gebhart/patrepeval huggingface dataset:
1T channel transmission field experiments and next generation DWDM network design (2012)

1T (an abbreviation for terabit per second) channel transmission field experiments are reviewed and the expected performance of 1T channels in deployed fiber networks is shown. The main change from 100G channel design to 1T channel design is introduction of the superchannel concept, in which multiple optical carriers are used for one channel. One of the main tasks of next generation ROADM based DWDM network designs involving superchannels is to maintain a balance between easy light path management and high spectral efficiency.
Using single-particle ICP-MS for monitoring metal-containing particles in tap water (2018)

This study provides the feasibility of using a single-particle ICP-MS technique for convenient and routine monitoring of engineered nanomaterials in tap water.
Embryo Implantation and Tumor Metastasis: Common Pathways of Invasion and Angiogenesis (1999)

Implantation of the embryo is one of the last great mysteries of reproductive biology. There are striking similarities present between the behavior of invasive placental cells and that of invasive cancer cells. In this review, we propose that cellular mechanisms used by the cells of the placenta during implantation are reused by cancer cells to invade and spread within the body. Integrins and other cell adhesion molecules, extracellular matrix and matrix metalloproteinases all appear to be involved and are regulated by the complex endocrine, autocrine and paracrine milieu within the uterus. Angiogenesis is a common feature of both implantation and cancer spread. Endothelial cells also use similar cellular mechanisms during angiogenesis to digest the surrounding matrix, migrate and form new blood vessels. A better understanding of the mechanism of trophoblast invasion will likely lead to insights of various diseases of pregnancy such as preeclampsia. An appreciation of the maternal mechanisms to control this invasive behavior may likewise lead to a better understanding of metastatic cancer cells and lead to better methods to control their growth and spread within host tissues.
HOPE-Graph: A Hypothesis Evaluation Service considering News and Causality Knowledge (2021)

Daily released news and analyst reports can affect economic activities such as product marketing and stock trading. At the same time, we often interpret news by using our domain knowledge to see what influence an event might have. Therefore, it is an important analytical task to evaluate hypotheses or opinions by considering simultaneously the public opinion formed by these news sources and one’s own causality knowledge. In this paper, we present HOPE-Graph: a hypothesis evaluation service that considers news and the knowledge of causal relationships between hypotheses. This service is implemented by integrating news analysis obtaining pro/con rates for hypotheses into a hypothesis evaluation framework that propagates pro/con rates based on positive/negative causal relationships. The framework is conceived as an abstract argumentation framework that evaluates arguments on the basis of the support/attack relationships between them. By using the causality knowledge, it is possible to obtain a score that preemptively incorporates the score of the causal hypothesis. To investigate the effectiveness of our service, we checked the Granger causality from the score of the hypothesis of a company’s performance to the stock price and found that proper consideration of causality knowledge can lead to scores that are more relevant to stock prices in more cases.
Metabolism of Monoterpenes: Conversion of l-Menthone to l-Menthol and d-Neomenthol by Stereospecific Dehydrogenases from Peppermint (Mentha piperita) Leaves (1982)

The monoterpene ketone l-menthone is specifically converted to l-menthol and l-menthyl acetate and to d-neomenthol and d-neomenthyl-beta-d-glucoside in mature peppermint (Mentha piperita L. cv. Black Mitcham) leaves. The selectivity of product formation results from compartmentation of the menthol dehydrogenase with the acetyl transferase and that of the neomenthol dehydrogenase with the glucosyl transferase. Soluble enzyme preparations, but not particulate preparations, from mature peppermint leaves catalyzed the NADPH-dependent reduction of l-menthone to both epimeric alcohols, and the two dehydrogenases responsible for these stereospecific transformations were resolved by affinity chromatography on Mātrex Gel Red A. Both enzymes have a molecular weight of approximately 35,000, possess a K(m) for NADPH of about 2 x 10(-5)m, are very sensitive to inhibition by thiol-directed reagents, and are not readily reversible. The menthol dehydrogenase showed a pH optimum at 7.5, exhibited a K(m) for l-menthone of about 2.5 x 10(-4)m, and also reduced d-isomenthone to d-neoisomenthol. The neomenthol dehydrogenase showed a pH optimum at 7.6, exhibited a K(m) for l-menthone of about 2.2 x 10(-5)m, and also reduced d-isomenthone to d-isomenthol. These stereochemically distinct, but otherwise similar, enzymes are of key importance in determining the metabolic fate of menthone in peppermint, and they are probably typical of the class of dehydrogenases thought to be responsible for the metabolism of monoterpene ketones during plant development.
Tunable rejection filters with ultra-wideband using zeroth shear mode plate wave resonators (2017)

