gebhart/patrepeval huggingface dataset:
Comparative Proteomic Analysis of Methanothermobacter themautotrophicus ΔH in Pure Culture and in Co-Culture with a Butyrate-Oxidizing Bacterium (2011)

To understand the physiological basis of methanogenic archaea living on interspecies H(2) transfer, the protein expression of a hydrogenotrophic methanogen, Methanothermobacter thermautotrophicus strain ΔH, was investigated in both pure culture and syntrophic coculture with an anaerobic butyrate oxidizer Syntrophothermus lipocalidus strain TGB-C1 as an H(2) supplier. Comparative proteomic analysis showed that global protein expression of methanogen cells in the model coculture was substantially different from that of pure cultured cells. In brief, in syntrophic coculture, although methanogenesis-driven energy generation appeared to be maintained by shifting the pathway to the alternative methyl coenzyme M reductase isozyme I and cofactor F(420)-dependent process, the machinery proteins involved in carbon fixation, amino acid synthesis, and RNA/DNA metabolisms tended to be down-regulated, indicating restrained cell growth rather than vigorous proliferation. In addition, our proteome analysis revealed that α subunits of proteasome were differentially acetylated between the two culture conditions. Since the relevant modification has been suspected to regulate proteolytic activity of the proteasome, the global protein turnover rate could be controlled under syntrophic growth conditions. To our knowledge, the present study is the first report on N-acetylation of proteasome subunits in methanogenic archaea. These results clearly indicated that physiological adaptation of hydrogenotrophic methanogens to syntrophic growth is more complicated than that of hitherto proposed.
The role of structural proteomics in vaccine development: recent advances and future prospects (2015)

Vaccines are the most effective way to fight infectious diseases saving countless lives since their introduction. Their evolution during the last century made use of the best technologies available to continuously increase their efficacy and safety. Mass spectrometry (MS) and proteomics are already playing a central role in the identification and characterization of novel antigens. Over the last years, we have been witnessing the emergence of structural proteomics in vaccinology, as a major tool for vaccine candidate discovery, antigen design and life cycle management of existing products. In this review, we describe the MS techniques associated to structural proteomics and we illustrate the contribution of structural proteomics to vaccinology discussing potential applications.
Cooling cycle test of DC superconducting power transmission cable (2010)

We constructed a test stand of a 20 m DC superconducting power transmission cable in Chubu University in 2006. The cable uses thirty-nine Bi-2223 tapes. Four cycles of a cooling and current-feeding test have been carried out after the construction of the test stand. The cable suffered rapid temperature decrease of 20 K/hour at the daytime during the cooling process by cold nitrogen gas and liquid to the liquid nitrogen temperature. Nineteen HTS tapes in the cable are electrically isolated from each other, and the superconducting characteristics of these HTS tapes can be measured separately. At every cooling cycle, critical current of these isolated HTS tapes were measured. Consequently, no reduction of the critical current characteristics was observed through the 4 cooling cycles. We considered that this endurance of the cable against the cooling cycle is due to unfixed cable end structure of the cable, and that the cable was free from the mechanical stress in spite of the 6 cm shrinkage of the cable length under the low temperature.
An Algorithmic Framework For Differentially Private Data Analysis on\n Trusted Processors (2018)

Differential privacy has emerged as the main definition for private data\nanalysis and machine learning. The {\\em global} model of differential privacy,\nwhich assumes that users trust the data collector, provides strong privacy\nguarantees and introduces small errors in the output. In contrast, applications\nof differential privacy in commercial systems by Apple, Google, and Microsoft,\nuse the {\\em local model}. Here, users do not trust the data collector, and\nhence randomize their data before sending it to the data collector.\nUnfortunately, local model is too strong for several important applications and\nhence is limited in its applicability. In this work, we propose a framework\nbased on trusted processors and a new definition of differential privacy called\n{\\em Oblivious Differential Privacy}, which combines the best of both local and\nglobal models. The algorithms we design in this framework show interesting\ninterplay of ideas from the streaming algorithms, oblivious algorithms, and\ndifferential privacy.\n
The Conical Catalytic Converter-Potential for Improvement of Catalytic Effectiveness (1998)

