gebhart/patrepeval huggingface dataset:
Breast Cancer Incidence in Women with Abnormal Cytology in Nipple Aspirates of Breast Fluid (1992)

This is a prospective study of breast cancer risk in relation to nipple aspirate fluid cytology in 2,701 volunteer white women from the San Francisco Bay Area first enrolled between 1973 and 1980. The women were not pregnant or lactating and were free of breast cancer within 6 months of entry into the study. The breast cancer status of this cohort was determined between June 1988 and April 1991. Follow-up was complete for 87% (n = 2,343) of the cohort, representing 29,961 person-years and an average of 12.7 years of follow-up. The overall breast cancer incidence was 4.4% (104 of 2,343) and rose with fluid cytology findings as follows: no fluid obtained, 2.6% (9 of 352); unsatisfactory specimen, 4.8% (15 of 315); normal cytology, 4.3% (56 of 1,291); epithelial hyperplasia, 5.5% (18 of 327); and atypical hyperplasia, 10.3% (6 of 58). Relative risks for breast cancer and their 95% confidence intervals were estimated by Cox regression, adjusting for age and year of entry. Compared with the relative risk for women who yielded no fluid, relative risks were: unsatisfactory specimen, relative risk (RR) = 1.4 (95% confidence interval (CI) 0.6-3.3); normal cytology, RR = 1.8 (95% CI 0.9-3.6); epithelial hyperplasia, RR = 2.5 (95% CI 1.1-5.5); and atypical hyperplasia, RR = 4.9 (95% CI 1.7-13.9). These findings were strongest for and were mainly confined to women aged 25-54 years. Women with atypical hyperplasia and a first-degree family history of breast cancer were six times more likely to develop breast cancer than were women with atypical hyperplasia but without a family history of breast cancer (95% CI 1.0-30.2). These findings provide strong support for our hypothesis that hyperplasia and atypical hyperplasia diagnosed in nipple aspirates of breast fluid are associated with an increased risk of breast cancer.
Thermal, mechanical, and physical properties of selected bituminous coals and cokes (1979)

Thermal, mechanical, and physical properties of virgin and heat-treated Pittsburgh seam coal were determined as part of a comprehensive study of combustion of monolithic coal block. The information was sought to help characterize pyrolysis and combustion processes in underground coal mine fires, but should also prove useful in the study of in situ and surface coal gasifiers. Measured properties include thermal conductivity, specific heat, thermal expansion, density, compressive and tensile strength, porosity, and permeability. The transport property data were obtained (when feasible) in 2 mutually perpendicular directions of the anisotropic virgin coal material, and coal samples carbonized for 5 hr at temperatures of 350 C, 475 C, 500 C, 650 CC, and 850 C. Other coals (Pocahontas No. 3, Sewell, and Illinois No. 6 seams) were investigated for porosity and relative permeability. 49 references.
<title>Adaptive optics system for solid state laser systems used in inertial confinement fusion</title> (1995)

Using adaptive optics we have obtained nearly diffraction-limited 5 kJ, 3 nsec output pulses at 1.053 micrometer from the Beamlet demonstration system for the National Ignition Facility (NIF). The peak Strehl ratio was improved from 0.009 to 0.50, as estimated from measured wavefront errors. We have also measured the relaxation of the thermally induced aberrations in the main beam line over a period of 4.5 hours. Peak-to-valley aberrations range from 6.8 waves at 1.053 micrometer within 30 minutes after a full system shot to 3.9 waves after 4.5 hours. The adaptive optics system must have enough range to correct accumulated thermal aberrations from several shots in addition to the immediate shot-induced error. Accumulated wavefront errors in the beam line will affect both the design of the adaptive optics system for NIF and the performance of that system.
Distinct Cellular Functions of MK2 (2002)

