gebhart/patrepeval huggingface dataset:
Neoplastic Transformation Induced by an Activated Lymphocyte-Specific Protein Tyrosine Kinase (pp56lck) (1988)

The lck proto-oncogene encodes a lymphocyte-specific member of the src family of protein tyrosine kinases. Here we demonstrate that pp56lck is phosphorylated in vivo at a carboxy-terminal tyrosine residue (Tyr-505) analogous to Tyr-527 of pp60c-src. Substitution of phenylalanine for tyrosine at this position resulted in increased phosphorylation of a second tyrosine residue (Tyr-394) and was associated with an increase in apparent kinase activity. In addition, this single point mutation unmasked the oncogenic potential of pp56lck in NIH 3T3 cell transformation assays. Viewed in the context of similar results obtained with pp60c-src, it is likely that the enzymatic activity and transforming ability of all src-family protein tyrosine kinases can be regulated by carboxy-terminal tyrosine phosphorylation. We further demonstrate that overexpression of pp56lck in the murine T-cell lymphoma LSTRA as a result of a retroviral insertion event produces a kinase protein that despite wild-type primary structure is nevertheless hypophosphorylated at Tyr-505. Thus, control of normal growth in this lymphoid cell line may have been abrogated through acquisition of a posttranslationally activated version of pp56lck.
From evidence to inference: Probing the evolution of protein interaction networks (2009)

The evolutionary mechanisms by which protein interaction networks grow and change are beginning to be appreciated as a major factor shaping their present-day structures and properties. Starting with a consideration of the biases and errors inherent in our current views of these networks, we discuss the dangers of constructing evolutionary arguments from naïve analyses of network topology. We argue that progress in understanding the processes of network evolution is only possible when hypotheses are formulated as plausible evolutionary models and compared against the observed data within the framework of probabilistic modeling. The value of such models is expected to be greatly enhanced as they incorporate more of the details of the biophysical properties of interacting proteins, gene phylogeny, and measurement error and as more advanced methodologies emerge for model comparison and the inference of ancestral network states.
Frequency Trimming of ZnO/Glass SAW Filters (1991)

In the process of producing ZnO/glass SAW filters, a desired frequency cannot always be obtained after sputtering ZnO thin films on IDT /glass substrates. It is therefore necessary to adjust the center frequency of each SAW filter within 0.05% tolerance after sputtering. We have developed a method to adjust the center frequency in a mass production process by overlaying organic polymer resin on the substrates. The frequency deviation then becomes very small not only in one lot, but also between lots, and the mass production cost of SAW filters can be reduced tremendously.
Design and implementation of distributed control architecture of an AC-stacked PV inverter (2015)

A control scheme for a distributed Inverter Molecule™ architecture is analyzed and implemented in this paper. An Inverter Molecule is a building block for a novel distributed inverter architecture suitable for PV/Battery applications which exceeds the performance metrics obtained by Central/String- inverters with or without DC/DC optimizers or by Micro-Inverters. The proposed transformerless architecture utilizes low-voltage semiconductor devices with much higher yields than their high-voltage counterparts. A group of Inverter Molecules operate autonomously and cooperatively to maintain the grid interconnection requirements while providing maximum power control on each molecule's PV panel. This paper overviews the state-of the-art control methods implemented mostly on cascaded H-bridge derived topologies and further establishes a distributed control scheme for Inverter Molecule architecture that does not need any high bandwidth communications except a heartbeat signal at line frequency. Experimental results are presented for a lab-scaled prototype.
CD200 Is Preferentially Expressed in CD138 dim Multiple Myeloma Cells: Implications for a Myeloma Stem Cell Subpopulation with Potential Immune-Resistance. (2009)

