gebhart/patrepeval huggingface dataset:
Nontargeted Analysis of DNA Adducts by Mass-Tag MS: Reaction of p-Benzoquinone with DNA (2012)

Using a method in which DNA adducts are discovered based on their conversion in a nucleotide form to phosphorimidazolides with isotopologue benzoylhistamines (or p-bromobenzoylhistamine) prior to detection by MALDI-TOF-MS, we have profiled the adducts that form when calf thymus DNA is reacted in vitro with p-benzoquinone (BQ). We find, as relative values normalized to 100% of adducts observed, 79% BQ-dCMP, 21% BQ-methyl-dCMP (a new DNA adduct), and trace amounts of BQ-dAMP and BQ-dGMP. Because mC is 5% of C in this DNA, the reaction of BQ with DNA in vitro is about five times faster at methyl-C than C. When equal amounts of dCMP and methyl-dCMP are reacted with BQ, equal amounts of the corresponding adducts are observed. Thus, the microenvironment of methyl-C in DNA enhances its reactivity relative to C with BQ. In a prior, similar study, but based on analysis by (32)P-postlabeling, the second most abundant adduct was assigned to BQ-A, apparently because of comigration of the BQ-A and BQ-methyl-C adducts (as bisphosphates) in the chromatographic step. Because the calf thymus DNA (used as received) was contaminated with RNA, we also detected the ribonucleotide adduct, BQ-CMP.
Using Real-Time Kinematics Algorithm in Mission Critical Communication for Accurate Positioning and Time Correction over 5G and Beyond Networks (2022)

At 5G and beyond networks, accurate localization services and nanosecond time synchronization are crucial to enabling mission-critical wireless communications technologies and techniques such as autonomous vehicles and distributed multiple-input and multiple-output (MIMO) antenna systems. This paper investigates how to improve wireless time synchronization by studying time correction based on the Real-Time Kinematics (RTK) positioning algorithm. Using the multiple Global Navigation Satellite System (GNSS) receiver references and the proposed binary GNSS satellite formation to reduce the effect of the ionosphere and troposphere delays and recede the measurement phase-range and pseudorange errors. As a result, it improves user equipment’s (UE) localization and measures the time difference between the Base Station (BS) and the UE local clocks. The results show that the positioning accuracy has been increased, and a millimetre accuracy has been achieved while attaining the sub-nanosecond time error (TE) between the UE’s and BS local clocks.
High‐Volume Postdilution Hemodiafiltration Is a Feasible Option in Routine Clinical Practice (2014)

Hemodiafiltration (HDF) with 20-22 L of substitution fluid is increasingly recognized as associated with significant benefits regarding patient outcome. However, some doubt exists as to whether these high volumes can be achieved in routine clinical practice. A total of 4176 sessions with 366 patients on postdilution HDF were analyzed in this 1-month observational cohort study with prospective data collection. All dialysis machines were equipped with AutoSub plus signal analysis software that automatically and continuously adapts the substitution fluid flow according to the blood flow, blood viscosity, and dialyzer characteristics. Percentages of sessions with different types of vascular access were compared regarding achievement of ≥21 L substitution fluid. Logistic regression analysis was conducted to study the independent relationship of selected variables with achievement of ≥21 L substitution volume. Patient- and dialysis-related variables that showed an association with the convection volume were entered in a multivariable model that included hematocrit up front. Respectively, 87%, 84%, and 33% of routine sessions conducted with fistulas, grafts, and catheters qualified as high-volume HDF. Serum albumin levels ≥4.2 g/dL were positively associated with the achievement of at least 21 L substitution volume. Positive associations were also observed for blood flows in the ranges 350-399 and ≥400 mL/min compared with the reference range (300-350 mL/min), for longer treatment time, for fistula versus catheter, for higher filtration fraction, and for dialysis conducted at the end of the week versus Monday. It can be concluded that implementation and sustainability of high-volume HDF is possible in routine clinical practice for almost all patients treated with fistulas and grafts.
Circulating markers of inflammation and endothelial function, and their relationship to diabetic retinopathy (2014)