This paper reports wide band rejection filters and tunable rejection filters using ultra-wideband zeroth shear mode (SH0) plate wave resonators. The frequency range covers the digital TV band in Japan that runs from 470 to 710 MHz. This range has been chosen to meet the TV white space cognitive radio requirements of rejection filters. Wide rejection bands were obtained using several resonators with different frequencies. Tunable rejection filters were demonstrated using Si diodes connected to the band rejection filters. Wide tunable ranges as high as 31% were measured by applying a DC voltage to the Si diodes.
Inhibition of inositol 1,4,5-trisphosphate metabolism in permeabilised SH-SY5Y human neuroblastoma cells by a phosphorothioate-containing analogue of inositol 1,4,5-trisphosphate (1990)

Electrically permeabilised [3H]inositol-labelled SH-SY5Y human neuroblastoma cells were employed to examine the effects of two synthetic, phosphatase-resistant analogues of inositol 1,4,5-trisphosphate [Ins(1,4,5)P3] on the metabolism of cell membrane-derived [3H]Ins(1,4,5)P3 or exogenous [5-32P]Ins(1,4,5)P3.&#13;\n&#13;\nIncubation of permeabilised SH-SY5Y cells for 5 min at 37°C with carbachol and guanosine 5′-[γ-thio]triphosphate caused a decrease in [3H]phosphoinositol phospholipid levels and an increase in [3H]inositol phosphate accumulation with inositol 4-phosphate, inositol 1,4-bisphosphate, Ins(1,4,5)P3 and inositol 1,3,4,5-tetrakisphosphate comprising approximately 79%, 16%, 3% and 2%, respectively, of the increase. Inositol 1-phosphate levels did not increase upon stimulation, nor was inositol 4-phosphate converted rapidly to inositol.&#13;\n&#13;\nIn parallel incubations, the analogues, DL-inositol 1,4,5-trisphosphorothioate (DL-InsP3S3) and DL-inositol 1,4-bisphosphate 5-phosphorothioate (DL-InsP3S), and synthetic racemic Ins(1,4,5)P3 (DL-InsP3), altered the profile of the [3H]inositol phosphates recovered and led, at millimolar concentrations, to a 10–15-fold increase in [3H]Ins(1,4,5)P3. The extent of inhibition of [3H]Ins(1,4,5)P3 metabolism was, however, greatest in the presence of synthetic D-Ins(1,4,5)P3 (geqslant R: gt-or-equal, slanted5 mM), when [3H]Ins(1,4,5)P3 comprised approximately 50% of the increase in total [3H]inositol phosphates. Thus, under these conditions, at least 50% of [3H]inositol phosphates were derived from [3H]phosphatidylinositol 4,5-bisphosphate. [32P]Pi release from exogenous [5-32P]Ins(1,4,5)P3 was also inhibited by DL-InsP3S3, DL-InsP3S and DL-InsP3, with half-maximal inhibition at approximately 50 μM, 160 μM and 240 μM respectively. These actions were approximately ten times more potent than the effects of these compounds on [3H]inositol phosphate accumulation, indicating that homogenous mixing of exogenous and cellmembrane-derived Ins(1,4,5)P3 does not occur.&#13;\n&#13;\nThese findings indicate that DL-InsP3S3 and DL-InsP3S inhibit Ins(1,4,5)P3 5-phosphatase. In contrast. the effects of synthetic DL-InsP3 and d-Ins(1,4,5)P3 are due to isotopic dilution. Whilst DL-InsP3S3 was the most potent inhibitor of dephosphorylation of exogenous or cell-membrane-derived Ins(1,4,5)P3, it was the weakest inhibitor of 3-kinase-catalysed Ins(1,4,5)P3 phosphorylation. Similarly, although approximately 50 times less potent than DL-InsP3S3, 2,3-diphosphoglycerate inhibited Ins(1,4,5)P3 5-phosphatase activity and was apparently without effect of Ins(1,4,5)P3 3-kinase activity.&#13;\n&#13;\nThese data show that both DL-InsP3S3 and DL-InsP3S are potent inhibitors of Ins(1,4,5)P3 5-phosphatase. In contrast, phosphorylation of Ins(1,4,5)P3 was inhibited potently only by DL-InsP3S.
Memory energy management for an enterprise decision support system (2011)

