gebhart/patrepeval huggingface dataset:
Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data (2015)

A hybrid de novo assembly pipeline was constructed to utilize both MiSeq and SOLiD short read data in combination in the assembly. The short read data were converted to a standard format of the pipeline, and were supplied to the pipeline components such as ABySS and SOAPdenovo. The assembly pipeline proceeded through several stages, and either MiSeq paired-end data, SOLiD mate-paired data, or both of them could be specified as input data at each stage separately. The pipeline was examined on the filamentous fungus Aspergillus oryzae RIB40, by aligning the assembly results against the reference sequences. Using both the MiSeq and the SOLiD data in the hybrid assembly, the alignment length was improved by a factor of 3 to 8, compared with the assemblies using either one of the data types. The number of the reproduced gene cluster regions encoding secondary metabolite biosyntheses (SMB) was also improved by the hybrid assemblies. These results imply that the MiSeq data with long read length are essential to construct accurate nucleotide sequences, while the SOLiD mate-paired reads with long insertion length enhance long-range arrangements of the sequences. The pipeline was also tested on the actinomycete Streptomyces avermitilis MA-4680, whose gene is known to have high-GC content. Although the quality of the SOLiD reads was too low to perform any meaningful assemblies by themselves, the alignment length to the reference was improved by a factor of 2, compared with the assembly using only the MiSeq data.
Ultrasonic experiments at ultra-high frequency with picosecond time-resolution (2002)

A method that can be used to make ultrasonic measurements with picosecond time resolution is described. In this method, short light pulses (duration <or=1 ps) are used to generate and detect ultrasonic waves. The excellent time resolution makes possible pulse-echo ultrasonic measurements in situations in which the acoustic path length is extremely short. It is possible to make ultrasonic pulse-echo measurements on thin-film microstructures of thicknesses down to a few hundred angstroms. As examples of the use of the method, measurements of sound propagation in glass films at frequencies up to 500 GHz, studies of the mechanical properties of microstructures, and investigations of high-frequency surface waves are described.<<ETX>>
ACAT1 regulates the dynamics of free cholesterols in plasma membrane which leads to the APP-&alpha;-processing alteration (2015)

Acyl-CoA:cholesterol acyltransferase 1 (ACAT1) is a key enzyme exclusively using free cholesterols as the substrates in cell and is involved in the cellular cholesterol homeostasis. In this study, we used human neuroblastoma cell line SK-N-SH as a model and first observed that inhibiting ACAT1 can decrease the amyloid precursor protein (APP)-α-processing. Meanwhile, the transfection experiments using the small interfering RNA and expression plasmid of ACAT1 indicated that ACAT1 can dependently affect the APP-α-processing. Furthermore, inhibiting ACAT1 was found to increase the free cholesterols in plasma membrane (PM-FC), and the increased PM-FC caused by inhibiting ACAT1 can lead to the decrease of the APP-α-processing, indicating that ACAT1 regulates the dynamics of PM-FC, which leads to the alteration of the APP-α-processing. More importantly, further results showed that under the ACAT1 inhibition, the alterations of the PM-FC and the subsequent APP-α-processing are not dependent on the cellular total cholesterol level, confirming that ACAT1 regulates the dynamics of PM-FC. Finally, we revealed that even when the Niemann-Pick-Type C-dependent pathway is blocked, the ACAT1 inhibition still obviously results in the PM-FC increase, suggesting that the ACAT1-dependent pathway is responsible for the shuttling of PM-FC to the intracellular pool. Our data provide a novel insight that ACAT1 which enzymatically regulates the dynamics of PM-FC may play important roles in the human neuronal cells.
Gene networks in Arabidopsis thaliana for metabolic and environmental functions (2008)

Transcript dynamics of the Arabidopsis genome is captured in a high-confidence, realistic GGM(Graphical Gaussian Model)-based gene network that identifies co-regulation correlation of 22 000 genes across >150 conditions in specific clusters.
Clinical benefits of partial circulatory support in New York Heart Association Class IIIB and Early Class IV patients (2010)

The Synergy device provides partial hemodynamic support and its use is associated with significantly improved hemodynamics, thus appearing to interrupt and partially reverse the progressive hemodynamic deterioration typical of end-stage heart failure. Ongoing efforts are aimed at demonstrating additional clinical benefits and continuing to further improve the risk/benefit ratio.
Sustainable Modification of Chitosan Binder for Capacitive Electrodes Operating in Aqueous Electrolytes (2023)