&lt;div class="htmlview paragraph"&gt;The development of the S-designed metallic catalytic converter and the flexibility of its production paved the &lt;b&gt;way for&lt;/b&gt; the first conical converter with continuous cell enlargement. This type of conical converter, installed upstream from a standard catalytic conversion system exerts a positive influence on flow distribution and converter efficiency, both during the cold start and under &lt;b&gt;operating&lt;/b&gt; conditions. The study results outlined in the following text demonstrate the potential for increased &lt;b&gt;catalytic&lt;/b&gt; effectiveness, taking the example of the &lt;b&gt;close-&lt;/b&gt;coupled application.&lt;/div&gt;
d- and l-2‘,3‘-Didehydro-2‘,3‘-dideoxy-3‘-fluoro-carbocyclic Nucleosides:  Synthesis, Anti-HIV Activity and Mechanism of Resistance (2007)

Introducing 2'-fluoro substitution on the 2',3'-double bond in carbocyclic nucleosides has provided biologically interesting compounds with potent anti-HIV activity. As an extension of our previous works in the discovery of anti-HIV agents, D- and L-2',3'-unsaturated 3'-fluoro carbocyclic nucleosides were synthesized and evaluated against HIV-1 in human peripheral blood mononuclear (PBM) cells. Among the synthesized L-series nucleosides, compounds 18, 19, 26 and 28 exhibited moderate antiviral activity (EC50 7.1 microM, 6.4 microM, 10.3 microM, and 20.7 microM, respectively), while among the D-series, the guanosine analogue (35, D-3'-F-C-d4G) exhibited the most potent anti-HIV activity (EC50 0.4 microM, EC90 2.8 microM). However, the guanosine analogue 35 was cross-resistant to the lamivudine-resistant variants (HIV-1M184V). Molecular modeling studies suggest that hydrophobic interaction as well as hydrogen-bonding stabilize the binding of compound 35 in the active site of wild type HIV reverse transcriptase (HIV-RT). In the case of L-nucleosides, these two effects are opposite which results in a loss of binding affinity. According to the molecular modeling studies, cross-resistance of D-3'-F-C-d4G (35) to M184V mutant may be caused by the realignment of the primer and template in the HIV-RTM184V interaction, which destabilizes the RT-inhibitor triphosphate complex, resulting in a significant reduction in anti-HIV activity of the D-guanine derivative 35.
Development of an Automated 30 Second Chair Stand Test Using Smartwatch Application (2019)

This paper presents development of the smartwatch application for automation of the standard 30 Second Chair Stand Test (30SCST). 30SCST is primarily used to test leg strength and endurance, but also speed and mobility and assess risk of falls. We use inertial signals on smartwatch to detect and count stands during the test. The application notifies the user to start and stop the test using vibration on the smartwatch. Synchronization of notifications and signal acquisition allows assessment of user's response time during the test. Our application monitors baseline heart rate before the test, heart rate increase during the test, and heart rate recovery after the test that might allow assessment of cardiovascular fitness of the user. The application is developed using Wear OS and tested on two smartwatch platforms: Fossil G4 and Polar M600. Pilot test included 12 subjects, six male and six female (mean age 39.1, S.D. 19 years). Overall accuracy of detection of the number of standups is 98.8%. Smartwatch application can be used for automated testing in clinical setups as well as for self-monitoring at home.
Toward Precisely Controllable Acoustic Response of Shell-Stabilized Nanobubbles: High Yield and Narrow Dispersity (2021)