Higher C-reactive protein levels, but not markers of endothelial function, may be related to more severe diabetic retinopathy. This finding suggests that inflammatory processes are involved in severe diabetic retinopathy, particularly in patients with a BMI ≥ 30 kg/m(2) .
Formability of C-Si-Mn-Al-Nb-Mo Ultra High-strength TRIP-aided Sheet Steels (2007)

Formable 980–1470 MPa grade ultra high-strength TRIP-aided sheet steels with bainitic ferrite matrix (TBF steels) have been developed for cold forming of automotive applications. Complex additions of 1.0%Al–0.05%Nb–0.2%Mo to 0.2%C–1.5%Si–1.5%Mn base steel increased both the volume fraction and carbon concentration of retained austenite films of the TBF steel, with refining of microstructure. Extremely much retained austenite was realized in the TBF steel austempered at 450–500°C, corresponding to hot-dip galvanization just after annealing. Good combinations of strength and elongation and strength and stretch-flangeability were achieved when the TBF steel was austempered at 450–500°C and 425–475°C, respectively. These good combinations were caused by fine lath structure and a large amount of metastable retained austenite film. It is noteworthy that the TBF steel exhibited an excellent combination of total elongation and stretch-flangeability when austempered at 325–350°C lower than MS.
B-102 Exosomal protein signatures: mechanistic insights and biomarker potential (2019)

In 1889, Stephen Paget first proposed that organ distribution of metastases is a non-random event, yet metastatic organotropism remains one of the greatest mysteries in cancer biology. A growing number of studies demonstrate that tumor-derived microvesicles, referred to as exosomes, may alter the tumor microenvironment at future sites of metastasis promoting pre-metastatic niche formation, and thus creating a favorable “soil” for incoming metastatic “seeds.” However, by what mechanism, and whether their role is significant in tumor progression remains unknown. We have recently demonstrated that exosomes released by lung-, liver- and brain-tropic tumor cells preferentially fuse with resident cells at their future metastatic sites, such as fibroblasts and epithelial cells in the lung, Kupffer cells in the liver, and endothelial cells in the brain. We found that tumor-derived exosome homing to organ-specific cell types prepares the pre-metastatic niche. Moreover, treatment with exosomes derived from lung-tropic models can redirect to the lung the metastatic distribution of cells that normally lack the capacity to form lung metastasis. Proteomic profiling of exosomes revealed distinct integrin expression patterns associated with each organ-specific metastatic site. Whereas exosomal α 6 β4 integrins were associated with lung metastasis, exosomal integrin α v β5 was linked to liver metastasis and α v β3 to brain metastasis. Targeting α 6 β4 and α v β5 integrins decreased exosome uptake and metastasis in the lung and liver, respectively. Moreover, our clinical data indicate that integrin expression profiles in circulating plasma exosomes from cancer patients could be used to predict organ-specific metastasis. To gain a more comprehensive understanding of the relationship between exosomal protein cargo and tumor progression, we have built one of the largest exosome proteomics databases, including human and murine normal, pre-cancer and cancer exosomes from a variety sources, from cell lines to plasma and other bodily fluids. Out of 490 human samples, 206 were isolated from normal subjects and 284 were from cancer patients. This dataset has allowed us to extend the list of markers that can be used to identify and isolate exosomes from human samples. When comparing the protein cargo of blood plasma exosomes isolated from normal subjects versus cancer patients with early stage pancreatic, colorectal, breast and lung cancer, we were able to define a cancer-specific proteomic signature that distinguishes cancer exosomes. Using paired samples from tumor tissue and plasma of the same cancer patients with breast, lung or pancreatic cancer, we were able to derive cancer type-specific exosomal signatures, which can be used as biomarkers to identify and classify tumors of unknown origin. Therefore, proteomic profiling of exosomes has great clinical potential as a non-invasive, rapid liquid biopsy that could aid in tumor detection classification.
Development of a Unique Surface Magneto-Optical Kerr Effect Magnetometer to Correlate Magnetism and Structure in Fe-Fe₃O₄ Thin Film Bilayers (2012)