Abstract Abstract 4877 Introduction The CD138negCD20+ cell population has been suggested as the putative multiple myeloma (MM) cancer stem cells, both in MM cell lines and in patient specimens. CD200 is an immunosuppressive membrane glycoprotein reported to be co-expressed with other stem-cell markers in prostate, breast, brain, and colon cancers. Also, CD200 is a negative prognostic factor for MM. It remains unknown whether CD200 is expressed in the CD138negCD20+ MM cell population, the putative MM cancer stem cells. Here we addressed this question by assessing CD200 expression in different subpopulations of MM cells according to their CD138 expression levels. Methods Two MM cell lines (RPMI8226 and NCI-H929) were co-stained with FITC-labeled anti-CD200, PE-labeled anti-CD20, and APC-labeled anti-CD138 antibodies for multicolor flow cytometry analysis. The cells were gated into 4 subpopulations (h1&gt;h2&gt;h3&gt;h4 corresponding to CD138 expression levels: high&gt;dim&gt;low&gt;negative). In each gated cell population, CD200 expression was assessed, and the CD200+ and CD200neg cell subpopulations were further gated for analysis of their CD20 expression levels. Results In the RPMI 8226 cell line, the distribution of gated h1, h2, h3, and h4 populations was 87.51%, 5.86%, 5.26%, and 1.29%, respectively. In the h2 (CD138dim) population, 22.88% of the cells were CD200+. In contrast, CD200 was expressed at much lower levels in the other three populations, ranging from 7.28% (h1), 6.65% (h3), to 0.48% (h4). In CD200+ cells from the gated h1, h2, h3, and h4 population, CD20+ cells were 19.50%, 23.03%, 27.67%, and 18.75%, respectively, while in the CD200neg cells, CD20+ cells were 20.79%, 22.50%, 25.08%, and 28.02%, respectively. In the NCI-H929 cell line, 18.59% of the cells in the h2 population were CD200+, whereas only 1.61%, 1.69%, and 0.47% of the cells in the h1, h3, and h4 populations were CD200+. In each population, there were more CD20+ cells in CD200+ cells than in CD200neg cells, which were 24.52% vs 0.04% (h1), 41.94% vs 11.34% (h2), 11.11% vs 3.06% (h3), and 50.00% vs 2.25% (h4), respectively. Conclusions These results demonstrate that the immunosuppressive molecule CD200 is preferentially expressed in a CD138dim subpopulation of multiple myeloma cells. Depending on cell line, the putative myeloma stem cell marker CD20 is either preferentially, or not preferentially, expressed in the CD200+ cells, suggesting that an immune-resistant subpopulation of MM stem cells might exist, which may have important implications for designing immunotherapeutic approaches to treat this disease. Disclosures Goldenberg: Immunomedics, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees, Patents &amp; Royalties.
MP12-06 LONG-TERM RISK OF METASTATIC PROSTATE CANCER IN MEN WITH GRADE GROUP 2 MANAGED WITH ACTIVE SURVEILLANCE (2018)

INTRODUCTION AND OBJECTIVES: There is now a growing trend toward expanding active surveillance (AS) inclusion criteria beyond low risk prostate cancer. We sought to study the long-term risk of metastatic development in men with Grade Group 2 being managed with initial AS at Memorial Sloan Kettering Cancer Center.
Fixed points of monotonic and (weakly) scalable neural networks (2021)

We derive conditions for the existence of fixed points of neural networks, an important research objective to understand their behavior in modern applications involving autoencoders and loop unrolling techniques, among others. In particular, we focus on networks with nonnegative inputs and nonnegative network parameters, as often considered in the literature. We show that such networks can be recognized as monotonic and (weakly) scalable functions within the framework of nonlinear Perron-Frobenius theory. This fact enables us to derive conditions for the existence of a nonempty fixed point set of the neural networks, and these conditions are weaker than those obtained recently using arguments in convex analysis, which are typically based on the assumption of nonexpansivity of the activation functions. Furthermore, we prove that the shape of the fixed point set of monotonic and weakly scalable neural networks is often an interval, which degenerates to a point for the case of scalable networks. The chief results of this paper are verified in numerical simulations, where we consider an autoencoder-type network that first compresses angular power spectra in massive MIMO systems, and, second, reconstruct the input spectra from the compressed signal.
Holographic Imaging-Based Functional Assessment of Macrophage Polarization in Co-Culture with Tumor Cells (2015)