Understanding the pressure dependence of the nonlinear behavior of ultrasonically excited phospholipid-stabilized nanobubbles (NBs) is important for optimizing ultrasound exposure parameters for implementations of contrast enhanced ultrasound, critical to molecular imaging. The viscoelastic properties of the shell can be controlled by the introduction of membrane additives, such as propylene glycol as a membrane softener or glycerol as a membrane stiffener. We report on the production of high-yield NBs with narrow dispersity and different shell properties. Through precise control over size and shell structure, we show how these shell components interact with the phospholipid membrane, change their structure, affect their viscoelastic properties, and consequently change their acoustic response. A two-photon microscopy technique through a polarity-sensitive fluorescent dye, C-laurdan, was utilized to gain insights on the effect of membrane additives to the membrane structure. We report how the shell stiffness of NBs affects the pressure threshold (<i>P</i><sub>t</sub>) for the sudden amplification in the scattered acoustic signal from NBs. For narrow size NBs with 200 nm mean size, we find <i>P</i><sub>t</sub> to be between 123 and 245 kPa for the NBs with the most flexible membrane as assessed using C-Laurdan, 465-588 kPa for the NBs with intermediate stiffness, and 588-710 kPa for the NBs with stiff membranes. Numerical simulations of the NB dynamics are in good agreement with the experimental observations, confirming the dependence of acoustic response to shell properties, thereby substantiating further the development in engineering the shell of ultrasound contrast agents. The viscoelastic-dependent threshold behavior can be utilized for significantly and selectively enhancing the diagnostic and therapeutic ultrasound applications of potent narrow size NBs.
Low-order statistical analysis of 1-D diffuse reflectance signals from cancer cells using 2-D scalogram images (2016)

The novelty of this study is seen in the efficient characterization of cancer cells through representation of 1-D backscattered signals from cancer cells using statistical analysis on 2-D scalogram images. The proposed approach allows one to obtain a rapid and accurate visualization of the frequency components associated with the backscattered signals; while enlightening the understanding and the physics of the diffuse reflectance light waves interactions with the lung cells, by performing texture characterization and pattern recognition analysis directly on the scalograms.
Synthesis of ligand-functionalized water-soluble [18F]YF3 nanoparticles for PET imaging (2013)

We report a simple, efficient synthesis of novel (18)F-labeled imaging agents based on YF3 nanoparticles. Targeting ligands and antitumor drug molecules can be introduced onto the YF3 nanoparticles in a one-pot synthesis. The (18)F-labeling reaction proceeds in aqueous solutions at room temperature with excellent radiolabeling yields (>80%) in a very short time (5-10 min). (18)F-labeled YF3 nanoparticles displayed high stability in mouse and human serum, and their application for mapping lymph nodes in live rats after local injection has also been demonstrated.
Manufacture of silicon-based devices having disordered sulfur-doped surface layers (2017)

The present invention provides methods of fabricating a radiation-absorbing semiconductor wafer by irradiating at least one surface location of a silicon substrate, e.g., an n-doped crystalline silicon, by a plurality of temporally short laser pulses, e.g., femtosecond pulses, while exposing that location to a substance, e.g., SF.sub.6, having an electron-donating constituent so as to generate a substantially disordered surface layer (i.e., a microstructured layer) that incorporates a concentration of that electron-donating constituent, e.g., sulfur. The substrate is also annealed at an elevated temperature and for a duration selected to enhance the charge carrier density in the surface layer. For example, the substrate can be annealed at a temperature in a range of about 700 K to about 900 K.
Water Desalination (2007)

Abstract This article addresses water availability and use with special emphasis on the role and current level of technology of water desalination. The major desalination processes, using membranes or distillation, are described. These are multistage flash evaporation (MSF), multi‐effect distillation (ME), vapor compression distillation (VC), freeze–desalination, reverse osmosis (RO), and electrodialysis (ED). Within the membrane processes category important features of major applications: nanofiltration, brackish RO, wastewater reclamation and seawater desalination are discussed. Description of desalination hybrid systems and key references are provided. The use of renewable energy for water desalination by solar stills, ocean–thermal energy conversion plants, wind, and photovoltaic cells is presented. Two of the key technical problems in desalination, scale deposition and prevention, and corrosion and the proper choice of materials to be used for construction of desalination system, are discussed. Basic equations are provided for the evaluation and preliminary design of MSF and RO, which are currently the leading water desalination processes. The leading professional and governmental organizations involved with desalination, and their activities, are described.
Cryogenic Adsorption of Hydrogen Isotopes over Nano-Structured Materials (2011)