Energy efficiency is an important factor in designing and configuring enterprise servers. In these servers, memory may consume 40% of the total system power. Different memory configurations (sizes, numbers of ranks, speeds, etc.) can have significant impacts on the performance and energy consumption of enterprise workloads. Many of these workloads, such as decision support systems (DSS), require large amounts of memory. This paper investigates the potential to save energy by making the memory configuration adaptive to workload behavior. We present a case study on how memory configurations affect energy consumption and performance for running DSS. We measure the energy consumption and performance of a commercial enterprise server, and develop a model to describe the conditions when energy can be saved with acceptable performance degradation. Using this model, we identify opportunities to save energy in future enterprise servers.
Dynamics of the Recycle Systems of Two Centrifugal Compressors Operating in Series in a Natural Gas Compressor Station (2014)

Compression systems employed in gas pipeline transmission systems and gas processing plants provide a vital function to the overall operation of both systems, and therefore must be vigilantly monitored in order to ensure a high level of operational reliability. The majority of these compression systems employ centrifugal compressors, driven by either gas turbines or electric motors with/without gearboxes. These systems are designed and operated in a manner to eliminate or minimize the potential for surge, which is a dynamic instability detrimental to the integrity of the unit. Surge can occur when compressors are subjected to rapid transients such as one following an emergency shutdown (ESD) or power failure. To prevent this, compressor stations are designed with recycle systems and special types of recycle valves required to open upon ESD. This paper describes the dynamics surrounding an ESD operation of a compression system composed of two units in series and two independent recycle systems, one for each unit. The conventional sizing of the recycle system applied to a single unit operation needs to be evaluated carefully when there are two units operating in series, and in particular sizing of the recycle system surrounding the higher pressure unit, i.e. the downstream unit. This paper provides an insight into the salient parameters that impact the operation of such system via several dynamic simulations of an ESD event. Different ‘what-if’ design scenarios are analyzed and results presented. The data was obtained from an actual station operation on TransCanada’s Alberta gas transmission system in Canada. This station also employs two large gas volume capacitance aerial coolers which are also involved in the dynamics of the system during ESD.
Relevance of DC-SIGN in DC-induced T cell proliferation (2006)

The role of dendritic cell-specific ICAM-3-grabbing nonintegrin (DC-SIGN) in DC-T cell communication was assessed by analyzing the effect of DC-SIGN-blocking mAb in MLR. The results show that the degree of inhibition by DC-SIGN and LFA-1 mAb depends on the magnitude of the MLR and the maturation status of the DC. Addition of DC-SIGN mAb at several time-points during MLR showed that DC-SIGN is involved early on in DC-T cell contacts. This initial role is masked by strong adhesive and costimulatory mechanisms, indicating a short-lived effect of DC-SIGN in DC-T cell interactions. To examine this concept in more detail, the percentage of PBL capable of binding DC-SIGN was determined. Analysis of several donors revealed that 1-20% PBL bind to beads coated with recombinant DC-SIGN, and the DC-SIGN-binding cells comprised all major cell subsets found in blood. PBL isolated from a donor with high DC-SIGN-binding capacity were more prone to blocking by DC-SIGN mAb in MLR than PBL from a donor with low DC-SIGN-binding capacity. This study indicates an initial and transient role for DC-SIGN in T cell proliferation, which becomes apparent when T cell proliferation is low and when the percentage of DC-SIGN binding PBL is high.
Telomerase: target for cancer treatment (2013)