Abstract Biopolymers emerged in recent years as a promising alternative for a more sustainable manufacturing of electrochemical energy storage systems. In fact, for environmentally friendly aqueous systems, fluorinated polymers are usually adopted. For this reason, substituting these polymers with water processable binders could improve the overall environmental impact of the device. In this study, a low – cost and environmentally friendly modification of chitosan binder for self‐standing activated carbon electrodes operating in Na ion, aqueous electrochemical double layer capacitors is reported and discussed.
Hydrodynamic passive separation under continuous flow in a microfluidic chip (2011)

Continuous passive separation based on laminar flow and creative geometries has advantages over traditional separation methods such as dielectrophoresis, hydrodynamic chromatography, and acoustic separations to name a few. One advantage in particular is the lack of constant energy supply needed and another advantage is the ability to continuously operate the device for larger sample volumes without much interruption. Adding external forces to a device also can increase its complexity and may limit an ability to function on biological samples. In this paper we demonstrate a passive separation device.
Effects of a Low Octane Gasoline Blended Fuel on Negative Valve Overlap Enabled HCCI Load Limit, Combustion Phasing and Burn Duration (2013)

Homogeneous charge compression iginition (HCCI) combustion allows for the use of fuels with octane requirements below that of spark-ignited engines. A reference gasoline was compared with iso-octane and a low octane blend of gasoline and 40% n-heptane, NH40. Experiments were conducted on a single cylinder engine operating with negative valve overlap (NVO). The fuel flow rate per cycle was compensated based on the lower heating value to maintain a constant energy addition across fuels. Iso-octane and gasoline demonstrated similar maximum load, achieving a gross IMEPg of ~430 kPa, whereas the NH40 demonstrated an increased IMEPg of ~460 kPa. The NH40 could be operated at a later phasing compared with the higher octane fuels, and exhibited a shorter burn duration at a given fueling rate and phasing. These results could be due to compositional differences, as NH40 required less NVO compared to iso-octane and gasoline, leading to less thermal and compositional stratification, as well as a higher O2 concentration and less residual gas. Additionally, the NH40 fuel demonstrated a higher intermediate temperature heat release than the higher octane fuels, potentially contributing to the shorter burn duration. Overall, these results demonstrate clear benefits to NVO enabled HCCI combustion with low octane fuels.
Abstract 4451: The effects of anthocyanins from the fruit of Vitis coignetiae Pulliat on NF-κB and NF-κB-regulated gene expressions in human lung cancer cells (2010)

Abstract Vitis coignetiae Pulliat (Meoru in Korea) has been used as a remedy for inflammatory diseases and various cancers. We isolated anthocyanins from Meoru. We previously suggested that anthocyanins from fruits of Vitis coignetiae Pulliat (Meoru in Korea) should have anti-invasive effects through suppression of NF-κB activation. Here, we investigated their effects on NF-κB-regulated gene products and cellular responses in human lung cancer cells. The anthocyanins inhibited NF-κB activation in a dose-dependent manner. TNF-α augmented proliferation, migration and invasion of A549 cells. The anthocyanins inhibited the augmented proliferation, migration and invasion of the cancer cells by TNF-α. We also found that the anthocyanins suppressed NF-κB-regulated proteins involved in caner proliferation, metastasis and anti-apoptosis. The anthocyanins inhibit NF-κB activity by inhibiting IκBα phosphorylation. Taken together, this study suggested that the anthocyanins isolated from fruits of Vitis coignetiae Pulliat inhibit the NF-κB activation and downstream proteins, which may be a factor in their anticancer activities of fruit of Vitis coignetiae Pulliat. Keywords: anthocyanins, Vitis coignetiae Pulliat, NF-κB, cancer * This study was supported by a grant from the National R&amp;D Program for Cancer Control, Ministry for Health, Welfare and Family affairs, Republic of Korea (0820050) Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4451.
Volatile Etch Species Produced during Thermal Al2O3 Atomic Layer Etching (2019)