Mitogen-activated protein kinase (MAPK)-activated protein kinase 2 (MK2) is activated upon stress by p38 MAPK alpha and -beta, which bind to a basic docking motif in the C terminus of MK2 and which subsequently phosphorylate its regulatory sites. As a result of activation MK2 is exported from the nucleus to the cytoplasm and cotransports active p38 MAPK to this compartment. Here we show that the amount of p38 MAPK is significantly reduced in cells and tissues lacking MK2, indicating a stabilizing effect of MK2 for p38. Using a murine knockout model, we have previously shown that elimination of MK2 leads to a dramatic reduction of tumor necrosis factor (TNF) production in response to lipopolysaccharide. To further elucidate the role of MK2 in p38 MAPK stabilization and in TNF biosynthesis, we analyzed the ability of two MK2 isoforms and several MK2 mutants to restore both p38 MAPK protein levels and TNF biosynthesis in macrophages. We show that MK2 stabilizes p38 MAPK through its C terminus and that MK2 catalytic activity does not contribute to this stabilization. Importantly, we demonstrate that stabilizing p38 MAPK does not restore TNF biosynthesis. TNF biosynthesis is only restored with MK2 catalytic activity. We further show that, in MK2-deficient macrophages, formation of filopodia in response to extracellular stimuli is reduced. In addition, migration of MK2-deficient mouse embryonic fibroblasts (MEFs) and smooth muscle cells on fibronectin is dramatically reduced. Interestingly, reintroducing catalytic MK2 activity into MEFs alone is not sufficient to revert the migratory phenotype of these cells. In addition to catalytic activity, the proline-rich N-terminal region is necessary for rescuing the migratory phenotype. These data indicate that catalytic activity of MK2 is required for both cytokine production and cell migration. However, the proline-rich MK2 N terminus provides a distinct role restricted to cell migration.
BCL-2 ONCOGENE BLOCKS DIFFERENTIATION AND EXTENDS VIABILITY BUT DOES NOT IMMORTALIZE NORMAL HUMAN KERATINOCYTES (1994)

To ascertain whether the bcl-2 oncogene plays a role in the initial stages of skin carcinogenesis by preventing differentiation of epidermal keratinocytes, we transfected primary human keratinocytes with the human bcl-2 gene and then determined whether these transfectants escape high calcium- and serum-induced differentiation. We found that the bcl-2 oncogene blocked differentiation and extended the life span of human keratinocytes in culture by over 24 weeks compared with cells transfected with pZip-neo DNA, which only grew for 5 weeks in culture. Keratinocytes transfected with the bcl-2 oncogene exhibited apoptotic bodies and telomere-telomere association between chromosomes toward the end of their life-span. These results suggest that die bcl-2 oncogene may be necessary but not sufficient for the immortalization of human keratinocytes.
Tyrosine Kinase Inhibitors. 10. Isomeric 4-[(3-Bromophenyl)amino]pyrido[d]- pyrimidines Are Potent ATP Binding Site Inhibitors of the Tyrosine Kinase Function of the Epidermal Growth Factor Receptor (1996)

Following the discovery of the very high inhibitory ability of the 4-[(3-bromophenyl)amino]-quinazolines against the tyrosine kinase activity of the epidermal growth factor receptor (EGFR) (e.g., 3, IC50 0.029 nM), four series of related pyrido[d]pyrimidines bearing electron-donating groups at the 6- or 7-positions have been synthesized and evaluated. The compounds were prepared by nucleophilic substitution of the corresponding 6- and 7-fluoro analogues. While members of all series showed potent inhibitory activity against isolated EGFR, there were important differences between the different isomeric pyrido[d]pyrimidines and the parent quinazolines. Overall, the [3,4-d] and [4,3-d] series were the most potent, followed by the [3,2-d] compounds, with the [2,3-d] analogues being least active. Whereas in the parent quinazoline series the addition of steric bulk to a 6- or 7-NH2 substituent (i.e., NHMe and NMe2 groups) dramatically decreased potency, no such trend was discernable in the [3,2-d] series. Furthermore, in the 7-substituted pyrido[4,3-d]- and 6-substituted pyrido[3,4-d]pyrimidine series, and to a limited extent in the 7-substituted pyrido[2,3-d] series, such substitution increased potency dramatically, to the extent that the 7-(methylamino)pyrido[4,3-d]pyrimidine (5f) (IC50 0.13 nM) and 6-(methylamino)pyrido[3,4-d]pyrimidine (7f) (IC50 0.008 nM) constitute important new leads. Selected compounds were evaluated for their ability to inhibit EGFR autophosphorylation in A431 cells, and a positive quantitative correlation was found between this activity and inhibitory activity against the isolated enzyme.
Fluid Inclusions trapped in Xenoliths from the Lower Crust/upperMantle Beneath Jeju Island (I); A Preliminary Study (2004)

