gebhart/patrepeval huggingface dataset:
Loss of growth responsiveness to epidermal growth factor and enhanced production of alpha‐transforming growth factors in <i>ras</i>‐transformed mouse mammary epithelial cells (1987)

A mouse mammary epithelial cell line, NMuMG, exhibits a low capacity to grow in semisolid medium as colonies and it is not tumorigenic in nude mice. In contrast, NMuMG cells which have been transformed by an activated c-Harvey ras proto-oncogene, NMuMG/rasH, or by the polyoma middle T-transforming gene, NMuMG/pyt, are able to grow in soft agar and, when injected into nude mice, produce undifferentiated carcinomas. Human epidermal growth factor (EGF) or human alpha-transforming growth factor (alpha TGF) can stimulate, in a dose-dependent fashion, the anchorage-independent growth of NMuMG and NMuMG/pyt cells in soft agar but fail to enhance the anchorage-independent growth of the NMuMGrasH cells. Likewise, human EGF or human alpha TGF is also able to stimulate the anchorage-dependent growth of normal NMuMG cells and NMuMG/pyt cells in a serum-free medium supplemented with insulin, transferrin, fetuin, and laminin, or in medium containing low concentrations of serum, whereas these same growth factors under comparable culture conditions have little or no effect upon the anchorage-dependent growth of the ras-transformed NMuMG-rasH cells. The biological refractoriness of the NMuMG/rasH cells to human EGF or human alpha TGF is reflected by a reduction in the total number of cell surface receptors for EGF and by an absence of a high-affinity population of binding sites for mouse [125l]EGF on these cells as compared to the NMuMG or NMuMG/pyt cells. In addition, concentrated conditioned medium (CM) obtained from NMuMG/rasH and NMuMG/pyt cells contains a relatively higher amount of biologically active TGFs than CM obtained from comparably treated NMuMG cells as measured by the ability to induce the anchorage-independent growth of normal rat kidney cells in soft agar. The higher levels of biologically active TGFs found in the CM from the transformed cells relative to the NMuMG cells is paralleled by a corresponding increase in the CM from these cells in the amount of immunoreactive alpha TGF, by an increase in the amount of EGF receptor-competing activity, and by an increase in the levels of alpha TGF mRNA in the NMuMG/rasH cells. These results demonstrate that mammary epithelial cells which have been transformed by an activated ras proto-oncogene, but not by the polyoma middle T-transforming gene, become unresponsive to exogenous EGF or alpha TGF.(ABSTRACT TRUNCATED AT 400 WORDS)
Circle Plus Partial Helical Scan Scheme for a Flat Panel Detector‐Based Cone Beam Breast X‐Ray CT (2009)

Flat panel detector-based cone beam breast CT (CBBCT) can provide 3D image of the scanned breast with 3D isotropic spatial resolution, overcoming the disadvantage of the structure superimposition associated with X-ray projection mammography. It is very difficult for Mammography to detect a small carcinoma (a few millimeters in size) when the tumor is occult or in dense breast. CBBCT featured with circular scan might be the most desirable mode in breast imaging due to its simple geometrical configuration and potential applications in functional imaging. An inherited large cone angle in CBBCT, however, will yield artifacts in the reconstruction images when only a single circular scan is employed. These artifacts usually manifest themselves as density drop and object geometrical distortion that are more noticeable in the reconstructed image areas that are further away from the circular scanning plane. In order to combat this drawback, a circle plus partial helical scan scheme is proposed. An exact circle plus straight line scan scheme is also conducted in computer simulation for the purpose of comparison. Computer simulations using a numerical breast phantom demonstrated the practical feasibility of this new scheme and correction to those artifacts to a certain degree.
Safety on the Roads: LTE Alternatives for Sending ITS Messages (2014)