Porous materials such as zeolites, activated carbon, silica gels, alumina and a number of industrial catalysts are compared and ranked for hydrogen and deuterium adsorption at liquid nitrogen temperature. All samples show higher D2 adsorption than that of H2, in which HY zeolite has the greatest isotopic effect while 13X zeolite has the highest hydrogen uptake capacity. Material’s moisture content has significant impact to its hydrogen uptake. A material without adequate drying could result in complete loss of its adsorption capacity. Even though some materials present higher H2 adsorption capacity at full pressure, their adsorption at low vapor pressure may not be as good as others. Adsorption capacity in a dynamic system is much less than in a static system, as expected. The same type of material from different vendors or lots may behave differently.
Hybrid modes in plasmonic cavity array for enhanced hot-electron photodetection (2017)

The plasmonic characteristics of a periodic array of cavities in a silicon substrate are investigated for hot-electron photodetection. Resonances of cavity surface plasmons bound to air cavities and silicon cavities, and resonance of Bragg-surface plasmon polaritons are illustrated by the map of metal absorption. Hybrid modes formed with combination of these modes can strongly enhance absorption in metal and be exploited to optimize hot-electron photodetectors for single-band and dual-band detection at optical communication wavelengths.
Coronary Stent Artifact Reduction with an Edge-Enhancing Reconstruction Kernel – A Prospective Cross-Sectional Study with 256-Slice CT (2016)

In vivo 256-slice CT assessment of coronary stents shows that the edge-enhancing CT reconstruction kernel generates thinner stent walls, less overestimation from nominal thickness, and better image quality scores than the standard kernel.
New current control scheme for the Vienna rectifier in discontinuous conduction mode (2014)

The Vienna rectifier (VR) is used in applications that require unidirectional, non-isolated, three-phase AC to DC conversion with constant output voltage and sinusoidal input currents. However, because of the unidirectional topology, the input currents become discontinuous at small output power values. As a consequence, the relationship between rectifier input voltage and duty cycle changes compared to continuous conduction mode. Therefore, if no additional measures are taken, the rectifier input currents will be distorted. This work describes a new control scheme that allows operation of the VR with sinusoidal input currents in discontinuous conduction mode (DCM). The limits of operation are described, concerning maximum mains voltage, maximum midpoint current and minimum resistance to the mains in DCM. Further, the noise emission in DCM is compared to continuous conduction mode (CCM) operation. Finally, the proposed scheme is experimentally verified on a hardware prototype.
Granular L1 FePt:TiO2 (001) nanocomposite thin films with 5nm grains for high density magnetic recording (2008)

Fe Pt : Ti O 2 (001) thin films were deposited on CrRu∕MgO underlayers by dc magnetron cosputtering. The effects of TiO2 content on microstructure and magnetic properties of the epitaxial FePt (001) films were studied. Experimental results showed that even with 20vol% TiO2 doping, FePt films could keep a (001) preferred orientation and perpendicular anisotropy. The FePt:TiO2 (001) film with 5nm grain size, adjustable coercivity, and reduced exchange coupling was obtained by doping 20vol% TiO2 into FePt film, showing great potential as low noise ultrahigh density perpendicular magnetic recording media.
RETRACTED: Prophylactic DNA vaccine for hepatitis C virus (HCV) infection: HCV-specific cytotoxic T lymphocyte induction and protection from HCV-recombinant vaccinia infection in an HLA-A2.1 transgenic mouse model (2000)

DNA vaccines express antigens intracellularly and effectively induce cellular immune responses. Because only chimpanzees can be used to model human hepatitis C virus (HCV) infections, we developed a small-animal model using HLA-A2.1-transgenic mice to test induction of HLA-A2.1-restricted cytotoxic T lymphocytes (CTLs) and protection against recombinant vaccinia expressing HCV-core. A plasmid encoding the HCV-core antigen induced CD8(+) CTLs specific for three conserved endogenously expressed core peptides presented by human HLA-A2.1. When challenged, DNA-immunized mice showed a substantial (5-12 log(10)) reduction in vaccinia virus titer compared with mock-immunized controls. This protection, lasting at least 14 mo, was shown to be mediated by CD8(+) cells. Thus, a DNA vaccine expressing HCV-core is a potential candidate for a prophylactic vaccine for HLA-A2.1(+) humans.
Hepatic Expression of the Catalytic Subunit of the Apolipoprotein B mRNA Editing Enzyme ( apobec -1) Ameliorates Hypercholesterolemia in LDL Receptor-Deficient Rabbits (1996)

