gebhart/patrepeval huggingface dataset:
Hormonal Markers in Breast Cancer: Coexpression, Relationship with Pathologic Characteristics, and Risk Factor Associations in a Population-Based Study (2007)

The objective of this study was to evaluate the coexpression patterns of hormonal markers in breast cancer tissue and their relationship with pathologic characteristics and epidemiologic risk factors. We evaluated the expression of 17 markers by immunohistochemistry in 842 invasive breast carcinomas collected in a population-based case-control study conducted in Poland. Based on marker correlations, factor analysis identified four major coexpression patterns (factors): "nuclear receptor factor" [estrogen receptor (ER)-alpha, progesterone receptor, androgen receptor, cyclin D1, and aromatase], "estrogen metabolism/ER-beta factor" (ER-beta, peroxisome proliferator-activated receptor-gamma, steroid sulfatase, estrogen sulfonotransferase, and cytochrome P450 1B1), "HER2 factor" (human epidermal growth factor receptor 2, E-cadherin, cyclooxygenase-2, aromatase, steroid sulfatase), and "proliferation factor" (cytokeratin 5, cytokeratin 5/6, epidermal growth factor receptor, P53). Three of these factors corresponded to molecular subtypes previously defined by expression profiling; however, the estrogen metabolism/ER-beta factor seemed to be distinctive. High scores for this factor were associated with high tumor grade (P heterogeneity = 0.02), younger age at menarche (P heterogeneity = 0.04), lower current body mass index among premenopausal women (P heterogeneity = 0.01), and older age at menopause (P heterogeneity = 0.04). High scores for the proliferation factor were also associated with early menarche (P heterogeneity < 0.0001), and in contrast to the estrogen metabolism/ER-beta factor, higher current body mass index among premenopausal women (P heterogeneity = 0.03). Our analysis of hormonal pathway markers independently confirmed several previously defined molecular subtypes identified by gene expression profiling and augmented these findings by suggesting the existence of additional relationships related to ER-beta and enzymes involved in hormone metabolism.
Promoter choice affects the potency of HIV-1 specific RNA interference (2003)

RNA interference (RNAi) is mediated by small interfering (si) RNAs that target and degrade mRNA in a sequence-specific manner. Cellular expression of siRNA can be achieved by the use of expression cassettes driven by RNA polymerase III (pol III) promoters. Here, we demonstrate that a modified tRNA(met)-derived (MTD) promoter effectively drives the cellular expression of HIV-1-specific siRNA. We observed up to 56% greater inhibition of virus production when the MTD promoter was used to drive the expression of short hairpin (sh) RNA targeting the HIV-1 transactivator protein tat compared to cassettes containing other pol III promoters such as H1, U6+1 and U6+27. We conclude that the MTD promoter is ideally suited to drive intracellular expression of HIV-1 specific siRNA and may serve as an important component of future RNAi vector delivery systems.
Solid-Phase Oligonucleotide Synthesis and Flow Cytometric Analysis with Microspheres Encoded with Covalently Attached Fluorophores (2000)

A novel combinatorial approach to synthesize oligonucleotides on fluorescently encoded microspheres based on flow sorting and segmental solid-phase synthesis is described. BODIPY dyes were covalently attached to polystyrene (8.8 microm, 55% DVB) microsphere particles to generate four fluorescently encoded sets. 20-mer oligonucleotide sequences can be synthesized on these microspheres with yields comparable to conventional CPG supports (80% overall yield, average stepwise yield = 99%). The concept of segmental solid-phase synthesis by flow sorting was demonstrated by synthesizing unique 20-mer oligonucleotide sequences on each of four fluorescently encoded microsphere sets by including a flow sorting step (after first eight base additions) and flow cytometric detection of sequences synthesized on each microsphere set by hybridization with fluorescently labeled complementary sequence.
Oxidation Resistive, CMOS Compatible Copper-Based Alloy Ultrathin Films as a Superior Passivation Mechanism for Achieving 150 °C Cu–Cu Wafer on Wafer Thermocompression Bonding (2017)

