gebhart/patrepeval huggingface dataset:
Wild-type p53 and v-Src exert opposing influences on human vascular endothelial growth factor gene expression. (1995)

Angiogenesis, the development of new capillaries, is tightly controlled by the balance of positive and negative regulatory pathways. A newly described angiogenic factor, vascular endothelial growth factor/vascular permeability factor (VEGF/VPF), binds exclusively to endothelial cells and promotes their proliferation. Here we have studied the role of p53, a tumor suppressor, and v-Src, an oncogene on VEGF regulation. Wild-type p53 down-regulated endogenous VEGF mRNA level, as well as VEGF promoter activity, in a dose-dependent manner, whereas mutant forms of p53 had no effect. Overexpression of v-Src, known to up-regulate VEGF expression, activated a VEGF promoter-luciferase construct in a dose-dependent manner. Moreover, v-Src, in the presence of wt-p53, was unable to activate transcription of the VEGF promoter. Collectively, these data suggest that wild-type p53 may play a role in suppressing angiogenesis.
CMP cross-correlation analysis of multi-channel surface-wave data (2004)

In this paper, we demonstrate that Common Mid-Point (CMP) cross-correlation gathers of multi-channel and multi-shot surface waves give accurate phase-velocity curves, and enable us to reconstruct two-dimensional (2D) velocity structures with high resolution. Data acquisition for CMP cross-correlation analysis is similar to acquisition for a 2D seismic reflection survey. Data processing seems similar to Common Depth-Point (CDP) analysis of 2D seismic reflection survey data, but differs in that the cross-correlation of the original waveform is calculated before making CMP gathers. Data processing in CMP cross-correlation analysis consists of the following four steps: First, cross-correlations are calculated for every pair of traces in each shot gather. Second, correlation traces having a common mid-point are gathered, and those traces that have equal spacing are stacked in the time domain. The resultant cross-correlation gathers resemble shot gathers and are referred to as CMP cross-correlation gathers. Third, a multi-channel analysis is applied to the CMP cross-correlation gathers for calculating phase velocities of surface waves. Finally, a 2D S-wave velocity profile is reconstructed through non-linear least squares inversion. Analyses of waveform data from numerical modelling and field observations indicate that the new method could greatly improve the accuracy and resolution of subsurface S-velocity structure, compared with conventional surface-wave methods.
Comparison of Lentiviral and Sleeping Beauty Mediated αβ T Cell Receptor Gene Transfer (2013)

Transfer of tumour antigen-specific receptors to T cells requires efficient delivery and integration of transgenes, and currently most clinical studies are using gamma retroviral or lentiviral systems. Whilst important proof-of-principle data has been generated for both chimeric antigen receptors and αβ T cell receptors, the current platforms are costly, time-consuming and relatively inflexible. Alternative, more cost-effective, Sleeping Beauty transposon-based plasmid systems could offer a pathway to accelerated clinical testing of a more diverse repertoire of recombinant high affinity T cell receptors. Nucleofection of hyperactive SB100X transposase-mediated stable transposition of an optimised murine-human chimeric T cell receptor specific for Wilm's tumour antigen from a Sleeping Beauty transposon plasmid. Whilst transfer efficiency was lower than that mediated by lentiviral transduction, cells could be readily enriched and expanded, and mediated effective target cells lysis in vitro and in vivo. Integration sites of transposed TCR genes in primary T cells were almost randomly distributed, contrasting the predilection of lentiviral vectors for transcriptionally active sites. The results support exploitation of the Sleeping Beauty plasmid based system as a flexible and adaptable platform for accelerated, early-phase assessment of T cell receptor gene therapies.
Infrared Spectroscopy of Plant Cell Cultures (1991)

Infrared spectroscopy was used to examine suspension-cultured pear (Pyrus communis L.) and Spartina pectinata cells. Noninvasive measurements were made using internal reflectance sampling. Spectra of actively growing cells exhibited a pronounced absorbance at 2343 reciprocal centimeters. The absorbance peak was identified and verified as CO(2) dissolved in water. This peak was absent in nonviable cells. Peak height was directly proportional to percent viability in artificial mixtures of viable and nonviable cells, indicating that the level of intracellular CO(2) production could be used as a viability determinant for plant cells. Suspension-cultured cells were slowly cooled to subzero temperatures and analyzed for viability using infrared spectroscopy and tetrazolium staining. Both methods showed similar trends in viability assessment. Infrared spectroscopy could provide a more detailed understanding of cell viability and allow measurement on a noninvasive basis.
V.42bis and other Ziv-Lempel variants (2002)