As the automotive industry moves steadily toward electric vehicles, there is an increasing need for more efficient electric motors. Currently, the state of the art in electric motor design is limited by silicon-steel laminations that restrict 3-dimensional flux-carrying capability. Oxide-coated ferrous powder metals offer the electrical resistivity and magnetic flux density needed for advanced electric motor design, but coating compatibility and performance are still the subject of much research. Here we have designed a unique magnetometer capable of characterizing this system in thin film form as well as future material systems. Additionally, we examine the microstructure and magnetic properties of Fe - Fe3O4, a promising system for this application. This study explores the structural compatibility between the core and coating material, as well as the magnetic hysteresis of the resulting composite, using a combination of electron microscopy and surface magneto-optical Kerr effect (SMOKE) magnetometry. We have designed a customized magnetometer with the ability to perform hysteresis measurements in a longitudinal geometry under magnetic fields up to 8 kOe with the option of adding modular improvements for in situ electric field application. This instrument allows for both static and dynamic measurements of thin film samples with high surface sensitivity. Structure-property relationships can be determined through this magnetic characterization and associated microstructural information provided by electron microscopy. The characterization of this system in thin film form will inform the eventual production of coated ferrous powders with improved electromagnetic properties.
Discovery of DS68702229 as a Potent, Orally Available NAMPT (Nicotinamide Phosphoribosyltransferase) Activator (2021)

Nicotinamide phosphoribosyltransferase (NAMPT) catalyzes the rate-limiting step of the nicotinamide adenine dinucleotide (NAD<sup>+</sup>) salvage pathway. Because NAD<sup>+</sup> plays a pivotal role in energy metabolism and boosting NAD<sup>+</sup> has positive effects on metabolic regulation, activation of NAMPT is an attractive therapeutic approach for the treatment of various diseases, including type 2 diabetes and obesity. Herein we report the discovery of 1-(2-phenyl-1,3-benzoxazol-6-yl)-3-(pyridin-4-ylmethyl)urea 12c (DS68702229), which was identified as a potent NAMPT activator. Compound 12c activated NAMPT, increased cellular NAD<sup>+</sup> levels, and exhibited an excellent pharmacokinetic profile in mice after oral administration. Oral administration of compound 12c to high-fat diet-induced obese mice decreased body weight. These observations indicate that compound 12c is a promising anti-obesity drug candidate.
Spatial Mapping of Plasma Sprayed Coating Thickness Using X-Ray Fluorescence (2015)

Abstract The measurement of the spatial distribution of coating thickness of thin coatings applied by thermal spraying can be challenging. For non-magnetic metallic substrates and coatings, X-Ray Fluorescence (XRF) was employed for measuring coating thicknesses in the range of 15 to 60 μm. XRF is used to measure the ratio of atomic fluorescence peaks for an element in the substrate to an element in the coating. With appropriate calibration, the ratio of peak intensities gives the coating thickness for the spot sampled. Mass gain and cross sectional metallography are compared to XRF to determine accuracies and sensitivities of the techniques for plasma sprayed coatings.
OFDM versus single-carrier: a multiple antenna comparison (2004)

info:eu-repo/semantics/published
Emulating Realistic Bidirectional Spatial Channels for MIMO OTA Testing (2015)

This paper discusses over the air (OTA) testing for multiple input multiple output (MIMO) capable terminals with emphasis on modeling bidirectional spatial channel models in multiprobe anechoic chamber (MPAC) setups. In the literature, work on this topic has been mainly focused on how to emulate downlink channel models, whereas uplink channel is often modeled as free space line-of-sight channel without fading. Modeling realistic bidirectional (i.e., both uplink and downlink) propagation environments is essential to evaluate any bidirectional communication systems. There have been works stressing the importance of emulating full bidirectional channel and proposing possible directions to implement uplink channels in the literature. Nevertheless, there is no currently published work reporting an experimental validation of such concepts. In this paper, a general framework to emulate bidirectional channels for time division duplexing (TDD) and frequency division duplexing (FDD) communication systems is proposed. The proposed technique works for MPAC setups with arbitrary uplink and downlink probe configurations, that is, possibly different probe configurations (e.g., number of probes or their configurations) in the uplink and downlink. The simulation results are further supported by measurements in a practical MPAC setup. The proposed algorithm is shown to be a valid method to emulate bidirectional spatial channel models.
A plasma membrane template for macropinocytic cups (2016)