Surface passivation plays a dual role of protecting copper (Cu) from getting oxidized and reducing the surface roughness of Cu thin film and thus enables low-temperature Cu-Cu bonding. In this paper, we utilized an oxidation resistive, CMOS compatible copper-nickel-based alloy, constantan as a passivation layer, as it does not get oxidized at room temperature and is also CMOS damascene process compatible. Systematically optimized ultrathin, constantan (2 nm) on Cu surface not only protected Cu from oxidation but also reduced the surface roughness to about 0.7 nm, which led to Cu-Cu bonding at a temperature as low as 150 °C at 4 bar pressure. Cross-sectional TEM of bonded Cu layer reveals very significant interdiffusion and grain growth between the Cu films resulting in a zigzag bonding interface and the presence of Cu grains that extend across the entire bonding layer. Furthermore, reliability investigation of passivated Cu bonded structure was demonstrated using current stressing, temperature cycling test, and relative humidity test, which suggest excellent stable bonding without electrical performance degradation. This method of alloy-based passivation is confirmed to be effective and enable low temperature, low-pressure Cu-Cu wafer on wafer bonding for 3-D integration applications.
Synthesis of a model protein of defined secondary and quaternary structure. Effect of chain length on the stabilization and formation of two-stranded alpha-helical coiled-coils. (1984)

Five polyheptapeptides (Ac-(Lys-Leu-Glu-Ala-Leu-Glu-Gly)n-Lys-amide, where n = 1-5) of 8, 15, 22, 29, and 36 residues were synthesized by the solid-phase method. The peptides were purified by reversed-phase high-performance liquid chromatography. The ability of these peptides to form two-stranded alpha-helical coiled-coils in benign medium (1.1 M KC1, 0.05 M PO4 buffer, pH 7.0) was monitored by molecular weight determinations and circular dichroism studies and their physical properties were compared to carboxamidomethylated alpha-tropomyosin at cysteine 190 (CM-tropomyosin). The peptides TM-8, TM-15, and TM-22 were shown to be monomeric in both denaturant (8 M urea) and benign medium by gel-filtration high-performance liquid chromatography on TSK G2000 SW while peptides TM-29 and TM-36 were shown to be dimeric in benign medium both by gel-filtration and sedimentation equilibrium experiments. The CD spectra of the polyheptapeptides TM-8, TM-15, and TM-22 show large increases in molar ellipticity at 220 nm on the addition of trifluoroethanol (helix-inducing solvent) to the benign buffer. By comparison, the two-stranded polyheptapeptides (TM-29 and TM-36) and CM-tropomyosin do not show any increase in molar ellipticity at 220 nm. The helicity of polyheptapeptides increases with increasing chain length, with TM-36 having a value comparable with CM-tropomyosin [( theta]220 = -31,800 degrees and -32,200 degrees, respectively) which is considered to be essentially 100% alpha-helical. These small two-stranded alpha-helical coiled-coils are considerably more stable to temperature and urea denaturation than CM-tropomyosin. Whereas CM-tropomyosin is almost completely denatured in the presence of 6 M urea, TM-29 and TM-36 maintain 22 and 70% of their helicity, respectively. The 30% denaturation values (t30) are 74, 62, and 37 degrees C for TM-36, TM-29, and CM-tropomyosin, respectively, in benign medium (1.1 M KC1:PO4 buffer, pH 7.0). The t30 values can be substantially decreased in the presence of denaturant (3 M urea, 0.1 M KC1, PO4 buffer, pH 7.0) to 62 and 43 degrees C for TM-36 and TM-29, respectively.(ABSTRACT TRUNCATED AT 400 WORDS)
Effect of Catalyst on Yield of Liquid Products from Biomass via Pyrolysis (2003)

The pyrolysis of biomass is a thermal treatment that results in the production of charcoal, liquid, and gaseous products. Among the liquid products, methanol is one of the most valuable products. Methanol can be used as one possible gasoline replacement for conventional gasoline and diesel fuel. Methanol can be produced by pyrolysis of biomass. Methanol mainly arises from methoxyl groups of uronic acid and from the breakdown of methyl esters and/or ethers from decomposition of pectin-like plant materials. The maximum methanol yields (12.19% at 825 K) for hazelnut shell was obtained from a Na2CO3 (30% of dried sample) catalytic flash pyrolysis run. The yields of liquid products from the samples increased with an increasing of the amount of Na2CO3 from 10% to 30%. The maximum liquid yield from yellow pine was 51.2% at 875 K. The yields of liquid products from the samples depended on the amount of K2CO3 and the temperature. The maximum liquid yield from yellow pine was 49.5% from a 30% K2CO3 catalytic run at 875 K. The catalytic effect of Na2CO3 was slightly higher than that of K2CO3 for hazelnut shell, tea waste, and yellow pine samples.
Vascular endothelial growth factor-C expression in human prostatic carcinoma and its relationship to lymph node metastasis (1999)