Summary form only given, substantially as follows. The V.42bis standard for data compressing modems is discussed from algorithmic, experimental, practical, theoretical, and marketing standpoints. On a test set of five 100-Kbyte text and executable files, the compression ratios are found to be markedly inferior to those of several other algorithms, notably the Cleary-Witten adaptive Markov code and the Fiala-Greene Ziv-Lempel variant. However, since all the better-compressing methods have much larger data structures none is superior to V.42bis for use in a contemporary modem.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Increased Expression of MicroRNA-221 in Gastric Cancer and Its Clinical Significance (2012)

These findings suggest that miR-221 is a novel prognostic indicator in gastric cancer and may be a potential target for diagnosis and gene therapy.
Advances in high-brightness fiber-coupled laser modules for pumping multi-kW CW fiber lasers (2017)

High-power continuous wave (CW) fiber lasers with excellent beam quality continue to drive demand for higher brightness pump modules at 920 nm and 976 nm. Over the last decade, the brightness requirement for pumping state-of-the-art CW fiber lasers (CWFLs) has risen from approximately 0.5 W/(mm-mR)<sup>2</sup> to ~2 W/(mm-mR)<sup>2 </sup>for today’s mutlikW CWFLs. The most advanced CWFLs demand even higher brightness pump modules in order to minimize design complexity, maximize efficiency, and maximize the stimulated Raman scattering threshold. This need has resulted in a reoptimization of the nLIGHT <i>element</i><sup>TM</sup> line to enable a commercial 200 W, 18-emitter package with a 0.15 NA beam in a 105 &mu;m fiber, corresponding to a brightness of 3.2 W/(mm-mR)<sup>2</sup> and a 25 % increase in power over the existing <i>element</i><sup>TM</sup> e14 at 155 W. Furthermore, we have demonstrated the further scalability of this reoptimized design with our next generation COS, resulting in a maximum of 272 W into 105 &mu;m fiber with a brightness of 3.8 W/(mm-mR)<sup>2</sup>.
Molecular physiology of cardiac potassium channels (1996)

The cardiac action potential results from the complex, but precisely regulated, movement of ions across the sarcolemmal membrane. Potassium channels represent the most diverse class of ion channels in heart and are the targets of several antiarrhythmic drugs. Potassium currents in the myocardium can be classified into one of two general categories: 1) inward rectifying currents such as IK1, IKACh, and IKATP; and 2) primarily voltage-gated currents such as IKs, IKr, IKp, IKur, and Ito. The inward rectifier currents regulate the resting membrane potential, whereas the voltage-activated currents control action potential duration. The presence of these multiple, often overlapping, outward currents in native cardiac myocytes has complicated the study of individual K+ channels; however, the application of molecular cloning technology to these cardiovascular K+ channels has identified the primary structure of these proteins, and heterologous expression systems have allowed a detailed analysis of the function and pharmacology of a single channel type. This review addresses the progress made toward understanding the complex molecular physiology of K+ channels in mammalian myocardium. An important challenge for the future is to determine the relative contribution of each of these cloned channels to cardiac function.
A new American Joint Committee on Cancer staging system for cutaneous melanoma (2000)

The Melanoma Staging Committee of the AJCC has proposed major revisions of the melanoma TNM and stage grouping criteria. The committee members represent most of the major cooperative groups and cancer centers worldwide with a special interest in melanoma; the committee also collectively has had clinical experience with over 40,000 patients. The new staging system better reflects independent prognostic factors that are used in clinical trials and in reporting the outcomes of various melanoma treatment modalities. Major revisions include 1) melanoma thickness and ulceration, but not level of invasion, to be used in the T classification; 2) the number of metastatic lymph nodes, rather than their gross dimensions, the delineation of microscopic versus macroscopic lymph node metastases, and presence of ulceration of the primary melanoma to be used in the N classification; 3) the site of distant metastases and the presence of elevated serum LDH, to be used in the M classification; 4) an upstaging of all patients with Stage I,II, and III disease when a primary melanoma is ulcerated; 5) a merging of satellite metastases around a primary melanoma and in-transit metastases into a single staging entity that is grouped into Stage III disease; and 6) a new convention for defining clinical and pathologic staging so as to take into account the new staging information gained from intraoperative lymphatic mapping and sentinel lymph node biopsy. The AJC Melanoma Staging Committee invites comments and suggestions regarding this proposed staging system before a final recommendation is made.
Interplay between promoter and structural gene variants control basal serum level of mannan-binding protein (1995)