This article discusses different alternatives for sending intelligent transportation systems (ITS) messages using long-term evolution (LTE) networks. Specifically, it compares the unicast and evolved Multimedia Broadcast Multicast Services (eMBMS) transmission modes by means of system-level simulations and a cost modeling analysis. The optimum configuration of the eMBMS carrier is studied for the case of ITS services. This article also includes some recommendations on the configuration of the ITS server in charge of distributing safety messages as well as on its interaction with the mobile network operator (MNO). The results show that eMBMS is significantly more efficient in terms of resource consumption than the unicast mode, implying an important reduction of the delivery costs.
[Interleukin 1 and hematopoiesis]. (1990)

Interleukin-1 mediates a broad spectrum of activities in the functional network of cytokines. In addition to its function as an inducer of the acute phase response IL-1 has many effects on hemopoiesis in normal and hematologically impaired organisms. This regulatory function is realized by its ability to stimulate the release of hematopoietic growth factors and by its recruiting property for cell cycles of different hemopoietic progenitors and stem cells. IL-1 acts synergistically with the colony-stimulating factors.
Solidification Analyses of Bulky Zr<SUB>60</SUB>Al<SUB>10</SUB>Ni<SUB>10</SUB>Cu<SUB>15</SUB>Pd<SUB>5</SUB> Glass Produced by Casting into Wedge-Shape Copper Mold (1995)

The liquid-crystalline transformation behavior during continuous cooling and the transformation-induced structure were examined for a Zr60Al10Ni10Cu15Pd5 molten alloy which was ejected into a wedge-shape cavity in a copper mold. The wedge-shape cavity has a constant depth of 50 mm and different vertical angles (θ) ranging from 5 to 15 degrees. The ejection temperature of the molten alloy was also changed in the range of 1273 to 1573 K. The cast structure consists only of a glassy phase in the θ range smaller than 10 degrees and changes to a mixed structure consisting of glassy and nonequilibrium crystalline Zr2Ni and Zr2Cu phases in the higher θ range. The glass transition temperature and crystallization temperature of the cast metal glass are 683 and 778 K, respectively, which agree with those for the melt-spun glassy ribbon. The start (Cs) and termination (Ct) points for the transformation from the supercooled liquid to crystalline phases during continuous cooling were determined from the thermal analytical data obtained at different sites in the wedge-shape cavity and the continuous-cooling-transformation (C.C.T.) curves were constructed. The nose temperature (Tn) and the time (tn) up to the nose point in the C.C.T. curves were 1018 K and 0.93 s respectively. The critical cooling rate for glass formation defined by (Tm−Tn)⁄tn is evaluated to be 110 K/s. Further, the time interval between Cs and Ct is as short as 0.2 s and the fast growth reaction is attributed to the easy formation of the nonequilibrium crystalline phases and the increase in temperature caused by the precipitation-induced recalescence.
How to drain without lymphatics? Dendritic cells migrate from the cerebrospinal fluid to the B-cell follicles of cervical lymph nodes (2005)

The lack of draining lymphatic vessels in the central nervous system (CNS) contributes to the so-called "CNS immune privilege." However, despite such a unique anatomic feature, dendritic cells (DCs) are able to migrate from the CNS to cervical lymph nodes through a yet unknown pathway. In this report, labeled bone marrow-derived myeloid DCs were injected stereotaxically into the cerebrospinal fluid (CSF) or brain parenchyma of normal rats. We found that DCs injected within brain parenchyma migrate little from their site of injection and do not reach cervical lymph nodes. In contrast, intra-CSF-injected DCs either reach cervical lymph nodes or, for a minority of them, infiltrate the subventricular zone, where neural stem cells reside. Surprisingly, DCs that reach cervical lymph nodes preferentially target B-cell follicles rather than T-cell-rich areas. This report sheds a new light on the specific role exerted by CSF-infiltrating DCs in the control of CNS-targeted immune responses.
Air Drilling Operations Improved by Percussion Bit/Hammer Tool Tandem (1985)