Lymph node dissemination is a major prognostic factor in human cancer. However, the molecular mechanisms underlying lymph node metastasis are poorly understood. Recently, vascular endothelial growth factor-C (VEGF-C) was identified as a ligand for VEGF receptor-3 (VEGFR-3/Flt-4) and the expression of VEGFR-3 was found to be highly restricted to the lymphatic endothelial cells. In this report, we investigated the expression of VEGF-C and VEGFR-3 in human prostatic carcinoma tissue by using in situ hybridization and immunohistochemical staining respectively. Expression of VEGF-C mRNA in prostatic carcinoma was significantly higher in lymph node-positive group than in lymph node-negative group. In addition, the number of VEGFR-3-positive vessels was increased in stroma surrounding VEGF-C-positive prostatic carcinoma cells. These results suggest that the expression of VEGF-C in prostatic carcinoma cells is implicated in the lymph node metastasis.
<title>Smart optical fiber probes for precise tissue treatment</title> (2002)

Optical features of a novel technique for fiber-optic-based laser delivery into a precise tissue area are investigated. As a key optical element, the technique includes a single delivery fiber with a specially angle shaped tip. Because of the frustrated-total-internal-reflectance caused by the refractive-index change of the surrounding medium, the angled fiber tip acts as a smart, tissue-activated probe. It provides a safe way for laser delivery that includes only two states of tissue illumination: (1) off-state (no tissue illumination), when the fiber tip is out of the tissue area and the laser emission is backreflected due to total-internal-reflection; and (2) on-state (maximum tissue illumination), when the fiber tip is on the absorbing tissue area and becomes transparent because of the frustrated-total-internal-reflectance and the laser energy is coupled into the absorber. Here, optical properties of tissue-activated fiber probes used for precise laser delivery are investigated both experimentally and theoretically by analyzing the backreflectance signal power. Optical fibers with various geometrical parameters are used and a spatial resolution of 2 micrometers is achieved when the fiber tip is moved toward the absorption tissue surface. The results confirm the system potential for on-the-spot laser delivery applicable to precise laser treatment, tissue diagnostics, and micro-scale surgical procedures.
Testing Medications in Children (2002)

To stimulate more evaluation of the safety and efficacy of medications in children, two federal regulations were established. The pediatric exclusivity provision gives an additional six months of patent protection to companies that voluntarily test a medication in children, whereas the pediatric rule requires pediatric studies if a drug is important for children.
Bone marrow as a source of circulating CXCR4+ tissue‐committed stem cells (2005)

Several studies have suggested that adult haematopoietic stem cells (HSCs) may be capable of transdifferentiating across tissue-lineage boundaries, giving rise to the concept that these stem cells are plastic in their differentiative capacity. This topic created much excitement in the scientific community, with the prospect of employing HSCs in tissue/organ regeneration (e.g. heart infarct, stroke, liver damage) as an alternative to multipotent embryonic stem cells. However, recent observations, and several alternative explanations of previously published data (e.g. cell fusion, epigenetic changes), do not support the concept of HSC plasticity. Our recent studies, in which we employed chemotactic isolation to a stromal-cell-derived-factor-1 (SDF-1) gradient combined with real-time reverse transcriptase (RT)-PCR/immuno-histochemical analyses, revealed that bone marrow (BM) contains a highly mobile population of CXCR4+ cells that express mRNA/proteins for various markers of early tissue-committed stem cells (TCSCs). Based on this we postulate that the BM is not only a home for HSCs, but also a 'hideout' for non-haematopoietic CXCR4+ TCSCs, and we suggest that their presence in BM tissue should be considered before experimental evidence is interpreted simply as transdifferentiation/plasticity of HSCs. Furthermore, our observation that the number of TCSCs is the highest in BM of young animals and decreases with age provides a novel insight into aging, and may explain why the regeneration process becomes less effective in older individuals.
NapGH components of the periplasmic nitrate reductase of Escherichia coli K-12: location, topology and physiological roles in quinol oxidation and redox balancing (2004)