Macropinocytosis is a fundamental mechanism that allows cells to take up extracellular liquid into large vesicles. It critically depends on the formation of a ring of protrusive actin beneath the plasma membrane, which develops into the macropinocytic cup. We show that macropinocytic cups in <i>Dictyostelium</i> are organised around coincident intense patches of PIP<sub>3</sub>, active Ras and active Rac. These signalling patches are invariably associated with a ring of active SCAR/WAVE at their periphery, as are all examined structures based on PIP<sub>3</sub> patches, including phagocytic cups and basal waves. Patch formation does not depend on the enclosing F-actin ring, and patches become enlarged when the RasGAP NF1 is mutated, showing that Ras plays an instructive role. New macropinocytic cups predominantly form by splitting from existing ones. We propose that cup-shaped plasma membrane structures form from self-organizing patches of active Ras/PIP<sub>3</sub>, which recruit a ring of actin nucleators to their periphery.
Modeling of HCCI Combustion and Emissions Using Detailed Chemistry (2001)

&lt;div class="htmlview paragraph"&gt;To help guide the design of homogeneous charge compression ignition (HCCI) engines, single and multi-zone models of the concept are developed by coupling the first law of thermodynamics with detailed chemistry of hydrocarbon fuel oxidation and NO&lt;sub&gt;x&lt;/sub&gt; formation. These models are used in parametric studies to determine the effect of heat loss, crevice volume, temperature stratification, fuel-air equivalence ratio, engine speed, and boosting on HCCI engine operation.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;In the single-zone model, the cylinder is assumed to be adiabatic and its contents homogeneous. Start of combustion and bottom dead center temperatures required for ignition to occur at top dead center are reported for methane, n-heptane, isooctane, and a mixture of 87% isooctane and 13% n-heptane by volume (simulated gasoline) for a variety of operating conditions. Detailed chemistry of NO&lt;sub&gt;x&lt;/sub&gt; formation is coupled with multi-step chemical kinetics of hydrocarbon fuel oxidation to gain insight into the ignition and NO&lt;sub&gt;x&lt;/sub&gt; formation processes.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A more detailed multi-zone model is also developed in an effort to explore the effects of temperature stratification, heat loss, and crevice volume on the combustion process and HC, CO, and NO&lt;sub&gt;x&lt;/sub&gt; emissions. The combustion chamber volume is divided into four types of zones: crevice, boundary layer, inner core, and outer core. The inner core zones are considered to be adiabatic and constant mass, while the outer core, boundary layer, and crevice zones are allowed to exchange mass and energy. The multi-zone model is used to conduct parametric studies to investigate the effect of changing engine operating conditions, crevice volume, and boundary layer thickness on engine performance and emissions. It is shown that CO emissions primarily arise from fuel flowing out of the crevices and boundary layer during expansion and being partially oxidized. The multi-zone model is hence shown to provide a much more physical representation of the ignition and emission formation processes in HCCI engines than the single-zone model.&lt;/div&gt;
Levels of cytotoxic reactivity to cultured normal skin fibroblasts in sera from normal and sarcoma-bearing patients. (1980)

