gebhart/patrepeval huggingface dataset:
Isozyme-Specific Abnormalities of PKC in Thyroid Cancer: Evidence for Post-Transcriptional Changes in PKC Epsilon (2002)

PKC isozymes are the major binding proteins for tumor-promoting phorbol esters, and PKC activity is abnormal in a number of different human cancers. Less is known about putative structural and functional changes of specific PKC isozymes in human neoplasms. A single-point mutation of PKCalpha at position 881 of the coding sequence has been observed in human pituitary adenomas and up to 50% of thyroid follicular neoplasms, and a rearrangement of PKCepsilon was reported in a thyroid follicular carcinoma cell line, suggesting that these signaling proteins may play a role in thyroid tumorigenesis. To explore this possibility, we examined thyroid neoplasms for mutations and changes in expression levels of PKCepsilon or alpha. None of the 57 follicular adenomas, 26 papillary carcinomas (PCs), 7 follicular carcinomas, or the anaplastic carcinoma harbored the PKCalpha 881A>G mutation. Moreover, none of 15 PCs, 10 follicular adenomas, or 6 follicular carcinomas showed evidence of mutations of PKCepsilon. However, 8 of 11 PCs had major isozyme-specific reductions of the PKCepsilon protein, which occurred through either translational or posttranslational mechanisms. These data indicate that post-transcriptional changes in PKCepsilon are highly prevalent in thyroid tumors and may play a significant role in their development.
Identification and Expression of the TREX1 and TREX2 cDNA Sequences Encoding Mammalian 3′→5′ Exonucleases (1999)

The 3'-->5' exonucleases catalyze the excision of nucleoside monophosphates from the 3' termini of DNA. We have identified the cDNA sequences encoding two 3'-->5' exonucleases (TREX1 and TREX2) from mammalian cells. The TREX1 and TREX2 proteins are 304 and 236 amino acids in length, respectively. Analysis of the TREX1 and TREX2 sequences identifies three conserved motifs that likely generate the exonuclease active site in these enzymes. The specific amino acids in these three conserved motifs suggest that these mammalian exonucleases are most closely related to the proofreading exonucleases of the bacterial replicative DNA polymerases and the RNase T enzymes. Expression of TREX1 and TREX2 in Escherichia coli demonstrates that these recombinant proteins are active 3'-->5' exonucleases. The recombinant TREX1 protein was purified, and exonuclease activity was measured using single-stranded, partial duplex, and mispaired oligonucleotide DNA substrates. The greatest activity of the TREX1 protein was detected using a partial duplex DNA containing five mispaired nucleotides at the 3' terminus. No activity was detected using single-stranded RNA or an RNA-DNA partial duplex. Identification of the TREX1 and TREX2 cDNA sequences provides the genetic tools to investigate the physiological roles of these exonucleases in mammalian DNA replication, repair, and recombination pathways.
Interferon α down-regulates telomerase reverse transcriptase and telomerase activity in human malignant and nonmalignant hematopoietic cells (2000)

Recently, the derepressed expression of the catalytic subunit of telomerase, human telomerase reverse transcriptase (hTERT), the enzyme that elongates telomeres, has been implicated as an important step in the immortalization process. The exact regulation of hTERT expression, which is the rate-limiting factor for telomerase activity, is at present unclear. As transformed cells seem to be dependent on a constitutive telomerase activity, the availability of inhibitors would potentially be of great value in antineoplastic therapy. Interferons (IFNs) have been successfully used in the treatment of several forms of malignancies, but the underlying molecular mechanisms responsible for the antitumor activity are poorly defined. In this study we have investigated the effects of IFNs on hTERT expression and telomerase activity. We found that IFN-alpha rapidly (commonly within 4 hours) and significantly down-regulates the expression of hTERT and telomerase activity in a number of human malignant hematopoietic cell lines, primary leukemic cells from patients with acute leukemia as well as T-lymphocytes from healthy donors. This effect of IFN-alpha did not seem to depend on IFN-alpha-mediated cell growth arrest or alterations in c-myc expression. The finding that IFN induces a repression of hTERT and a decrease in telomerase activity suggests a novel mechanism that may play a significant role in the antitumor action of IFN. (Blood. 2000;96:4313-4318)
Pyrolyzable Nanoparticle Tracers for Environmental Interrogation and Monitoring (2017)