Mannan-binding protein (MBP) is a serum lectin participating in the innate immune defense by opsonizing various microorganisms for phagocytosis. Opsonization defect due to MBP deficiency and low levels of the protein can partially be explained by the dominant effect of three different mutations in the structural part of the MBP gene. Large interracial differences in the frequencies of these variants have previously been described, but they cannot explain the large interindividual variation in MBP serum concentration. We describe the existence of additional polymorphisms at positions -550 (H/L variants) and -221 (X/Y variants) in the promoter region of the gene. The promoter haplotypes, HY, LY, and LX, show associations with high, medium, and low levels of MBP serum concentrations, respectively. Moreover, this represents a genetic system with additive effect of haplotypes in which a low producing LX haplotype in the homozygous state down-regulates the basal expression of MBP as effectively as a single structural variant. Populations of pure Eskimos, Caucasoids, and black Africans show marked interethnic differences in the frequencies of promoter haplotypes regulating the expression of the normal peptide, with the HY haplotype frequency varying from 0.83 in Eskimos via 0.33 in Caucasoids to 0.08 in Africans. The LY haplotype frequency varies from 0.04 in Eskimos via 0.39 in Caucasoids to 0.23 in Africans. The LX haplotype frequency varies from 0.03 in Eskimos via 0.24 in Caucasoids to 0.23 in Africans. The effect of the promoter variants can explain almost all of the ethnic differences not explainable by the structural variants alone.
Developmental role of the SNF1-related kinase Hunk in pregnancy-induced changes in the mammary gland (2000)

The steroid hormones 17 beta-estradiol and progesterone play a central role in the pathogenesis of breast cancer and regulate key phases of mammary gland development. This suggests that developmental regulatory molecules whose activity is influenced by ovarian hormones may also contribute to mammary carcinogenesis. In a screen designed to identify protein kinases expressed in the mammary gland, we previously identified a novel SNF1-related serine/threonine kinase, Hunk (hormonally upregulated Neu-associated kinase). During postnatal mammary development, Hunk mRNA expression is restricted to a subset of mammary epithelial cells and is temporally regulated with highest levels of expression occurring during early pregnancy. In addition, treatment of mice with 17 beta-estradiol and progesterone results in the rapid and synergistic upregulation of Hunk expression in a subset of mammary epithelial cells, suggesting that the expression of this kinase may be regulated by ovarian hormones. Consistent with the tightly regulated pattern of Hunk expression during pregnancy, mammary glands from transgenic mice engineered to misexpress Hunk in the mammary epithelium manifest temporally distinct defects in epithelial proliferation and differentiation during pregnancy, and fail to undergo normal lobuloalveolar development. Together, these observations suggest that Hunk may contribute to changes in the mammary gland that occur during pregnancy in response to ovarian hormones.
Distortion in linearized electrooptic modulators (1995)

Intermodulation and harmonic distortion are calculated for a simple fiber-optic link with a representative set of link parameters and a variety of electrooptic modulators: simple Mach-Zehnder, linearized dual and triple Mach-Zehnder, simple directional coupler (two operating points), and linearized directional coupler with one and two dc electrodes. The resulting dynamic ranges, gains, and noise figures are compared for these modulators. A new definition of dynamic range is proposed to accommodate the more complicated variation of intermodulation with input power exhibited by linearized modulators. The effects of noise bandwidth, preamplifier distortion, and errors in modulator operating conditions are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Data Integration in the Geospatial Semantic Web (2009)

Geospatial decision makers have to be aware of the varying interests of all stakeholders. One crucial task in the process is to identify relevant information available from the Web. In this chapter the authors introduce an application in the quarrying domain which integrates Semantic Web technologies to provide new ways to discover and reason about relevant information. The authors discuss the daily struggle of the domain experts to create decision-support maps helping to find suitable locations for opening up new quarries. After explaining how semantics can help these experts, they introduce the various components and the architecture of the software which has been developed in the European funded SWING project. In the last section, the different use cases illustrate how the implemented tools have been applied to real world scenarios.
Response to Programmed Cell Death-1 Blockade in a Murine Melanoma Syngeneic Model Requires Costimulation, CD4, and CD8 T Cells (2016)