Apolipoprotein (apo) B48, a protein contained in intestinally derived lipoprotein particles, is synthesized by post-transcriptional editing of apoB100 mRNA. This reaction is mediated by an enzyme complex that includes the catalytic subunit, apobec-1. The liver of most mammals, by contrast, contains only unedited apoB mRNA and secretes apoB100, the major protein component of plasma low-density lipoprotein (LDL). Because rabbits, like humans, fail to edit hepatic apoB100 mRNA, we introduced a recombinant adenovirus encoding apobec-1 into the livers of LDL receptor-defective rabbits to determine the impact on lipoprotein metabolism of hepatic apoB48 secretion. Transgene expression was mainly confined to the liver and was sustained for up to 3 weeks following virus administration, as evidenced by the presence of apobec-1 mRNA and the ability of hepatic S100 extracts to edit a synthetic apoB RNA template in vitro. The transient induction of hepatic apoB mRNA editing accompanied alterations in very-low-density lipoprotein (VLDL) size, the presence of apoB48 in fractions spanning the VLDL and LDL range, and modest reductions in total plasma cholesterol levels.
Kiss and spit metabolomics highlights the role of host purine metabolism during pathogen infection (2022)

Abstract Intracellular bacteria and protists are auxotrophic for many metabolites and must rely on the host cell to supply these nutrients. The mechanisms of how pathogens manipulate host metabolism to their benefit are not understood. These questions are difficult to address for intracellular pathogens because one cannot easily distinguish the origin of the metabolite as host or pathogen derived. The obligate intracellular parasite Toxoplasma gondii manipulates the host cell by a pre-invasion process called “kiss and spit”, where the contents of the parasite rhoptry organelles are secreted into the host cytoplasm before invasion occurs. Here, we demonstrated that rhoptry contents from kiss and spit altered metabolite abundance in nucleotide synthesis, the pentose phosphate pathway, glycolysis, and amino acid synthesis. An increase in 2,3-bisphosphoglycerate (2,3-BPG) abundance led us to investigate the activation of host cytosolic nucleosidase II (cN-II) to provide purines for the parasite.
IOctopus (2020)

In a multi-CPU server, memory modules are local to the CPU to which they are connected, forming a nonuniform memory access (NUMA) architecture. Because non-local accesses are slower than local accesses, the NUMA architecture might degrade application performance. Similar slowdowns occur when an I/O device issues nonuniform DMA (NUDMA) operations, as the device is connected to memory via a single CPU. NUDMA effects therefore degrade application performance similarly to NUMA effects.
Resetting the Epigenetic Histone Code in the MRL-lpr/lpr Mouse Model of Lupus by Histone Deacetylase Inhibition (2005)

The baseline level of gene expression varies between healthy controls and systemic lupus erythematosus (SLE) patients, and among SLE patients themselves. These variations may explain the different clinical manifestations and severity of disease observed in SLE. Epigenetic mechanisms, which involve DNA and histone modifications, are predictably associated with distinct transcriptional states. To understand the interplay between various histone modifications, including acetylation and methylation, and lupus disease, we performed differential expression histone modification analysis in splenocytes from the MRL-lpr/lpr mouse model of lupus. Using stable isotope labeling in combination with mass spectrometry, we found global site-specific hypermethylation (except H3 K4 methylation) and hypoacetylation in histone H3 and H4 MRL-lpr/lpr mice compared to control MRL/MPJ mice. Moreover, we have identified novel histone modifications such as H3 K18 methylation, H4 K31 methylation, and H4 K31 acetylation that are differentially expressed in MRL-lpr/lpr mice compared to controls. Finally, in vivo administration of the histone deacetylase inhibitor trichostatin A (TSA) corrected the site-specific hypoacetylation states on H3 and H4 in MRL-lpr/lpr mice with improvement of disease phenotype. Thus, this study is the first to establish the association between aberrant histone codes and pathogenesis of autoimmune disease SLE. These aberrant post-translational histone modifications can therefore be reset with histone deacetylase inhibition in vivo.