Environmental tracing applications require materials that can be detected in complex fluids composed of multiple phases and contaminants. Moreover, large libraries of tracers are necessary in order to mitigate memory effects and to deploy multiple tracers simultaneously in complex oil fields. Herein, we disclose a novel approach based on the thermal decomposition of polymeric nanoparticles comprised of styrenic and methacrylic monomers. Polymeric nanoparticles derived from these monomers cleanly decompose into their constituent monomers at elevated temperatures, thereby maximizing atom economy wherein the entire nanoparticle mass contributes to the generation of detectable units. A total of ten unique single monomer particles and three dual-monomer particles were synthesized using semicontinuous monomer starved addition polymerization. The pyrolysis gas chromatography-flame ionization detection/mass spectrometry (GC-FID/MS) behavior of these particles was studied using high-pressure mass spectrometry. The programmable nature of our methodology permits simultaneous removal of contaminants and subsequent identification and quantification in a single analytical step.
RNAs Containing Modified Nucleotides Fail To Trigger RIG-I Conformational Changes for Innate Immune Signaling (2016)

The innate immune system provides the first response to virus infections and must distinguish between host and pathogen nucleic acids to mount a protective immune response without activating autoimmune responses. While the presence of nucleotide modifications in RNA is known to correlate with diminished innate immune signaling, the underlying mechanisms have not been explored. The data reported here are important for defining mechanistic details to explain signaling suppression by RNAs containing modified nucleotides. The results suggest that RNAs containing modified nucleotides interrupt signaling at early steps of the RIG-I-like innate immune activation pathway and also that nucleotide modifications with similar chemical structures can be organized into classes that suppress or evade innate immune signaling steps. These data contribute to defining the molecular basis for innate immune signaling suppression by RNAs containing modified nucleotides. The results have important implications for designing therapeutic RNAs that evade innate immune detection.
Oberflächenschutzverfahren und ihr Einsatz in der Werkstoff‐ und Tribo‐Technik (1984)

Abstract Die geschilderten Oberflachenschutzverfahren wurden entwickelt, um im Maschinen‐ und Apparatebau mit billigeren Grundwerkstoffen weiterzuarbeiten, aber bei hohem Verschleiß und Korrosionsbeanspruchungen noch eine technische und wirtschaftliche Nutzungsdauer zu erreichen. Durch die laufende Verknappung und damit Verteuerung der Rohstoffe werden die einzelnen Verfahren in Zukunft noch eine wesentliche Steigerung erfahren.
Tetracycline-Regulatable System To Tightly Control Gene Expression in the Pathogenic Fungus Candida albicans (2000)

Conventional tools for elucidating gene function are relatively scarce in Candida albicans, the most prevalent human fungal pathogen. To this end, we developed a convenient system to control gene expression in C. albicans by the tetracycline-regulatable (TR) promoters. When the sea pansy Renilla reniformis luciferase gene (RLUC1) was placed under the control of this system, doxycycline (DOX) inhibited the luciferase activity almost completely. In the absence of DOX, the RLUC1 gene was induced to express luciferase at a level 400- to 1,000-fold higher than that in the presence of DOX. The same results were obtained in hypha-forming cells. The replacement of N-myristoyltransferase or translation elongation factor 3 promoters with TR promoters conferred a DOX-dependent growth defect in culture media. Furthermore, all the mice infected with these mutants, which are still virulent, survived following DOX administration. Consistently, we observed that the number of these mutant cells recovered from the mouse kidneys was significantly reduced following DOX administration. Thus, this system is useful for investigating gene functions, since this system is able to function in both in vitro and in vivo settings.
Human Herpesvirus Type 8 Interleukin-6 Homologue Is Functionally Active on Human Myeloma Cells (1998)