This paper describes the textural relations of mantle xenoliths and fluid inclusions in mantlederived rocks found in alkaline basalts from Jeju Island which contain abundant ultramafic, felsic, and cumulate xenoliths. Most of the ultramafic xenoliths are spinel-lherzolites, composed of olivine, orthopyroxene, clinopyroxene and spinel. The felsic xenoliths considered as partially molten buchites consist of quartz and plagioclase with black veinlets, which are the product of ultrahigh-temperature metamorphism of lower crustal materials. The cumulate xenoliths, clinopyroxene-rich or clinopyroxene megacrysts, are also present. Textural examination of these xenoliths reveals that the xenoliths are typically coarse grained with metamorphic characteristics, testifying to a complex history of evolution of the lower crust/upper mantle source region. The ultramafic xenoliths contain protogranular, Porphyroclastic and equigranular textures with annealing features, indicating the presence of shear regime in upper mantle of the Island. The preferential associations of spinel and olivine with large orthopyroxenes suggest a previous high temperature equilibrium in the high-Al field and the original rock-type was a Al-rich OrthOPyrOXene-bearing peridotite without garnet. Three types of fluid inclusions trapped in mantle-derived xenoliths include C0,-rich fluid (Type I), multiphase silicate melt (glass I: devitrified crystals d= one or more daughter crystals + one or more vapor bubbles) (Type II), and sulfide (melt) inclusions (Type III). COi-rich inclusions are the most abundant volatile species in mantle xenoliths, supporting the presence of a separate C0,-rich phase. These C0,-nch inclusions are spatially associated with silicate and sulfide melts, suggesting immiscibility between them. Most multiphase silicate melt inclusions contain considerable amount of silicic glass, reflecting the formation of silicic melts in the lower crust/upper mantle, Combining fluid and melt inclusion data with conventional petrological and geochemical information will help to constrain the fluid regime, fluid-melt-mineral interaction processes in the mantle of the Korean Peninsula and pressure-temperature history of the host xenoliths in future studies
Antigen retrieval in formalin-fixed, paraffin-embedded tissues: an enhancement method for immunohistochemical staining based on microwave oven heating of tissue sections. (1991)

We describe a new approach for retrieval of antigens from formalin-fixed, paraffin-embedded tissues and their subsequent staining by immunohistochemical techniques. This method of antigen retrieval is based on microwave heating of tissue sections attached to microscope slides to temperatures up to 100 degrees C in the presence of metal solutions. Among 52 monoclonal and polyclonal antibodies tested by this method, 39 antibodies demonstrated a significant increase in immunostaining, nine antibodies showed no change, and four antibodies showed reduced immunostaining. In particular, excellent immunostaining results were obtained with a monoclonal antibody to vimentin as well as several different keratin antibodies on routine formalin-fixed tissue sections after pre-treatment of the slides with this method. These results showed that after antigen retrieval: (a) enzyme predigestion of tissues could be omitted; (b) incubation times of primary antibodies could be significantly reduced, or dilutions of primary antibodies could be increased; (c) adequate staining could be achieved in long-term formalin-fixed tissues that failed to stain by conventional methods; and (d) certain antibodies which were typically unreactive with formalin-fixed tissues gave excellent staining.
Semitransparent Nanostructured Films for Imaging Mass Spectrometry and Optical Microscopy (2012)

Semitransparent porous silicon substrates have been developed for pairing nanostructure-initiator mass spectrometry (NIMS) imaging with traditional optical-based microscopy techniques. Substrates were optimized to generate the largest NIMS signal while maintaining sufficient transparency to allow visible light to pass through for optical microscopy. Using these substrates, both phase-contrast and NIMS images of phospholipids from a scratch-wounded cell monolayer were obtained. NIMS images were generated using a spatial resolution of 14 μm. Coupled with further improvements in spatial resolution, this approach may allow for the localization of intact biological molecules within cells without the need for labeling.
Prognostic values of tumor endothelial markers in patients with colorectal cancer (2005)