The thermal atomic layer etching (ALE) of Al2O3 can be achieved using sequential fluorination and ligand-exchange reactions. Although previous investigations have characterized the etch rates and surface chemistry, no reports have identified the volatile etch products. This study explored the volatile etch species during thermal Al2O3 ALE at 300 °C using quadrupole mass spectrometry (QMS). HF was the fluorination reactant; Al(CH3)3 (trimethylaluminum (TMA)) and AlCl(CH3)2 (dimethylaluminum chloride, (DMAC)) were the metal precursors for ligand exchange. When TMA was used as the metal precursor after the fluorination of Al2O3 powder, the QMS measurements revealed that the main ion species were consistent with dimers of AlF(CH3)2 (dimethylaluminum fluoride (DMAF)) with itself (DMAF + DMAF) or with TMA (DMAF + TMA). These ion species were observed after loss of a methyl group as Al2F2(CH3)3+ at m/z = 137 and Al2F(CH3)4+ at m/z = 133, respectively. In addition, an ion species consistent with a trimer was also observed as Al3F3(CH3)5+ at m/z = 213. Very similar results were observed for TMA exposures on AlF3 powder. Comparable results were also obtained using DMAC as the metal precursor for ligand exchange. In contrast, SiCl4 and TiCl4 are not successful metal precursors because they do not lead to thermal Al2O3 ALE at 300 °C. QMS measurements revealed no Al-containing etch species after SiCl4 and TiCl4 exposures on AlF3 powder. However, SiFxCly+ and TiFxCly+ species were observed which suggested that ligand-exchange reactions can occur without the release of Al-containing etch species. Density functional theory (DFT) and coupled cluster singles, doubles, and perturbative triples (CCSD(T)) calculations were performed to support the preference for dimer products. The theoretical results confirmed the stability of the dimer products and showed that dimers with two Al–F–Al bridging bonds are the most stable and dimers with two Al–CH3–Al bridging bonds are the least stable. In addition, the calculations suggested that dimers with terminal CH3 ligands are most able to desorb from the surface because these dimers need to break weak Al–CH3–Al bridging bonds. Transmission electron microscopy (TEM) studies confirmed the thermal Al2O3 ALE of Al2O3 films on W powders. The TEM images revealed that the etch process was uniform and conformal after various numbers of thermal Al2O3 ALE cycles using HF and TMA as the reactants.
Prospects for Clinical Application of Synthetic Gene Delivery Vectors (2000)

I. INTRODUCTION In many respects synthetic (‘‘nonviral’’) gene transfer vectors, comprised of either naked DNA or DNA complexed with a cationic lipid or polymer, are in a formative stage of development for use in vivo. Several diverse chemical compounds and physical methods of gene delivery are under evaluation, the mechanisms of gene transfer into different tissues are still being elucidated, and the acute and long-term toxicological consequences in vivo have not been fully characterized. Thus, it is perhaps surprising that almost one-fourth of the clinical gene therapy trials to date have used synthetic vectors, involving more than 700 patients (Fig. 1A). However, the overwhelming number of these protocols has been for the treatment of different cancers and far fewer noncancer trials have been initiated (Fig. 1B, Table 1). This chapter reviews some of the recent preclinical and clinical applications of synthetic vectors, highlighting a few disease targets that are representative of current synthetic gene delivery strategies. Included will be some discussion on the realistic prospects for synthetic vectors to be an effective therapeutic for a given disease indication and the technical challenges remaining to achieve that goal.
Unraveling Overlapping Multiplets in Two‐Dimensional NMR Correlation Spectra by Selective Inversion of Coupling Partners (1990)

Clean and simple two‐dimensional multiplet pallerns instead of overlapping multiplets can be generated in an NMR experiment by employing selective pulses that single out small segments of a complete spectrum. The pattern of the selected multiplet is in this case manipulated by altering the apparent signs of the coupling constants. The technique is suitable not only for separating overlapping signals, but also for testing hypotheses associated with particular coupling networks.
A 350W, 2GHz, 44% efficient LDMOS power amplifier design with capability to handle a wideband 65MHz envelope signal (2012)