Seroepidemiology and polymerase chain reaction studies have strongly suggested that human herpesvirus type 8 (HHV-8) is associated with Kaposi's sarcoma, Castleman's disease, and body cavity-based lymphoma. The genome of HHV-8 harbors a viral analogue of the interleukin-6 (IL-6) gene. The amino acid sequence of the viral IL-6 (vIL-6) protein is 24.7% identical to human IL-6 (hIL-6). IL-6 as a B-cell growth and differentiation factor is known to play an essential role in the pathophysiology of B-cell tumors. Thus, it seems possible that virus-encoded IL-6 contributes to malignant growth of HHV-8-positive B-cell lymphatic tumors. We have tested a preparation of HHV-8-derived IL-6 for the ability to promote the proliferation of the human myeloma cell line INA-6, which is strictly dependent on exogenous IL-6 for growth and survival. Viral IL-6 significantly induced DNA synthesis of INA-6 cells, but required much more protein on a weight basis when compared with hIL-6 for maximal proliferation. The proliferative effect of vIL-6 was almost completely inhibited by a combination of anti-IL-6 receptor (IL-6R) and anti-gp130 antibodies or IL-6R superantagonist Sant7 and anti-gp130 antibodies. This report demonstrates that vIL-6 has proliferative activity on human cells and that the IL-6R and gp130 are involved in vIL-6 signaling in the myeloma cell line INA-6.
GTPase-activating protein and phosphatidylinositol 3-kinase bind to distinct regions of the platelet-derived growth factor receptor beta subunit. (1992)

In response to binding of platelet-derived growth factor (PDGF), the PDGF receptor (PDGFR) beta subunit is phosphorylated on tyrosine residues and associates with numerous signal transduction enzymes, including the GTPase-activating protein of ras (GAP) and phosphatidylinositol 3-kinase (PI3K). Previous studies have shown that association of PI3K requires phosphorylation of tyrosine 751 (Y751) in the kinase insert and that this region of receptor forms at least a portion of the binding site for PI3K. In this study, the in vitro binding of GAP to the PDGFR was investigated. Like PI3K, GAP associates only with receptors that have been permitted to autophosphorylate, and GAP itself does not require tyrosine phosphate in order to stably associate with the phosphorylated PDGFR. To define which tyrosine residues are required for GAP binding, a panel of PDGFR phosphorylation site mutants was tested. Mutation of Y771 reduced the amount of GAP that associates to an undetectable level. In contrast, the F771 (phenylalanine at 771) mutant bound wild-type levels of PI3K, whereas the F740 and F751 mutants bound 3 and 23%, respectively, of the wild-type levels of PI3K but wild-type levels of GAP. The F740/F751 double mutant associated with wild-type levels of GAP, but no detectable PI3K activity, while the F740/F751/F771 triple mutant could not bind either GAP or PI3K. The in vitro and in vivo associations of GAP and PI3K activity to these PDGFR mutants were indistinguishable. The distinct tyrosine residue requirements suggest that GAP and PI3K bind different regions of the PDGFR. This possibility was also supported by the observation that the antibody to the PDGFR kinase insert Y751 region that blocks association of PI3K had only a minor effect on the in vitro binding of GAP. In addition, highly purified PI3K and GAP associated in the absence of other cellular proteins and neither cooperated nor competed with each other's binding to the PDGFR. Taken together, these studies indicate that GAP and PI3K bind directly to the PDGFR and have discrete binding sites that include portions of the kinase insert domain.
Comments on Brasseur's fill pattern article (1994)

Lee Brasseur has conducted some important and useful research from which program designers and documentation designers can draw some useful advice. But there are areas of her paper that raise questions we need Brasseur or others to answer before we can be sure we travel the right track to software and document design that improves users' qualitative performance as well as their quantitative. My comments, then, are a series of questions and observations about the paper itself. The answers to these questions and the clarification of these observations might be the basis for further research.
Specific immunotherapy proposed for hepatitis B virus infection. (1975)