ABSTRACT Tenneco and other operators air drill whenever possible to improve rate of penetration. This is done with pneumatic hammer tools and various bit types used with standard rotary air rigs. The recent application of a "flatbottom" percussion bit combined with a custom designed hammer tool originally developed for mining operations has significantly improved air drilling operations in the Arkoma Basin. The improvements include a large increase in ROP, improved hole geomotry, reduced drillstring stresses and a substantial reduction in cost/ft. This paper provides: Discussion of the engineering design and operation of the flatbottom bit/hammer tool tandem Applications and limitations of the tools Guidelines for optimization of performance Documentation of field performance on Tenneco wells in the Arkoma Basin to demonstrate the improvements in air drilling operations provided by the flatbottom bit/hammer tool tandem.
Emergence and Pathogenicity of Highly Virulent Cryptococcus gattii Genotypes in the Northwest United States (2010)

Cryptococcus gattii causes life-threatening disease in otherwise healthy hosts and to a lesser extent in immunocompromised hosts. The highest incidence for this disease is on Vancouver Island, Canada, where an outbreak is expanding into neighboring regions including mainland British Columbia and the United States. This outbreak is caused predominantly by C. gattii molecular type VGII, specifically VGIIa/major. In addition, a novel genotype, VGIIc, has emerged in Oregon and is now a major source of illness in the region. Through molecular epidemiology and population analysis of MLST and VNTR markers, we show that the VGIIc group is clonal and hypothesize it arose recently. The VGIIa/IIc outbreak lineages are sexually fertile and studies support ongoing recombination in the global VGII population. This illustrates two hallmarks of emerging outbreaks: high clonality and the emergence of novel genotypes via recombination. In macrophage and murine infections, the novel VGIIc genotype and VGIIa/major isolates from the United States are highly virulent compared to similar non-outbreak VGIIa/major-related isolates. Combined MLST-VNTR analysis distinguishes clonal expansion of the VGIIa/major outbreak genotype from related but distinguishable less-virulent genotypes isolated from other geographic regions. Our evidence documents emerging hypervirulent genotypes in the United States that may expand further and provides insight into the possible molecular and geographic origins of the outbreak.
A PCR-RFLP method for detection of the LNPEP encoding human insulin-regulated aminopeptidase (IRAP) rs4869317 polymorphism (2016)

The PCR-RFLP is a simple and reliable method that allows a quick genotyping for the rs4869317 SNP of LNPEP gene. The study of this polymorphism could be useful in future investigations to analyze the role of genetic variants of IRAP in several physiological/pathological conditions.
Phase sensitive degenerate parametric amplification using directly-bonded PPLN ridge waveguides (2011)

We constructed the first CW pumped degenerate parametric amplifier based on periodically poled and ZnO-doped LiNbO3 ridge waveguides. An in-phase gain of + 11 dB was achieved owing to the high conversion efficiency and high damage resistance of the waveguide obtained by employing direct bonding and dry etching techniques. Nearly identical amplification and deamplification were obtained owing to a sufficient spatial and temporal overlap between the pump and signal beams. No secondary wavelength conversion process was observed, and a maximum output of 22 dBm was obtained. We also successfully demonstrated the phase sensitive amplification of a modulated signal light.
Elevated stromal chondroitin sulfate glycosaminoglycan predicts progression in early-stage prostate cancer. (1997)

Curative therapies for clinically localized prostate cancer have significant morbidity, and those patients who might be cured by aggressive management are not easily identified using current clinical information. Better biomarkers of tumor behavior need to be identified to improve clinical outcome. Chondroitin sulfate (CS), a glycosaminoglycan, may be a potentially useful biomarker as it is known to influence cell growth and differentiation and might influence malignant progression. In this study, CS was immuno-localized to the periacinar and peritumoral fibromuscular stromal tissue of nonmalignant and malignant prostates. The CS concentration was increased in the prostate tissue of men with early-stage prostate cancer compared with tissue from men without cancer (P < 0.0001). Using Cox's univariate analysis, CS concentration, tumor grade, preoperative serum prostate-specific antigen (PSA), extracapsular extension of disease, positive surgical margins, and patient age were associated with an increased risk of PSA failure. The CS concentration was compared with the other features in two-variable regression analyses. CS and preoperative serum PSA concentrations were independent predictors of PSA failure. CS was a stronger prognostic feature than tumor grade and could predict outcome for patients with moderately differentiated tumors. Patients with a low CS concentration had significantly better progression-free survival following radical prostatectomy than patients with high levels of CS (Kaplan-Meier plot, 91% versus 49% PSA progression free at 5 years, respectively, P = 0.0038). Only postoperative pathological indices (extracapsular extension, surgical margins) were stronger predictors than CS. We conclude that measurement of prostatic CS concentrations at diagnosis may allow stratification of patients with early-stage prostate cancer for adjunctive or alternate therapies.
Graphene Oxide: Structural Analysis and Application as a Highly Transparent Support for Electron Microscopy (2009)