In this paper we demonstrate high gain, high efficiency, single and balanced Doherty power amplifiers (PAs) that have the ability to transmit signals which occupy the full frequency band from 1930MHz–1995MHz. The PAs have been designed using a new generation of Freescale LDMOS power transistors [1], in which the drain side video-bandwidth (VBW) has been enhanced. For the first time we will show the ability of the PA to handle wideband envelope signals (> 80MHz) with excellent nonlinearity correction using Digital Pre-distortion (DPD). Narrow band as well as wideband DPD measurement results will be presented for single and balanced Doherty PAs including driver stages. These RF Doherty PAs are targeted for use in next generation wideband wireless communication systems.
Data from Tumor Cell–Autonomous SHP2 Contributes to Immune Suppression in Metastatic Breast Cancer (2023)

&lt;div&gt;&lt;p&gt;SH2 containing protein tyrosine phosphatase-2 (SHP2) is recognized as a druggable oncogenic phosphatase that is expressed in both tumor cells and immune cells. How tumor cell–autonomous SHP2 contributes to an immunosuppressive tumor microenvironment (TME) and therapeutic failure of immune checkpoint blockades in metastatic breast cancer (MBC) is not fully understood. Herein, we utilized systemic SHP2 inhibition and inducible genetic depletion of SHP2 to investigate immune reprogramming during SHP2 targeting. Pharmacologic inhibition of SHP2 sensitized MBC cells growing in the lung to α-programmed death ligand 1 (α-PD-L1) antibody treatment via relieving T-cell exhaustion induced by checkpoint blockade. Tumor cell–specific depletion of SHP2 similarly reduced pulmonary metastasis and also relieved exhaustion markers on CD8&lt;sup&gt;+&lt;/sup&gt; and CD4&lt;sup&gt;+&lt;/sup&gt; cells. Both systemic SHP2 inhibition and tumor cell–autonomous SHP2 depletion reduced tumor-infiltrated CD4&lt;sup&gt;+&lt;/sup&gt; T cells and M2-polarized tumor-associated macrophages. Analysis of TCGA datasets revealed that phosphorylation of SHP2 is important for immune-cell infiltration, T-cell activation and antigen presentation. To investigate this mechanistically, we conducted &lt;i&gt;in vitro&lt;/i&gt; T-cell killing assays, which demonstrated that pretreatment of tumor cells with FGF2 and PDGF reduced the cytotoxicity of CD8&lt;sup&gt;+&lt;/sup&gt; T cells in a SHP2-dependent manner. Both growth factor receptor signaling and three-dimensional culture conditions transcriptionally induced PD-L1 via SHP2. Finally, SHP2 inhibition reduced MAPK signaling and enhanced STAT1 signaling, preventing growth factor–mediated suppression of MHC class I. Overall, our findings support the conclusion that tumor cell–autonomous SHP2 is a key signaling node utilized by MBC cells to engage immune-suppressive mechanisms in response to diverse signaling inputs from TME.&lt;/p&gt;Significance:&lt;p&gt;Findings present inhibition of SHP2 as a therapeutic option to limit breast cancer metastasis by promoting antitumor immunity.&lt;/p&gt;&lt;/div&gt;
'Omic approaches to preventing or managing metastatic breast cancer (2011)

Early detection of metastasis-prone breast cancers and characterization of residual metastatic cancers are important in efforts to improve management of breast cancer. Applications of genome-scale molecular analysis technologies are making these complementary approaches possible by revealing molecular features uniquely associated with metastatic disease. Assays that reveal these molecular features will facilitate development of anatomic, histological and blood-based strategies that may enable detection prior to metastatic spread. Knowledge of these features also will guide development of therapeutic strategies that can be applied when metastatic disease burden is low, thereby increasing the probability of a curative response.
Ambient‐ and High‐Temperature Properties of Titanium Carbide–Titanium Boride Composites Fabricated by Transient Plastic Phase Processing (1999)

Ambient‐ and high‐temperature properties of a class of titanium carbide‐titanium boride composites that have been produced by transient plastic phase processing are presented. The composites produced are comprised of Ti 3 B 4 , TiB 2 , and TiC 0.65 at their equilibrium composition (34.5, 30.5, and 34.9 vol%, respectively), and the Ti 3 B 4 phase in these composites occurs either as equiaxed grains or as platelets, depending on the starting mixture composition. Measurements of the ambient‐ and high‐temperature flexure strength and fracture toughness, thermal shock susceptibility, oxidation resistance, and wear resistance of this class of composites are presented. The role of various microstructural parameters—such as the morphology of the Ti 3 B 4 phase, the length scale of the microstructure, and the volume fraction of borides—on these properties has been identified.
A procedure for generating infinite series identities (2004)