macrophage re-polarization from predom - inant M2 to M1 phenotype can be an effective approach to achieve anti-tumor immunity and therapeutic response. Ho - lographic time-lapse imaging cytometer HoloMonitor® M4 (Phase Holographic Imaging, Sweden) was used to assess the efficacy of reprogramming M2 polarized macrophages to a M1 polarized state in a macrophage-tumor co-culture system. Also, the miR-155 polarized macrophages were seen to cause tumor cells morphological changes suggesting cell death after co-culture indicating potential anti-tumor activity. INTRODUCTIONare one of the important micro-environmental components of solid tumors, whose polarization to M2 phe - notype aids in regulation of all steps of tumor pathogenesis 1 . Thus prevention of these pro-tumoral macrophage functions can be an important strategy to attain anti-tumor activity. Out of many approaches available, the phenotypic reprogram- ming or repolarization to the anti-tumoral M1 state is a prom - ising approach 2 . HoloMonitor M4 based imaging modality can be used to track unstained macrophages by monitoring their morphology and motility. In this study, we have explored the potential of genetic (microRNA mediated) phenotypic repro - gramming of macrophages using non-viral water-in-oil-in-water (WOW) multiple emulsion-based intracellular delivery system.
Micro Chiplet Printer Development for MOSAIC Program (2017)

The micro-CPV concept being developed under the ARPA-E MOSAIC (Micro-scale Optimized Solar-cell Arrays with Integrated Concentration) program uses arrays of micro unit cells (or elements) such that the material usage, weight, and the required structural strength can all be scaled down favorably. Unfortunately, one of the essential unfavorable scaling factors is the assembly cost due to the many micro scale components that must be deposited, positioned, oriented, and connected over large areas. PARC and Sandia are developing a prototype platform that uses dynamic electric field micro-assembly to demonstrate micro chiplet printing - assembling a desired solar cell chip at a designated location with well controlled orientation. Xerographic printing systems utilizing this method can be extended to provide high-throughput, on-demand heterogeneous assembly of micro-CPV systems.
Performance and yield stability of maize hybrids in stress-prone environments in eastern Africa (2019)

Identification and deployment of high-yielding and stress-tolerant maize hybrids adapted to stress-prone agro-ecologies is important for improving the food security and livelihoods of smallholder farmers in eastern Africa. The objectives of this study were to (i) assess the performance of maize hybrids under well-watered and drought stress conditions; (ii) evaluate grain yield stability of 65 intermediate-maturing and 55 early-maturing hybrids in 24 well-watered locations and seven drought stress locations; and (iii) identify representative and/or discriminative testing locations for increasing genetic gains for the target traits. There were significant differences for grain yield among early- and intermediate-maturing hybrids tested under well-watered and drought stress environments. Among the early-maturing hybrids, the top 10 hybrids produced 46.8%–73.9% and 31.2%–42.1% higher mean grain yields than the best commercial check under drought and well-watered conditions, respectively. Among the intermediate-maturing hybrids, the top 10 hybrids produced 25.2%–47.7% and 8.5%–13.5% higher grain yield than commercial checks under drought stress and well-watered conditions, respectively, suggesting improvement in the levels of drought tolerance in both early- and intermediate-maturing hybrids. GGE biplot analysis and a bi-segmented regression linear method identified specific early-maturing and intermediate-maturing hybrids that performed well under both well-watered and drought stress conditions. These hybrids could be recommended for commercial production in eastern Africa. Kakamega in Kenya was found to be the most representative and highly discriminating site among well-watered testing locations, while Kabuku in Tanzania was the least representative of test locations. For testing under drought stress conditions, Kiboko in Kenya was identified as the most representative location. This information could be useful for allocating resources and streamlining CIMMYT maize hybrid testing in eastern Africa.
Intelligent Prediction of The Equivalent Circulating Density From Surface Data Sensors During Drilling By Employing Machine Learning Techniques (2021)