We report on the structural analysis of graphene oxide (GO) by transmission electron microscopy (TEM). Electron diffraction shows that on average the underlying carbon lattice maintains the order and lattice-spacings of graphene; a structure that is clearly resolved in 80 kV aberration-corrected atomic resolution TEM images. These results also reveal that single GO sheets are highly electron transparent and stable in the electron beam, and hence ideal support films for the study of nanoparticles and macromolecules by TEM. We demonstrate this through the structural analysis of physiological ferritin, an iron-storage protein.
Adiabatic Quantum Simulation of Quantum Chemistry (2014)

Abstract We show how to apply the quantum adiabatic algorithm directly to the quantum computation of molecular properties. We describe a procedure to map electronic structure Hamiltonians to 2-body qubit Hamiltonians with a small set of physically realizable couplings. By combining the Bravyi-Kitaev construction to map fermions to qubits with perturbative gadgets to reduce the Hamiltonian to 2-body, we obtain precision requirements on the coupling strengths and a number of ancilla qubits that scale polynomially in the problem size. Hence our mapping is efficient. The required set of controllable interactions includes only two types of interaction beyond the Ising interactions required to apply the quantum adiabatic algorithm to combinatorial optimization problems. Our mapping may also be of interest to chemists directly as it defines a dictionary from electronic structure to spin Hamiltonians with physical interactions.
Characterization of plasmid burden and copy number in<i>Saccharomyces cerevisiae</i>for optimization of metabolic engineering applications (2012)

Many metabolic engineering and genetic engineering applications in yeast rely on the use of plasmids. Despite their pervasive use and the diverse collections available, there is a fundamental lack of understanding of how commonly used DNA plasmids affect the cell's ability to grow and how the choice of plasmid components can influence plasmid load and burden. In this study, we characterized the major attributes of the 2 micron and centromeric plasmids typically used in yeast by examining the impact of choice of selection marker, promoter, origin of replication, and strain ploidy on conferred growth rates and plasmid copy number. We conclude that the 'plasmid burden', as demonstrated by a reduced growth rate, is primarily due to the choice of selection marker, especially when auxotrophic markers are utilized. The plasmid burden traditionally attributed to replication and maintenance of plasmid DNA plays only a minor role in haploid yeast yet is much more significant in diploid strains. The selection marker can also significantly change plasmid copy number. In fact, plasmid copy number can be influenced to some extent by all of the parameters tested. The information presented in this study will allow for more rational design and selection of plasmids for engineering applications.
Vitamin D-regulated gene expression. (1993)

The major emphasis of this review is on the molecular events that occur in target tissues when stimulated by 1,25-dihydroxyvitamin D3. The vitamin D receptor is a 55,000-kDa protein whose domains have been described roughly for human and rat. A single receptor appears to carry out all of the known functions of vitamin D and is likely a nucleoprotein. The receptor binds to vitamin D response elements found in the promoter region of responsive genes. An accessory protein is required for the binding of the receptor to these response elements. The accessory protein has a molecular weight of approximately 62,000 kDa but has not been cloned. The response elements are two repeat sequences separated by three bases. A negative response element is known for the parathyroid gene and is a single arm homologous to one arm of the osteopontin response element. Phosphorylation in the ligand binding domain of the receptor follows binding of 1,25-(OH)2D3. The receptor then becomes transcriptively active and interacts with other transcription factors to bring about gene expression. It is unknown, if following phosphorylation, the ligand is released, and final proof that the phosphorylated receptor is the transcriptively active form of the protein is not yet available.
Evidence for <i>trans‐cis</i> isomerization of the <i>p</i>‐coumaric acid chromophore as the photochemical basis of the photocycle of photoactive yellow protein (1996)

