanoma cytotoxic T-cell (CTL) responses after vaccinations with autologous peptide-pulsed dendritic cells. Such potent CTL responses to multiple tumor antigens have, to the best of our knowledge, not been described previously in melanoma patients, neither spontaneously nor after any therapy. This patient first experienced a transient response to therapy but finally succumbed to disease progression and died. Progression was associated with the decline of the numbers of tumor-reactive T cells in circulation and at skin metastases in addition to the loss of MHC class I antigens. The immunologic analysis revealed that fully functional tumor-specific T cells were present in the peripheral blood of this patient during the phase of a relatively stable disease, and in situ tetramer staining demonstrated that these cells were also accumulated at cutaneous and visceral tumor sites. Furthermore, comparative clonotype mapping of PBMC and TIL depicted an overlapping TCR repertoire usage among these 2 compartments. Since strong CTL responses as observed in this patient are the goal of cancer vaccination but are so far only rarely observed, the thorough analysis of patients exhibiting either exceptional clinical and/or immunologic responses appears critical to understanding how vaccine therapies work and can be further improved.
Circumvention of breast cancer resistance protein (BCRP)-mediated resistance to camptothecins in vitro using non-substrate drugs or the BCRP inhibitor GF120918. (2001)

This study was aimed at characterizing the role of BCRP/MXR/ABCP (BCRP) in resistance of the human ovarian tumor cell lines T8 and MX3 to camptothecins more extensively and investigating whether resistance can be reversed by inhibiting BCRP by GF120918. Camptothecins studied were topotecan, CPT-11, and its active metabolite SN-38, 9-aminocamptothecin, and the novel experimental camptothecins NX211, DX8951f, and BNP1350. Notably, DX8951f and BNP1350 appeared to be very poor substrates for BCRP, with much lower resistance factors observed both in T8 and MX3 cells than observed for the other camptothecins tested. In the presence of a nontoxic dose level of GF120918, the intracellular accumulation of topotecan in the T8 and MX3 cells was completely restored to the intracellular levels observed in the sensitive IGROV1 parental cell line. This resulted in almost complete reversal of drug resistance to topotecan and to most of the other topoisomerase I drugs tested in the T8 cell line and to complete reversal in the MX3 cells. However, coincubation of DX8951f or BNP1350 with GF120918 did not affect the cytotoxicity of either of these drugs significantly. From the combined data, we conclude that the affinities of topoisomerase I drugs for BCRP are, in decreasing order: SN-38 > topotecan > 9-aminocamptothecin approximately CPT-11 > NX211 > DX8951f > BNP1350. Furthermore, GF120918 appears to be a potent reversal agent of BCRP-mediated resistance to camptothecins, with almost complete reversal noted at 100 nM. Potential BCRP-mediated resistance to topoisomerase I inhibitors can also be avoided by using the BCRP-insensitive drugs DX8951f or BNP1350. This observation may have important clinical implications for future development of novel camptothecins.
Controlled Defects in Semiconducting Carbon Nanotubes Promote Efficient Generation and Luminescence of Trions (2014)

We demonstrate efficient creation of defect-bound trions through chemical doping of controlled sp(3) defect sites in semiconducting, single-walled carbon nanotubes. These tricarrier quasi-particles luminesce almost as brightly as their parent excitons, indicating a remarkably efficient conversion of excitons into trions. Substantial populations of trions can be generated at low excitation intensities, even months after a sample has been prepared. Photoluminescence spectroscopy reveals a trion binding energy as high as 262 meV, which is substantially larger than any previously reported values. This discovery may have important ramifications not only for studying the basic physics of trions but also for the application of these species in fields such as photonics, electronics, and bioimaging.
Effect of Ag photodoping on deep-level emission spectra of ZnO epitaxial films (2003)

Effect of Ag photodoping into ZnO films grown by molecular beam epitaxy has been examined via the real-time measurement of photoluminescence (PL) spectra using a HeCd laser at room temperature. While an asymmetric deep-level (green-yellow) broadband (D) is observed in PL of as-grown ZnO, it appears to change to two distinct bands (at 2.29 and 2.50 eV) in the illuminated Ag/ZnO. From the result of a Gaussian fitting, the yellow band at 2.29 eV is evaluated to relate with photodoped Ag atoms. With increasing the laser illumination time (photodoping), the PL intensity of broadband (ID) decreases and contrarily, the intensity of the near band edge emission observed at 3.297 eV (INB) shows a tendency to increase. We believe that the Ag can be photodoped into ZnO at 300 K and it contributes to the suppression of deep-level band, which results in an increase of INB.
4,5-Dianilinophthalimide: a protein-tyrosine kinase inhibitor with selectivity for the epidermal growth factor receptor signal transduction pathway and potent in vivo antitumor activity. (1994)

Deregulated signal transduction via the epidermal growth factor receptor (EGF-R) family of protein-tyrosine kinase growth factor receptors is associated with proliferative diseases. We describe a class of compounds (4,5-dianilinophthalimides) that inhibit the EGF-R protein-tyrosine kinase in vitro with high selectivity. In cells, 4,5-dianilinophthalmide selectively inhibited both ligand-induced EGF-R and p185c-erbB2 autophosphorylation and c-fos mRNA induction. Antitumor activity could be demonstrated in vivo against xenografts of the A431 and SK-OV-3 tumors, which overexpress the EGF-R and p185c-erbB2, respectively. In contrast, a platelet-derived growth factor-driven tumor was not inhibited by 4,5-dianilinophthalimide, which is compatible with its cellular selectivity and hypothesized mechanism of action. No overt cumulative toxicity was observed during treatment even though high efficacy was observed, indicating a good therapeutic window. 4,5-Dianilinophthalimides may offer therapeutic agents for the treatment of hyperproliferative diseases that overexpress EGF-R family protein-tyrosine kinases or their ligands.
Gigahertz speed operation of epsilon-near-zero silicon photonic modulators (2018)

Optical communication systems increasingly require electro-optical modulators that deliver high modulation speeds across a large optical bandwidth with a small device footprint and a CMOS-compatible fabrication process. Although silicon photonic modulators based on transparent conducting oxides (TCOs) have shown promise for delivering on these requirements, modulation speeds to date have been limited. Here, we describe the design, fabrication, and performance of a fast, compact electroabsorption modulator based on TCOs. The modulator works by using bias voltage to increase the carrier density in the conducting oxide, which changes the permittivity and hence optical attenuation by almost 10 dB. Under bias, light is tightly confined to the conducting oxide layer through nonresonant epsilon-near-zero (ENZ) effects, which enable modulation over a broad range of wavelengths in the telecommunications band. Our approach features simple integration with passive silicon waveguides, the use of stable inorganic materials, and the ability to modulate both transverse electric and magnetic polarizations with the same device design. Using a 4-μm-long modulator and a drive voltage of <math display="inline" id="m1"><mrow><mn>2</mn><mtext> </mtext><msub><mrow><mi mathvariant="normal">V</mi></mrow><mrow><mi>p</mi><mi>p</mi></mrow></msub></mrow></math>, we demonstrate digital modulation at rates of 2.5 Gb/s. We report broadband operation with a 6.5 dB extinction ratio across the 1530–1590 nm band and a 10 dB insertion loss. This work verifies that high-speed ENZ devices can be created using conducting oxide materials and paves the way for additional technology development that could have a broad impact on future optical communications systems.