AIM: Tumor endothelial markers (TEMs) are a newly discovered family of endothelial markers associated with tumor specific angiogenesis. This study sought to examine the levels of expression (qualitatively and quantitatively) for TEMs in human colon cancer.
Reproducible, Ultra High-Throughput Formation of Multicellular Organization from Single Cell Suspension-Derived Human Embryonic Stem Cell Aggregates (2008)

The mechanisms of early human embryogenesis are poorly understood. We report an ultra high throughput (UHTP) approach for generating spatially and temporally synchronised hEB. Aggregates generated in this manner exhibited aspects of peri-implantation tissue-level morphogenesis. These results should advance fundamental studies into early human developmental processes, enable high-throughput screening strategies to identify conditions that specify hESC-derived cells and tissues, and accelerate the pre-clinical evaluation of hESC-derived cells.
Comparative analysis of murine marrow–derived dendritic cells generated by Flt3L or GM-CSF/IL-4 and matured with immune stimulatory agents on the in vivo induction of antileukemia responses (2002)

Bone marrow (BM)-derived dendritic cells (DCs) cultured in granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin 4 (IL-4) have been used to generate antitumor immune responses. The cytokine Flt3 ligand (Flt3L) also has been shown to generate BM DCs. We sought to determine if DCs generated by using Flt3L then matured with lipopolysaccharide (LPS) could lead to DCs with in vivo anti-acute myelogenous leukemia (anti-AML) activity. LPS and tumor necrosis factor alpha (TNF-alpha) are effective agents for maturing DCs; however, they have potential in vivo toxicities. Cytosine-phosphorothioate-guanine oligodeoxynucleotides (CpGs) are considered relatively nontoxic, potent activators of DC function and maturation in vitro and in vivo. We investigated whether CpGs would be comparable to TNF-alpha or LPS for the maturation of GM-CSF/IL-4-generated DCs. DCs cultured with GM-CSF/IL-4 and matured with TNF-alpha, LPS, or CpG produced a greater allogeneic T-cell response compared with Flt3L/LPS-generated DCs. All 4 distinct DC types were pulsed with AML-lysate and administered before tumor challenge produced an increase in the total number of splenic anti-AML-specific cytotoxic T-lymphocyte precursors and led to significantly (P < or =.0001) improved survival compared with nonvaccinated controls. GM-CSF/IL-4/LPS was superior to Flt3L/LPS for generating anti-AML effects in vivo. Whereas TNF-alpha was comparable to LPS in conferring on GM-CSF/IL-4 DCs anti-AML effects in vivo, CpGs were superior to LPS. These data have important clinical implications and are the first to show that Flt3L-generated DCs can provide antitumor protection and that nontoxic agents such as CpGs and Flt3L may be useful in the clinical development of DC vaccines.
Global Gene Expression Profiling in Escherichia coli K12 (2003)

The work presented here is a first step toward a long term goal of systems biology, the complete elucidation of the gene regulatory networks of a living organism. To this end, we have employed DNA microarray technology to identify genes involved in the regulatory networks that facilitate the transition of Escherichia coli cells from an aerobic to an anaerobic growth state. We also report the identification of a subset of these genes that are regulated by a global regulatory protein for anaerobic metabolism, FNR. Analysis of these data demonstrated that the expression of over one-third of the genes expressed during growth under aerobic conditions are altered when E. coli cells transition to an anaerobic growth state, and that the expression of 712 (49%) of these genes are either directly or indirectly modulated by FNR. The results presented here also suggest interactions between the FNR and the leucine-responsive regulatory protein (Lrp) regulatory networks. Because computational methods to analyze and interpret high dimensional DNA microarray data are still at an early stage, and because basic issues of data analysis are still being sorted out, much of the emphasis of this work is directed toward the development of methods to identify differentially expressed genes with a high level of confidence. In particular, we describe an approach for identifying gene expression patterns (clusters) obtained from multiple perturbation experiments based on a subset of genes that exhibit high probability for differential expression values.
Novel insight into neutral medium as electrolyte for high-voltage supercapacitors (2011)