Telomerase, a cellular reverse transcriptase that adds DNA to the ends of chromosomes, is reactivated or up-regulated in the vast majority of human advanced malignancies, and is thus an almost universal target for human cancer. Most human tumors not only express telomerase, but also have very short telomeres, whereas telomerase activity is absent or at lower levels in normal tissues, which also have longer telomeres. This relationship between activation of telomerase activity and short telomeres in human malignancies makes the inhibition of telomerase a novel target for cancer therapeutics. Importantly, the mode of action of telomerase inhibitors predicts minimal side effects on normal stem cells that can express telomerase. Here we summarize the role of telomeres and telomerase in cancer and review the current status of ongoing telomerase clinical trials. This chapter will also discuss the relationship of telomerase to cancer stem cells. Central questions remaining include: What are the key safety concerns, such as the effect of telomerase inhibitors on normal stem cells that express some telomerase? Do cancer stem cells express telomerase activity? What effect will telomerase inhibitors have if cancer stem cells are more quiescent than the bulk of the more differentiated tumor cells? Will human cancers become resistant to telomerase inhibitors?
B-cell receptors expressed by lymphomas of hepatitis C virus (HCV)–infected patients rarely react with the viral proteins (2014)

Chronic hepatitis C virus (HCV) infection has been implicated in the induction and maintenance of B-cell lymphomas. The strongest evidence for this derives from clinical observations of tumor regressions upon antiviral treatments. Here we used multiple methods to test the hypothesis that the expansion of HCV-specific B cells gives rise to lymphomas. We obtained lymphoma tissues from HCV-infected lymphoma patients, including some that later regressed upon antiviral treatments. We expressed the lymphoma B-cell receptors as soluble immunoglobulin Gs and membrane IgMs, and analyzed their reactivity with HCV proteins and with HCV virions. We confirmed previous reports that HCV-associated lymphomas use a restricted immunoglobulin variable region gene repertoire. However, we found no evidence for their binding to the HCV antigens. We conclude that most lymphomas of HCV-infected patients do not arise from B cells aimed at eliminating the virus.
EEG-GNN: Graph Neural Networks for Classification of Electroencephalogram (EEG) Signals (2021)

Convolutional neural networks (CNN) have been frequently used to extract subject-invariant features from electroencephalogram (EEG) for classification tasks. This approach holds the underlying assumption that electrodes are equidistant analogous to pixels of an image and hence fails to explore/exploit the complex functional neural connectivity between different electrode sites. We overcome this limitation by tailoring the concepts of convolution and pooling applied to 2D grid-like inputs for the functional network of electrode sites. Furthermore, we develop various graph neural network (GNN) models that project electrodes onto the nodes of a graph, where the node features are represented as EEG channel samples collected over a trial, and nodes can be connected by weighted/unweighted edges according to a flexible policy formulated by a neuroscientist. The empirical evaluations show that our proposed GNN-based framework outperforms standard CNN classifiers across ErrP, and RSVP datasets, as well as allowing neuroscientific interpretability and explainability to deep learning methods tailored to EEG related classification problems. Another practical advantage of our GNN-based framework is that it can be used in EEG channel selection, which is critical for reducing computational cost, and designing portable EEG headsets.
Exploiting Additive Manufacturing Infill in Topology Optimization for Improved Buckling Load (2016)

Additive manufacturing (AM) permits the fabrication of functionally optimized components with high geometrical complexity. The opportunity of using porous infill as an integrated part of the manufacturing process is an example of a unique AM feature. Automated design methods are still incapable of fully exploiting this design freedom. In this work, we show how the so-called coating approach to topology optimization provides a means for designing infill-based components that possess a strongly improved buckling load and, as a result, improved structural stability. The suggested approach thereby addresses an important inadequacy of the standard minimum compliance topology optimization approach, in which buckling is rarely accounted for; rather, a satisfactory buckling load is usually assured through a post-processing step that may lead to sub-optimal components. The present work compares the standard and coating approaches to topology optimization for the MBB beam benchmark case. The optimized structures are additively manufactured using a filamentary technique. This experimental study validates the numerical model used in the coating approach. Depending on the properties of the infill material, the buckling load may be more than four times higher than that of solid structures optimized under the same conditions.
Coordinated Leading and Lagging Strand DNA Synthesis on a Minicircular Template (2021)