Immune response to hepatitis B surface antigen (HBsAg), coinciding with removal of HBsAg from the circulation, has been shown to be a cell-mediated response assessed by leukocyte migration inhibition assay. Immune response to HBsAg is a T-cell dependent phenomenon in the nude mouse model. Immunological tolerance in man appears to stem from the absence of cellular and humoral immune response to HBsAg, causing a chronic carrier state which serves as an epidemiological reservior for the transmission of viral hepatitis type B. Specific immunotherapy in hepatitis may consist of adoptive transfer of immunity to HBsAg. It is proposed to be accomplished by administration of anti-HBs, transfer factor or 'immune-RNA'. The efficacy and safety of 'immune-RNA' administration to chronic carriers can be validated by leukocyte migration inhibition techniques in vitro and in HBsAg positive chimpanzees in vivo.
In vivostudy of the tissue distribution and immunosuppressive response of cyclosporin a-loaded polyester micro- and nanospheres (1995)

In an attempt to elucidate the biopharmaceutical and clinical interest of new formulations of cyclosporin A (CyA) based on poly(d,l-lactide-co-glycolide) (PLGA) micro- and nanospheres, different in vivo studies were performed. On the one hand, tritium-labeled CyA was loaded into the microspheres (30 and 1 μm) and nano-spheres (0.2 μm) or diluted into a commercial injectable solution and then injected subcutaneously into mice. CyA kinetic profiles in blood and several tissues, i.e, liver, spleen, kidney, and adipose, were determined and compared for up to 21 days. The close relation observed between blood and tissue CyA profiles and the absence of significant differences between the distribution patterns of encapsulated CyA and the free drug led us to the following conclusions. First, subcutaneously injected microspheres and nanospheres act as a “depot,” from which CyA releases, attaining the blood and tissue compartments in the free form. Second, in addition to prolonging the residence time of the drug in the blood circulation, a single dose of microencapsulated CyA provides increased levels of the peptide in these tissues for up to several weeks. On the other hand, the immunosuppressive response after intraperitoneal injection of a single dose of the above-mentioned formulations was evaluated. Humoral immunosuppressive responses within day 0 and within day 7 postadministration were related to the in vivo kinetic profiles. Thus, nanospheres and 1-μm microspheres displayed a higher response at early times (0–24 h), while 30-μm microspheres led to an important level of immunosuppression at a later date (day 7). Consequently, these controlled release systems modulate the inununosuppression in terms of duration and intensity, suggesting their utility as promising CyA forms to achieve long-term immunosuppressive therapy.
Growth of Human Schwannomas in the Subrenal Capsule of the Nude Mouse (1990)

To develop a reproducible in vivo model for the growth of human schwannomas we implanted tumor specimens from 14 different patients (13 acoustic neurinomas; 1 trigeminal schwannoma) into the subrenal capsule of 108 nude mice. In 11 experiments, the animals were implanted with only solid tumor from the surgical specimens. In two experiments, the tumor implants were made from solid tumors and cell clusters. In one experiment, the tumor implants were made from cell clusters alone. The size and neovascularization of these tumors were serially determined during a 1.5- to 3-month period. The percentages of tumors that survived or grew were 77.3% from solid tumors and 70% from cell clusters. Maximum tumor volume varied as did the time span to reach that volume. Tumor enlargement and stability correlated well with neovascularity; regressing tumor showed minimal or no neovascularity. Histological analysis of the implanted tumors showed spindle cells that are similar to the original tumor. Immunohistochemical staining for S100 demonstrated the Schwann cell nature of the implants. Analysis of genomic DNA from an acoustic neurinoma that had been implanted for 3 weeks was consistent with its human origin. There were no significant microscopic differences among groups receiving solid tumor implants or cell clusters. These studies suggest that implantation of human schwannomas into the subrenal capsule of the nude mouse is a reproducible method to study tumor growth that may be useful in testing potential therapeutic regimens or genetic modulation of schwannomas. (Neurosurgery 26:598-605, 1990)
Modeling and Health Monitoring of DC Side of Photovoltaic Array (2015)

In this paper, a health monitoring method for photovoltaic (PV) systems based on probabilistic neural network (PNN) is proposed that detects and classifies short- and open-circuit faults in real time. To implement and validate the proposed method in computer programs, a new approach for modeling PV systems is proposed that only requires information from manufacturers datasheet reported under normal-operating cell temperature (NOCT) conditions and standard-operating test conditions (STCs). The proposed model precisely represents characteristics of PV systems at different temperatures, as the temperature dependency of parameters such as ideality factor, series resistance, and thermal voltage is considered in the proposed model. Although this model can be applied to a variety of applications, it is specifically used to test and validate the performance of the proposed fault detection and classification method.
Detection of Rice Stripe Virus using RT-PCR (2004)