Nap (periplasmic nitrate reductase) operons of many bacteria include four common, essential components, napD, napA, napB and napC (or a homologue of napC ). In Escherichia coli there are three additional genes, napF, napG and napH, none of which are essential for Nap activity. We now show that deletion of either napG or napH almost abolished Nap-dependent nitrate reduction by strains defective in naphthoquinone synthesis. The residual rate of nitrate reduction (approx. 1% of that of napG+ H+ strains) is sufficient to replace fumarate reduction in a redox-balancing role during growth by glucose fermentation. Western blotting combined with beta-galactosidase and alkaline phosphatase fusion experiments established that NapH is an integral membrane protein with four transmembrane helices. Both the N- and C-termini as well as the two non-haem iron-sulphur centres are located in the cytoplasm. An N-terminal twin arginine motif was shown to be essential for NapG function, consistent with the expectation that NapG is secreted into the periplasm by the twin arginine translocation pathway. A bacterial two-hybrid system was used to show that NapH interacts, presumably on the cytoplasmic side of, or within, the membrane, with NapC. As expected for a periplasmic protein, no NapG interactions with NapC or NapH were detected in the cytoplasm. An in vitro quinol dehydrogenase assay was developed to show that both NapG and NapH are essential for rapid electron transfer from menadiol to the terminal NapAB complex. These new in vivo and in vitro results establish that NapG and NapH form a quinol dehydrogenase that couples electron transfer from the high midpoint redox potential ubiquinone-ubiquinol couple via NapC and NapB to NapA.
Release kinetics of transforming growth factor‐β1 from fibrin clots (2003)

In any therapeutic model involving a tissue-engineering approach to the repair of partial-thickness articular cartilage defects, a chondrogenic differentiation factor is required to ensure tissue-specific healing. Transforming growth factor-beta1 (TGF-beta1) is known to act in this capacity, but at such high concentrations as to render its direct injection into the joint cavity inadvisable. This situation calls for a delivery system that can be applied directly to the defect site and that will release the drug gradually over a period of some weeks. Liposome encapsulation represents one such system, and has been recently implemented with some success in an animal model for cartilage repair. However, the kinetics of TGF-beta1 release have not been determined, it was the purpose of the present study to characterize these. The liberation of [(125)I]-labeled TGF-beta1 from fibrin matrices containing this agent in either a free or liposome-encapsulated form was monitored by liquid scintillation counting for 25 days in vitro. During the initial 5 days, fibrin clots containing liposome-encapsulated TGF-beta1 released this cytokine at a slower rate (2% to 4% per day) than did those containing the free molecules (10% to 20% per day); thereafter, the release rates were similar. At the end of the incubation period, only 40% of the liposome-encapsulated TGF-beta1 had been released from the fibrin clots, as compared with 68% from those containing the free molecules. Liposome encapsulation thus represents a suitable means of establishing a slow-delivery system in tissue-engineering approaches to articular cartilage repair.
Specific Double-Stranded RNA Interference in Undifferentiated Mouse Embryonic Stem Cells (2001)

Specific mRNA degradation mediated by double-stranded RNA (dsRNA) interference (RNAi) is a powerful way of suppressing gene expression in plants, nematodes, and fungal, insect, and protozoan systems. However, only a few cases of RNAi have been reported in mammalian systems. Here, we investigated the feasibility of the RNAi strategy in several mammalian cells by using the enhanced green fluorescent protein gene as a target, either by in situ production of dsRNA from transient transfection of a plasmid harboring a 547-bp inverted repeat or by direct transfection of dsRNA made by in vitro transcription. Several mammalian cells including differentiated embryonic stem (ES) cells did not exhibit specific RNAi in transient transfection. This long dsRNA, however, was capable of inducing a sequence-specific RNAi for the episomal and chromosomal target gene in undifferentiated ES cells. dsRNA at 8.3 nM decreased the cognate gene expression up to 70%. However, RNAi activity was not permanent because it was more pronounced in early time points and diminished 5 days after transfection. Thus, undifferentiated ES cells may lack the interferon response, similar to mouse embryos and oocytes. Regardless of their apparent RNAi activity, however, cytoplasmic extracts from mammalian cells produced a small RNA of 21 to 22 nucleotides from the long dsRNA. Our results suggest that mammalian cells may possess RNAi activity but nonspecific activation of the interferon response by longer dsRNA may mask the specific RNAi. The findings offer an opportunity to use dsRNA for inhibition of gene expression in ES cells to study differentiation.
Glycolysis in quiescent cultures of 3T3 cells. Stimulation by serum, epidermal growth factor, and insulin in intact cells and persistence of the stimulation after cell homogenization. (1978)