The programmed cell death protein 1 (PD-1) limits effector T-cell functions in peripheral tissues, and its inhibition leads to clinical benefit in different cancers. To better understand how PD-1 blockade therapy modulates the tumor-host interactions, we evaluated three syngeneic murine tumor models, the BRAF<sup>V600E</sup>-driven YUMM1.1 and YUMM2.1 melanomas, and the carcinogen-induced murine colon adenocarcinoma MC38. The YUMM cell lines were established from mice with melanocyte-specific BRAF<sup>V600E</sup> mutation and PTEN loss (BRAF<sup>V600E</sup>/PTEN<sup>-/-</sup>). Anti-PD-1 or anti-PD-L1 therapy engendered strong antitumor activity against MC38 and YUMM2.1, but not YUMM1.1. PD-L1 expression did not differ between the three models at baseline or upon interferon stimulation. Whereas mutational load was high in MC38, it was lower in both YUMM models. In YUMM2.1, the antitumor activity of PD-1 blockade had a critical requirement for both CD4 and CD8 T cells, as well as CD28 and CD80/86 costimulation, with an increase in CD11c<sup>+</sup>CD11b<sup>+</sup>MHC-II<sup>high</sup> dendritic cells and tumor-associated macrophages in the tumors after PD-1 blockade. Compared with YUMM1.1, YUMM2.1 exhibited a more inflammatory profile by RNA sequencing analysis, with an increase in expression of chemokine-trafficking genes that are related to immune cell recruitment and T-cell priming. In conclusion, response to PD-1 blockade therapy in tumor models requires CD4 and CD8 T cells and costimulation that is mediated by dendritic cells and macrophages. Cancer Immunol Res; 4(10); 845-57. ©2016 AACR.
Regulatory mechanism of 92 kDa type IV collagenase gene expression which is associated with invasiveness of tumor cells. (1993)

92-kDa Type IV collagenase, a member of matrix metalloproteinases, is believed to play a critical role in physiological tissue-remodeling processes and also in many pathological conditions such as tumor invasion. We analyzed the 5'-flanking sequence of the 92 kDa type IV collagenase gene that controls the expression of the gene by ligating it to the chloramphenicol acetyltransferase gene. Deletion and mutation analysis revealed that three motifs, homologous to the binding sites for AP-1, NF-kappa B, and Sp-1 proteins, contributed positively to induction by 12-O-tetradecanoyl-phorbol-13-acetate (TPA) and tumor necrosis factor alpha (TNF alpha). The AP-1 site was indispensable but not sufficient for the induction and required synergistic cooperation with either the kappa B or the Sp-1 site. In OST cells, a nuclear factor which bound to Sp-1 was constitutively expressed, and those bound to AP-1 and kappa B elements were rapidly induced by TNF alpha treatment. Comparison of the findings with those for the promoters of other TPA-inducible matrix metalloproteinases, interstitial collagenase and stromelysin 1, revealed that the signal to the AP-1 sites is common for the TPA-inducibility of the genes but that the signals to the kappa B or Sp-1 sites, which are not present in interstitial collagenase and stromelysin 1 promoters, are the unique determinant for the inducibility of the 92 kDa type IV collagenase gene.
20-Gb/s OFDM Transmission over 4,160-km SSMF Enabled by RF-Pilot Tone Phase Noise Compensation (2007)

We introduce a novel method to compensate for local oscillator offset and phase-noise in coherent-OFDM systems and report continuously detectable transmission at 20-Gb/s data rate (25.8 Gb/s before coding) over 4,160-km SSMF without dispersion compensation.
Spatiotemporal Effects of Microstimulation in Rat Neocortex: A Parametric Study Using Multielectrode Recordings (2003)