현재까지 벼 줄무의잎마름병(Rice stripe virus, RSV)은 남부지방에 국한되어 발생되어 왔다. 그러나 최근에는 RSV의 발생이 충청도, 경기도를 포함한 중부지방까지 확산되는 경향을 나타내고 있다. 이병의 병징은 육안으로는 생리적인 장해 현상과 구분하기가 힘들다 본 실험에서는 이병주 및 애멸구(Laodelphax striatellus)로 부터 viral RNA를 추출한 후 RNA복제효소 및 외피단백질유전자에 특이적인 primer를 제작하여 RT-PCR법에 의해 RSV를 검정하였다. 그결과 이병식물체 및 보독 애멸구로부터 RNA복제효소 유전자에 특이적인 band(1,023 bp) 및 외피단백질유전자에 특이적인 band(969 bp)가 관찰되었다. Until now, occurrence of rice stripe virus (RSV) is limitted in southern part of Korea. However, recently the occurrence of RSV is increased and spreaded in central part of Korea including Chungcheong and Kyonggi province. It is very difficult to distinguish RSV symptoms on virus symptom physiological damage of rice. We detected RSV viral RNA from infected rice and its insect vector Laodelphax striatellus using specific primer of RSV-polymerase and coat protein gene with reverse transcription (RT)-PCR. The result of RT-PCR, we observed specific band including RSV-polymerase (1,,023 bp) and CP (969 bp) in both host of rice and insect vector.
Holographic photonic crystals (2004)

Following the realization of photonic crystals in the late 1980s and fueled by the vision of photonic "highways" and all-optical switching, the field has grown into one of the most exciting and fertile areas of cross-disciplinary research spanning the scientific and engineering communities. We focus on the state of the art in holographic fabrication of photonic crystals by providing a unified framework of design principles for the creation of two- and three-dimensional optical lattices, with an emphasis on how all five two-dimensional and all fourteen three-dimensional Bravais lattices may be formed with three and four coherent laser beams, respectively. Additionally, we discuss quasiperiodic crystal interference profiles and aspects of the relevant holographic materials. After firmly establishing the general relationship between the holographic parameters and the resulting optical interference profiles, we offer a comprehensive literature review and set forth the most pressing research issues in holographic photonic crystals.
Cathepsin B expression in colorectal carcinomas correlates with tumor progression and shortened patient survival. (1994)

Cathepsin B is a lysosomal cysteine proteinase that has the ability to degrade several extracellular matrix components at both neutral and acidic pH and has been implicated in the progression of several human and rodent tumors. We have studied the expression of cathepsin B in human colorectal tissues using a monospecific polyclonal rabbit antibody raised against human liver cathepsin B. In immunoblots of normal and neoplastic colorectal tissues this antibody specifically recognized only cathepsin B. We studied 101 cases of formalin-fixed, paraffin-embedded tissue (15 normal mucosa, 17 adenomas, and 69 carcinomas). Epithelial cells of normal mucosa and adenomas were either negative or showed a weak granular reactivity located in the paranuclear and apical cytoplasm of superficial cells. Small clusters of histiocytes were also positive in the region of the superficial area of the lamina propria. In carcinomas, increased expression of cathepsin B correlated with advanced stage of the disease. Increased immunoreactivity of cathepsin B in malignant cells was associated with either a diffuse cytoplasmic staining or was polarized to the basal pole of the cells. This is in contrast to the punctate paranuclear staining pattern observed in normal colonic mucosal cells. In tumor stromal cells, increased expression of the enzyme correlated with neoplastic progression. Expression of high levels of cathepsin B in the tumor epithelial cells was associated with a significantly shorter survival of the patients. In conclusion, our results indicate that cathepsin B expression is up-regulated in human colorectal carcinomas compared with normal mucosa and adenomas and correlates with tumor progression.