This paper is focused on neutral aqueous medium, i.e.lithium, sodium and potassium sulfate solutions in a wide range of concentrations (0.1–2.5 mol L−1) as promising electrolytes for electrochemical capacitors because they are cheap, non-corrosive and allow applying diverse current collectors. These properties make the capacitor assembling process much easier and cheaper. Additionally, such electrolytes are electrochemically stable and environmentally friendly. Electrochemical investigations carried out especially for 1 mol L−1Li2SO4 aqueous solution confirmed the possibility of efficient capacitor work in a wider voltage range, i.e. even at 2.2 V without any significant capacitance fade during 15 000 cycles. The physicochemical properties of ions (i.e. solvation, diffusion or mobility) and their influence on the capacitor electrochemical behaviour are considered.
Recombinant Expression, Purification, and Biochemical Characterization of Chondroitinase ABC II from Proteus vulgaris (2008)

Chondroitin lyases (or chondroitinases) are a family of enzymes that depolymerize chondroitin sulfate (CS) and dermatan sulfate (DS) galactosaminoglycans, which have gained prominence as important players in central nervous system biology. Two distinct chondroitinase ABC enzymes, cABCI and cABCII, were identified in Proteus vulgaris. Recently, cABCI was cloned, recombinantly expressed, and extensively characterized structurally and biochemically. This study focuses on recombinant expression, purification, biochemical characterization, and understanding the structure-function relationship of cABCII. The biochemical parameters for optimal activity and kinetic parameters associated with processing of various CS and DS substrates were determined. The profile of products formed by action of cABCII on different substrates was compared with product profile of cABCI. A homology-based structural model of cABCII and its complexes with CS oligosaccharides was constructed. This structural model provided molecular insights into the experimentally observed differences in the product profile of cABCII as compared with that of cABCI. The critical active site residues involved in the catalytic activity of cABCII identified based on the structural model were validated using site-directed mutagenesis and kinetic characterization of the mutants. The development of such a contaminant-free cABCII enzyme provides additional tools to decode the biologically important structure-function relationship of CS and DS galactosaminoglycans and offers novel therapeutic strategies for recovery after central nervous system injury.
Characteristics of Probe Electrospray Generated from a Solid Needle (2008)

Probe electrospray ionization (PESI) has recently been developed, in which the electrospray was generated from a solid needle instead of by using a capillary. In this paper, the characteristics of probe electrospray ionization were studied based on the measurement of spray current, optical microscopy, and PESI mass spectrometry. In the experiment, the solid needle was moved up and down a vertical axis, and a small amount of sample was repeatedly loaded to the needle when the tip of the needle touched the surface of the liquid sample at the lowest position. After the application of high voltage, a liquid droplet was formed on the tip of the solid needle probe, with its size was determined by the size of the needle tip. The liquid flow rate to the tip, as indicated by the spray current, depends on the voltage applied to the needle as well as the loaded liquid amount. Stable electrospray can be maintained until the total consumption of liquid sample. The kilohertz current pulsation takes place in the case of overloading the sample to the needle. The influences of the applied voltage and the liquid flow rate on the PESI mass spectra were also examined.
VCSE laser transmitters for parallel data links (1993)

The major issues associated with using vertical cavity surface emitting laser (VCSEL)-based transmitter arrays for parallel data links are examined. An assumption is made that only limited optimization of the individual links is permitted, and to the extent that the required circuits are shared by many channels. An analysis of bit-error ratios, based on measured laser parameter variations across the array, and their theoretical effect on noise margins indicates that a 5-dB penalty may be expected. This leads to a tradeoff between laser tolerances and receiver complexity. Experimental work towards a VCSEL-CMOS transmitter is described. A 622-Mb/s operation is demonstrated with a small hybrid transmitter array. Power dissipation and electrical crosstalk problems are assessed. Block coding of data before transmission significantly improves some aspects of laser transmitter performance. A statistical treatment of crosstalk noise is presented and compared to experimental results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lewis acid-induced ene-cyclization of ω-olefinic trifluoromethyl ketones: access to alicyclic compounds bearing a CF3group (1991)

Several catalysts (Me2AlCl, MeAlCl2, EtAlCl2 and TiCl4) for the ene carbocyclization of olefinic trifluoromethyl ketonic compounds have been compared. Thus, five-, six-, seven- and eight-membered-ring compounds were obtained. Olefin regiochemistry and stereoselectivity are better controlled than in related non-fluorinated series. High yields of cyclic trifluoromethyl alcohols were obtained by the achievement of type-I, -II or -III ene processes, concerted or otherwise. The first example of an eight-membered cyclization is described.