Addition of serum to quiescent cultures of 3T3 cells rapidly increases lactic acid formation and subsequently stimulates cell division. The stimulation of lactic acid production is seen at high, saturating concentrations of extra-cellular glucose. It is dependent on the time of exposure and on the dose of serum and is not blocked by the addition of cycloheximide, puromycin, or actinomycin D. In contrast, serum only marginally affects glycolysis by rapidly growing 3T6 or SV40-3T3 cells. In addition to serum, epidermal growth factor (0.1 to 10 ng/ml) and insulin (10 to 500 ng/ml) cause a striking stimulation of glycolysis in quiescent 3T3 cells. Neither exogenous cyclic nucleotides nor ouabain effect the glycolytic response, but the presence of Ca2+ markedly influences the activation of glycolysis by epidermal growth factor and by insulin. A novel finding in this study is that homogenates prepared from quiescent cells treated with serum, epidermal growth factor, or insulin show increased glycolysis as compared with homogenates from nonstimulated cultures. This finding will allow further experimental analysis of the cause of increased glycolysis in rapidly proliferating cells.
Expression of the messenger RNAs for luteinizing hormone-releasing hormone (LHRH) and its receptor in human ovarian epithelial carcinoma. (1995)

Recently we reported the presence of specific high affinity binding sites for luteinizing hormone-releasing hormone (LHRH) and its analogues (Kd = 1.5 or 1.7 nM) in the human epithelial ovarian cancer cell lines EFO-21 and EFO-27. The proliferation of these cell lines was inhibited by nM concentrations of a LHRH agonist. This study was performed to ascertain whether these ovarian cancer cell lines produce LHRH and whether the high affinity LHRH binding site found previously was identical to the pituitary LHRH receptor. Significant amounts of immunoreactive LHRH were found in the extracts of both the EFO-21 cell line (449 +/- 56 fmol/10(6) cells) and the EFO-27 line (409 +/- 76 fmol/10(6) cells). LHRH bioactivity of these extracts, assessed in terms of release of luteinizing hormone by rat pituitary cells, was comparable to that of authentic LHRH. EFO-21 and EFO-27 cells expressed the mRNAs for both human LHRH and human LHRH receptor as assessed by reverse transcriptase-PCR using oligonucleotide primers according to published sequences. In addition, in eight of eight biopsy samples of human epithelial ovarian cancers we detected mRNA for LHRH, six of these specimens expressed the mRNA representing the LHRH receptor. These data support the concept that human epithelial ovarian cancers might have a local system based on LHRH to regulate cell proliferation. It is still obscure at present whether LHRH produced locally has a stimulatory, inhibitory, or no impact on the proliferation of ovarian cancer cells. However, exogenous LHRH agonists seem to have clear antiproliferative activity, probably mediated through LHRH receptors. This finding might provide the base for novel approaches in the therapy of epithelial ovarian cancer.
Bleomycin-induced pulmonary fibrosis in the rat: inhibition by indomethacin. (1979)

A model for pulmonary fibrosis in the rat has been developed using intratracheal administration of bleomycin. The histopathologic features of the reaction are similar to those reported in the hamster model. Increases in vascular permeability are seen in the lung within 24 hours and persist over a 2-month period. Extractable collagen, as measured by hydroxyproline, increases during this time by a factor greater than 1.5 times the reference control values of normal lung. During this same period, a prominent eosinophilia develops. The continued treatment of bleomycin-injected rats with indomethacin markedly diminishes the amount of extractable lung collagen at 60 days and the histopathologic evidence of pulmonary fibrosis. The eosinophilia over the first 3 weeks is also markedly suppressed. Less dramatic effects were seen with the permeability changes. These findings indicate that the rat is a reliable and useful model for the study of blemoycin-induced pulmonary fibrosis and that treatment with indomethacin ameliorates the lung changes.
85. Co-expression of fractalkine and its receptor in human endometrium supports a role for fractalkine in leukocyte recruitment and endometrial remodelling (2003)

Reproduction, Fertility and Development is an international journal publishing original research , review and comment in the fields of reproduction and developmental biology in humans, domestic animals and wildlife
Reliable Data Protocol (1984)

The Reliable Data Protocol (RDP) is designed to provide a reliable
data transport service for packet-based applications. This RFC
specifies a proposed protocol for the ARPA-Internet and DARPA research
community, and requests discussion and suggestions for improvemts.