Abstract The precise control for the equivalent circulating density (ECD) will lead to evade well control issues like loss of circulation, formation fracturing, underground blowout, and surface blowout. Predicting the ECD from the drilling parameters is a new horizon in drilling engineering practices and this is because of the drawbacks of the cost of downhole ECD tools and the low accuracy of the mathematical models. Machine learning methods can offer a superior prediction accuracy over the traditional and statistical models due to the advanced computing capacity. Hence, the objective of this paper is to use the artificial neural network (ANN) and adaptive neuro-fuzzy inference system (ANFIS) techniques to develop ECD prediction models. The novel contribution for this study is predicting the downhole ECD without any need for downhole measurements but only the available surface drilling parameters. The data in this study covered the drilling data for a horizontal section with 3,570 readings for each input after data preprocessing. The data covered the mud rate, rate of penetration, drill string speed, standpipe pressure, weight on bit, and the drilling torque. The data used to build the model with a 77:23 training to testing ratio. Another data set (1,150 data points) from the same field was used for models` validation. Many sensitivity analyses were done to optimize the ANN and ANFIS model parameters. The prediction of the developed machine learning models provided a high performance and accuracy level with a correlation coefficient (R) of 0.99 for the models' training and testing data sets, and an average absolute percentage error (AAPE) less than 0.24%. The validation results showed R of 0.98 and 0.96 and AAPE of 0.30% and 0.69% for ANN and ANFIS models respectively. Besides, a mathematical correlation was developed for estimating ECD based on the inputs as a white-box model.
Vascular endothelial growth factor receptor 2 inhibition in-vivo affects tumor vasculature in a tumor type-dependent way and downregulates vascular endothelial growth factor receptor 2 protein without a prominent role for miR-296 (2011)

The precise molecular effects that antiangiogenic drugs exert on tumor vasculature remain to be poorly understood. We therefore set out to investigate the molecular and architectural changes that occur in the vasculature of two different tumor types that both respond to vascular endothelial growth factor receptor 2 (VEGFR2) inhibitor therapy. Mice bearing Lewis lung carcinoma (LLC) or B16.F10 melanoma were treated with vandetanib (ZD6474), a VEGFR2/epidermal growth factor receptor (EGFR)/REarranged during Transfection (RET) kinase inhibitor, resulting in a significant 80% reduction in tumor outgrowth. Although in LLC the vascular density was not affected by vandetanib treatment, it was significantly decreased in B16.F10. In LLC, vandetanib treatment induced a shift in vascular gene expression toward stabilization, as demonstrated by upregulation of Tie2 and N-cadherin and downregulation of Ang2 and integrin β3. In contrast, only eNOS and P-selectin responded to vandetanib treatment in B16.F10 vasculature. Strikingly, vandetanib reduced protein expression of VEGFR2 in both models, whereas mRNA remained unaffected. Analysis of miR-296 expression allowed us to exclude a role for the recently proposed microRNA-296 in VEGFR2 posttranslational control in LLC and B16.F10 in vivo. Our data demonstrate that VEGFR2/EGFR inhibition through vandetanib slows down both LLC and B16.F10 tumor growth. Yet, the underlying molecular changes in the vasculature that orchestrate the antitumor effect differ between tumor types. Importantly, in both models, vandetanib treatment induced loss of its pharmacological target, which was not directly related to miR-296 expression. Validation of our observations in tumor biopsies from VEGFR2 inhibitor-treated patients will be essential to unravel the effects of VEGFR2 inhibitor therapy on tumor vasculature in relation to therapeutic efficacy.
Double Deficiency of Tetraspanins CD9 and CD81 Alters Cell Motility and Protease Production of Macrophages and Causes Chronic Obstructive Pulmonary Disease-like Phenotype in Mice (2008)