Analysis of the chromophore p-coumaric acid, extracted from the ground state and the long-lived blue-shifted photocycle intermediate of photoactive yellow protein, shows that the chromophore is reversibly converted from the trans to the cis configuration, while progressing through the photocycle. The detection of the trans and cis isomers was carried out by high performance capillary zone electrophoresis and further substantiated by 1H NMR spectroscopy. The data presented here establish the photo-isomerization of the vinyl double bond in the chromophore as the photochemical basis for the photocycle of photoactive yellow protein, a eubacterial photosensory protein. A similar isomerization process occurs in the structurally very different sensory rhodopsins, offering an explanation for the strong spectroscopic similarities between photoactive yellow protein and the sensory rhodopsins. This is the first demonstration of light-induced isomerization of a chromophore double bond as the photochemical basis for photosensing in the domain of Bacteria.
Angiotensin II and IV Stimulate Expression and Release of Plasminogen Activator Inhibitor-1 in Cultured Human Coronary Artery Endothelial Cells (2002)

There is increasing evidence that angiotensin II influences thrombogenesis by regulating the expression of plasminogen activator inhibitor-1 (PAI-1). In this study, the effects of angiotensin II and its receptors on the expression and release of PAI-1 and tissue-type plasminogen activator (t-PA) were examined in human coronary artery endothelial cells (HCAECs). As control, cells were treated with angiotensin IV. HCAECs incubated with angiotensin II increased the expression of PAI-1 mRNA in a concentration (10-9-10-5 M)- and time (6-24 h)-dependent manner. PAI-1 protein release was also increased in the culture medium of HCAECs treated with angiotensin II. The effects of angiotensin II (10-6 M) were blocked completely by the AT1 receptor blocker losartan (10-6 M) but not by the AT2 receptor blocker PD123319 (10-6 M). Angiotensin II pretreatment also slightly, but significantly, increased t-PA mRNA expression. This effect of angiotensin II on t-PA mRNA was blocked by losartan but not by PD123319. HCAECS treated with angiotensin II revealed large amounts of the lipid peroxidation product, malonaldehyde (MDA). The effects of angiotensin II on PAI-1 expression and MDA release were blocked by pretreatment of cells with alpha-tocopherol (10-5 M). In control experiments, treatment of HCAECs with angiotensin IV markedly increased PAI-1 mRNA expression and protein release. This effect of angiotensin IV was blocked by the AT4 receptor blocker divalinal (10-6 M). These observations indicate that AT1 receptor activation plays an important role in the stimulation of PAI-1 expression and release in response to angiotensin II. Upregulation of t-PA gene may reflect autoregulation in response to PAI-1 release. Angiotensin II-mediated activation of oxidation pathways may relate to uupregulation of PAI-1. This study also confirms that angiotensin IV upregulates PAI-1 expression in HCAECs.
<i>Coccidioides posadasii</i> Contains a Single 1,3-β-Glucan Synthase Gene That Appears To Be Essential for Growth (2005)

1,3-beta-Glucan synthase is responsible for the synthesis of beta-glucan, an essential cell wall structural component in most fungi. We sought to determine whether Coccidioides posadasii possesses genes homologous to known fungal FKS genes that encode the catalytic subunit of 1,3-beta-glucan synthase. A single gene, designated FKS1, was identified, and examination of its predicted protein product showed a high degree of conservation with Fks proteins from other filamentous fungi. FKS1 is expressed at similar levels in mycelia and early spherulating cultures, and expression decreases as the spherules mature. We used Agrobacterium-mediated transformation to create strains that harbor DeltaFKS1::hygB, a null allele of FKS1, and hypothesize that Fks1p function is essential, due to our inability to purify this allele away from a complementing wild-type FKS1 allele in a heterokaryotic strain. The heterokaryon appears normal with respect to growth rate and arthroconidium production; however, microscopic examination of strains with DeltaFKS1::hygB alleles revealed abnormal swelling of hyphal elements.