The coordinated synthesis of both leading and lagging DNA strands is thought to involve a dimeric DNA polymerase and a looping of the lagging strand so that both strands can be synthesized in the same direction. We have constructed a minicircle with a replication fork that permits an assessment of the stoichiometry of the proteins and a measurement of the synthesis of each strand. The replisome consisting of bacteriophage T7 DNA polymerase, helicase, primase, and single-stranded DNA-binding protein mediates coordinated replication. The criteria for coordination are fulfilled: (1) a replication loop is formed, (2) leading and lagging strand synthesis are coupled, (3) the lagging strand polymerase recycles from one Okazaki fragment to another, and (4) the length of Okazaki fragments is regulated. T7 single-stranded DNA-binding protein is essential for coordination.
Ethanol-Induced Condensation and Decondensation in DNA-Linked Nanoparticles: A Nucleosome-like Model for the Condensed State (2022)

Inspired by the conventional use of ethanol to induce DNA precipitation, ethanol condensation has been applied as a routine method to dynamically tune "bond" lengths (i.e., the surface-to-surface distances between adjacent nanoparticles that are linked by DNA) and thermal stabilities of colloidal crystals involving DNA-linked nanoparticles. However, the underlying mechanism of how the DNA bond that links gold nanoparticles changes in this class of colloidal crystals in response to ethanol remains unclear. Here, we conducted a series of all-atom molecular dynamic (MD) simulations to explore the free energy landscape for DNA condensation and decondensation. Our simulations confirm that DNA condensation is energetically much more favorable under 80% ethanol conditions than in pure water, as a result of ethanol's role in enhancing electrostatic interactions between oppositely charged species. Moreover, the condensed DNA adopts B-form in pure water and A-form in 80% ethanol, which indicates that the higher-order transition does not affect DNA's conformational preferences. We further propose a nucleosome-like supercoiled model for the DNA condensed state, and we show that the DNA end-to-end distance derived from this model matches the experimentally measured DNA bond length of about 3 nm in the fully condensed state for DNA where the measured length is 16 nm in water. Overall, this study provides an atomistic understanding of the mechanism underlying ethanol-induced condensation and water-induced decondensation, while our proposed nucleosome-like model allows the design of new strategies for interpreting experimental studies of DNA condensation.
Field emitters with nanoscale tips based on Mo oxide fabricated by electrochemical methods (2016)

Abstract Field emitters with nanoscale tips and a fabrication technique using a nanoscale gap are described. Each fabrication technique makes it possible to form emitters on a meter-scale glass substrate. The emitter has a configuration with one side gate to reduce the electron scattering losses at the counter electrode to improve the emission efficiency. All thin film layers constituting the emitter are fabricated by plasma-enhanced chemical vapor deposition and sputtering deposition. Nanoscale tips are formed between a shallow gap less than 7 nm deep by the joule heating of a Mo complex oxide, which is produced by the electro chemical etching of a deposited Mo layer. To our knowledge, this is the first work that shows a uniform efficiency of 5% or more achieved at an anode voltage of 10 kV and an operation voltage of 23 V.
Tumor Infiltrating Immune Cells and Outcome of Merkel Cell Carcinoma: A Population-Based Study (2012)

High intratumoral T-lymphocyte counts are associated with favorable survival in MCC. Although the numbers of T cells are generally higher in MCPyV-positive than in MCPyV-negative MCC, high intratumoral T-cell counts are also associated with favorable survival in MCPyV-negative MCC.
Supplementary Figure S3 from Ubiquitinated PCNA Drives USP1 Synthetic Lethality in Cancer (2023)

&lt;p&gt;CRISPR-UMI analysis and characterization of PCNA dynamics - related to Figure 3&lt;/p&gt;
Simple method for MR gradient system characterization and k‐space trajectory estimation (2011)

Fast imaging trajectories are used in MRI to speed up the acquisition process, but imperfections in the gradient system create artifacts in the reconstructed images. Artifacts result from the deviation between k-space trajectories achieved on the scanner and their original prescription. Measuring or approximating actual k-space trajectories with predetermined gradient timing delays reduces the artifacts, but are generally based on a specific trajectory and scan orientation. A single linear time-invariant characterization of the gradient system provides a method to predict k-space trajectories scanned in arbitrary orientations through convolution. This is done efficiently, by comparing the Fourier transforms of the input and measured waveforms of a single high-bandwidth test gradient waveform. This new method is tested for spiral, interleaved echo-planar, and three-dimensional cones imaging, demonstrating its ability to reduce reconstructed image artifacts for various k-space trajectories.