Using microstimulation to imprint meaningful activity patterns into intrinsically highly interconnected neuronal substrates is hampered by activation of fibers of passage leading to a spatiotemporal "blur" of activity. The focus of the present study was to characterize the shape of this blur in the neocortex to arrive at an estimate of the resolution with which signals can be transmitted by multielectrode stimulation. The horizontal spread of significant unit activity evoked by near-threshold focal electrical stimulation (charge transfer 0.8-4.8 nC) and multielectrode recording in the face representation of the primary somatosensory cortex of ketamine anesthetized rats was determined to be about 1,350 microm. The evoked activity inside this range consisted in a sequence of fast excitatory response followed by an inhibition lasting >100 ms. These 2 responses could not be separated by varying the intensity of stimulation while a slow excitatory rebound after the inhibitory response was restricted to higher stimulus intensities (>2.4 nC). Stimulation frequencies of 20 and 40 Hz evoked repetitive excitatory response standing out against a continuous background of inhibition. At 5- and 10-Hz stimulation, the inhibitory response showed a complex interaction pattern attributed to highly sublinear superposition of individual inhibitory responses. The present data help to elucidate the neuronal underpinnings of behavioral effects of microstimulation. Furthermore, they provide essential information to determine spatiotemporal constraints for purposeful multielectrode stimulation in the neocortex.
Molecular-Dynamics Studies of Single-Stranded Hexitol, Altritol, Mannitol, and Ribose Nucleic Acids (HNA, MNA, ANA, and RNA, Resp.) and of the Stability of HNA⋅RNA, ANA⋅RNA, and MNA⋅RNA Duplexes (2000)

The influence of the orientation of a 3′-OH group on the conformation and stability of hexitol oligonucleotides in complexes with RNA and as single strands in aqueous solution was investigated by molecular-dynamics (MD) simulations with AMBER 4.1. The particle mesh Ewald (PME) method was used for the treatment of long-range electrostatic interactions. An equatorial orientation of the 3′-OH group in the single-stranded D-mannitol nucleic acid (MNA) m(GCGTAGCG) and in the complex with the RNA r(CGCAUCGC) has an unfavorable influence on the helical stability. Frequent H-bonds between the 3′-OH group and the O−C(6′) of the phosphate backbone of the following nucleotide explain the distorted conformation of the MNA⋅RNA complex as well as that of the single MNA strand. This is consistent with experimental results that show lowered hybridization potentials for MNA⋅RNA complexes. An axial orientation of the 3′-OH group in the D-altritol nucleic acid (ANA) a(GCGTAGCG) leads to a stable complex with the complementary RNA r(CGCAUCGC), as well as to a more highly preorganized single-stranded ANA chain. The averaged conformation of the ANA⋅RNA complex is similar to that of A-RNA, with only minor changes in groove width, helical curvature, and H-bonding pattern. The relative stabilities of ANA⋅RNA vs. HNA⋅RNA (HNA=D-hexitol nucleic acid without 3′-OH group) can be explained by differences in restricted movements, H-bonds, and solvation effects.
Chronic Lymphocytic Leukemia B Cells Express Functional CXCR4 Chemokine Receptors That Mediate Spontaneous Migration Beneath Bone Marrow Stromal Cells (1999)

Chemokines play a central role for lymphocyte trafficking and homing. The mechanisms that direct the tissue localization of B cells from patients with chronic lymphocytic leukemia (B-CLL) are unknown. We found that CLL B cells express functional CXCR4 receptors for the chemokine stromal cell-derived factor-1 (SDF-1), as demonstrated by receptor endocytosis, calcium mobilization, and actin polymerization assays. Moreover, CLL B cells displayed chemotaxis to this chemokine that could be inhibited by monoclonal antibodies (MoAbs) against CXCR4, pertussis toxin, or Wortmannin, a phosphatidylinositol 3-kinase inhibitor. That this chemotaxis may be involved in the homing of CLL cells is argued by studies in which CLL B cells were cocultured with a murine marrow stromal cell line that secretes SDF-1. Within 2 hours, CLL B cells spontaneously migrated beneath such stromal cells in vitro (pseudoemperipolesis). This migration could be inhibited by pretreatment of CLL B cells with anti-CXCR4 MoAbs, SDF-1alpha, or pertussis-toxin. Furthermore, we noted strong downmodulation of CXCR4 on CLL B cells that migrated into the stromal cell layer. These findings demonstrate that the chemokine receptor CXCR4 on CLL B cells plays a critical role for heterotypic adherence to marrow stromal cells and provide a new mechanism to account for the marrow infiltration by neoplastic B cells.