A procedure for generating infinite series identities makes use of the generalized method of exhaustion by analytically evaluating the inner series of the resulting double summation. Identities are generated involving both elementary and special functions. Infinite sums of special functions include those of the gamma and polygamma functions, the Hurwitz Zeta function, the polygamma function, the Gauss hypergeometric function, and the Lerch transcendent. The procedure can be automated with Mathematica (or equivalent software).
Integrated Downhole Multiphase Flowmeter and Autonomous Inflow Control Valve (2019)

Abstract The Smart Autonomous Inflow Control Valve (S-AICV) technology is presented. This smart well sensor will prevent water and gas breakthrough and at the same time operate as a multiphase flow meter. The single compact system can be used in both mature and new field to map fluid flows along the well in oil reservoirs and at the same time autonomously controlling the production of unwanted fluid in the individual zones. This will provide the oil companies with detailed reservoir conditions data to have a better understanding of well production and drainage, and hence optimize future AICV well installations. A multiphase flow model is developed which correlate the three pressures located inside the S-AICV (P1, P2 and P3) to flow rates of gas, water and oil going through the valve. At breakthrough of gas and/or water the S-AICV will detect pressure changes when the fluid composition changes. This model utilizes this pressure changes to distinguish between the different fluids and determine the flow rate and composition of inflowing fluid. The S-AICV application is designed for each specific field to achieve the desired functionality, and the user input parameters for this model need to be determined and individually adjusted accordingly to the fluid properties and the configuration of the valve. This smart well sensor will extract data from the well and transfer the data to the surface via an optical fiber. The multiphase flow model will convert the signals to flow rates and composition, without compromising the autonomous and reliable AICV to meet the oil industry needs. Existing measurement systems as tracers or various production logging tool are costly and complex. Separate multiphase flow meters can be installed in addition to the AICVs, but this is an expensive solution where only a fraction of the data can be gathered. The benefits of the S-AICV system are its ability to prevent water and gas production and at the same time continuously measure the flow rate and composition to register breakthrough within a low-cost package with maximizing data gathering.
Endoscopic scoring indices for evaluation of disease activity in Crohn’s disease (2016)

Although they are used in clinical trials, the CDEIS and SES-CD remain incompletely validated. Future research is required to determine the operating properties and to define the optimal index.
Charging Effect by Fluorine-Treatment and Recess Gate for Enhancement-Mode on AlGaN/GaN High Electron Mobility Transistors (2020)

An enhancement-mode AlGaN/GaN metal-insulator-semiconductor high-electron- mobility-transistor was fabricated using a recess gate and CF<sub>4</sub> plasma treatment to investigate its reliable applicability to high-power devices and circuits. The fluorinated-gate device showed hysteresis during the DC current-voltage measurement, and the polarity and magnitude of hysteresis depend on the drain voltage. The hysteresis phenomenon is due to the electron trapping at the Al<sub>2</sub>O<sub>3</sub>/AlGaN interface and charging times longer than milliseconds were obtained by pulse I-V measurement. In addition, the subthreshold slope of the fluorinated-gate device was increased after the positive gate bias stress because of the two-dimensional electron gas reduction by ionized fluorine. Our systematic observation revealed that the effect of fluorine ions should be considered for the design of AlGaN/GaN power circuits.
An Improved Analytical Model for Carrier Multiplication Near Breakdown in Diodes (2016)

The charge carrier contributions to impact ionization and avalanche multiplication are analyzed in detail. A closed-form analytical model is derived for the ionization current before the onset of breakdown induced by both injection current components. This model shows that the ratio of both injection current components affects the multiplication factor at relatively low fields before breakdown, but does not affect the reverse breakdown voltage. Furthermore, the model indicates that in case the ionization coefficients of electrons and holes are quite different in value, which depends upon the semiconductor material, the ionization coefficient of the charge carrier with the highest value can be extracted at those low fields. The one with the lowest value can be obtained by fitting the current close to breakdown. The model is compared and verified with TCAD simulations, and to some extent with experimental data, for silicon p-i-n diodes.