CD9 and CD81 are closely related tetraspanins that regulate cell motility and signaling by facilitating the organization of multimolecular membrane complexes, including integrins. We show that CD9 and CD81 are down-regulated in smoking-related inflammatory response of a macrophage line, RAW264.7. When functions of CD9 and CD81 were ablated with monoclonal antibody treatment, small interfering RNA transfection, or gene knock-out, macrophages were less motile and produced larger amounts of matrix metalloproteinase (MMP)-2 and MMP-9 than control cells in vitro. In line with this, CD9/CD81 double-knock-out mice spontaneously developed pulmonary emphysema, a major pathological component of chronic obstructive pulmonary disease (COPD). The mutant lung contained an increased number of alveolar macrophages with elevated activities of MMP-2 and MMP-9 and progressively displayed enlarged airspace and disruption of elastic fibers in the alveoli. Secretory cell metaplasia, a finding similar to goblet cell metaplasia in cigarette smokers, was also observed in the epithelium of terminal bronchioles. With aging, the double-knockout mice showed extrapulmonary phenotypes, including weight loss, kyphosis, and osteopenia. These results suggest that the tetraspanins CD9 and CD81 regulate cell motility and protease production of macrophages and that their dysfunction may underlie the progression of COPD.
<title>High-performance polyimide waveguide array with micromirror coupler for guided-wave optoelectronic interconnects</title> (2000)

We report the formation of high-performance polyimide waveguide arrays with 45 degree(s) micro mirror coupler fabricated at each end, which provides a high-efficiency output or input surface-normal light couple for the waveguide. This fully embedded integration provides an efficient method of optical interconnection for the board-level data communication and the multi-layer connection. We employed the Si CMOS process compatible polyimide as the fabrication material, which is relatively easy to process and has low propagation loss for light at 850 nm wavelength. A 1 X 12 waveguide array with 45 degree(s) micro mirror coupler fabricated at each end is experimentally demonstrated.
HiperLAN 5.4 GHz low power CMOS synchronous oscillator (2002)

A 5.4 GHz 0.25 /spl mu/m VLSI CMOS synchronous oscillator is proposed, which is designed to act as a local oscillator for HiperLAN systems. The design strategy is described, including the synchronization range optimization approach. A chip is presented, which provides a 150 MHz synchronization range and a -97 dBc/Hz phase noise at 10 kHz offset from the carrier, while only consuming 5 mA from a 2.5 V supply.
BCR and Endosomal TLR Signals Synergize to Increase AID Expression and Establish Central B Cell Tolerance (2017)

Activation-induced cytidine deaminase (AID) is required to purge autoreactive immature and transitional-1 (immature/T1) B cells at the first tolerance checkpoint, but how AID selectively removes self-reactive B cells is unclear. We now show that B cell antigen receptor (BCR) and endosomal Toll-like receptor (TLR) signals synergize to elicit high levels of AID expression in immature/T1 B cells. This synergy is restricted to ligands for endocytic TLR and requires phospholipase-D activation, endosomal acidification, and MyD88. The first checkpoint is significantly impaired in AID- or MyD88-deficient mice and in mice doubly heterozygous for AID and MyD88, suggesting interaction of these factors in central B cell tolerance. Moreover, administration of chloroquine, an inhibitor of endosomal acidification, results in a failure to remove autoreactive immature/T1 B cells in mice. We propose that a BCR/TLR pathway coordinately establishes central tolerance by hyper-activating AID in immature/T1 B cells that bind ligands for endosomal TLRs.
Tau (MAPT) mutation Arg406Trp presenting clinically with Alzheimer disease does not share a common founder in Western Europe (2003)

The Supplementary Material referred to in this article can be found at http://www.mrw.interscience.wiley.com/suppmat/1059-7794/suppmat/2003/v22.html Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A two-dimensional channel simulation model for shadowing processes (2003)

A Gaussian random process with a given power spectral density (PSD) function can be modeled as a sum of sinusoids (SOS), and has been widely used to simulate Rayleigh-fading communication channels. The conventional one-dimensional (1D) channel model cannot capture the spatial correlation of shadowing processes. We here develop a two-dimensional (2D) SOS-based channel model to simulate the shadowing process. Three methods to fit the PSD of the simulated process to the true channel's PSD are explored. Performance of the proposed channel simulator is analyzed in terms of the autocorrelation function of the simulated shadowing process. Simulations illustrate the potential of the proposed channel simulation model.