Human sera possess complement-dependent cytotoxic reactivity against autologous and allogeneic cultured normal skin fibroblasts. Previous studies indicated that the natural antibody reactivity is directed against fetal antigens expressed on these cells in tissue culture. The reactivity was further characterized in the present study. Chromatographic analysis of a normal serum indicated that its reactivity belonged to the immunoglobulin M (19S) class of immunoglobulins. Sera from 22 preoperative tumor-bearing osteogenic sarcoma patients, 30 tumor-bearing soft-tissue sarcoma patients, and 52 age- and sex-matched normal individuals were tested against allogeneic skin fibroblasts. The patient and normal groups displayed wide, overlapping ranges of cytotoxicity. The osteogenic sarcoma group showed a small but significant increase in mean cytotoxicity compared to the controls, whereas the soft-tissue sarcoma sera were not significantly different from the controls. Reactivities in the sera of patients whose tumors recurred were not significantly different from those of the patients who remained disease free. Cytotoxic levels in sera from eight osteogenic sarcoma patients followed throughout the clinical course remained constant up to the time of documented recurrence and were not affected by surgical removal of the primary tumor or Bacillus Calmette-Guérin immunotherapy. In three of four patients whose tumors recurred, cytotoxic levels fell, but only after documented recurrence. The natural antibody reactivity against normal fibroblasts does not appear useful as a marker for diagnosis, prognosis, or monitoring tumor presence in sarcoma patients.
Characterization and Cell Cycle Regulation of the Major Kaposi’s Sarcoma-Associated Herpesvirus (Human Herpesvirus 8) Latent Genes and Their Promoter (1999)

Retinoblastoma tumor suppressor protein (pRB) inhibition by tumor virus oncoproteins has been attributed to the need for these viruses to promote lytic viral nucleic acid synthesis by unscheduled entry into the S phase of the cell cycle. Kaposi's sarcoma-associated herpesvirus (KSHV or HHV8) encodes a functional cyclin (vCYC) which is expressed during latency and can direct phosphorylation of pRB. We mapped the two major latent transcripts encoding vCYC, latent transcript 1 (LT1) and LT2, by cDNA sequencing, 5' rapid amplification of cDNA ends, and primer extension analyses. Both LT1 and LT2 transcripts are spliced, originate from the same start site, and encode ORF K13 (vFLIP) as well as ORF72 (vCYC). The latency-associated nuclear antigen (LANA, ORF73) is encoded by LT1 but spliced from LT2. While differential expression of the two transcripts was not found, the promoter controlling LT1/LT2 transcription is regulated in a cell cycle-dependent manner. Activities of both KSHV LT1/LT2 and huCYC D1 luciferase promoter reporters transfected into NIH 3T3 cells increase 11- and 4-fold, respectively, after release from cell cycle arrest by serum starvation. Further, vCYC and huCYC D2 mRNA levels are low in naturally infected BCBL-1 cells arrested in late G1 with L-mimosine but increase in parallel during a 24-h period after release from cell cycle arrest. Cell cycle regulation of KSHV vCYC expression mimics cellular D cyclin regulation and may maintain infected cell cycling. This is consistent with an alternative hypothesis that tumor viruses have developed specific responses to innate cellular defenses against latent virus infection that include pRB-induced cell cycle arrest.
24.6 A CMOS micro-flow cytometer for magnetic label detection and classification (2014)

Flow cytometry is widely used in medicine for hematology, immunology, chemotherapy and pathology, as well as in food and water safety. While present instruments are predominantly used in laboratory environments, there is a growing and unmet need for devices that can be used in point-of-care (PoC) settings. The main impediments to PoC solutions are the fluorescent labels, which require sophisticated sample pre-processing and calibration to reduce background, and optics that are difficult to miniaturize. Label-free approaches such as reported in [1] eliminate this problem but have limited applications due to a lack of specificity. Substituting magnetic labels avoids this limitation and eliminates the need for preprocessing, but present solutions use μHall sensors [2] or giant-magneto-resistors (GMRs) [3], which are not available in standard CMOS technology. CMOS LC-tank spectrometry [4] is amenable to integration but does not achieve the bandwidth and sensitivity required for flow cytometry. In this paper, we present a magnetic flow cytometer integrated in standard CMOS technology assembled in a single-use microfluidic cartridge that meets all the above-mentioned requirements.
Vaccination of calves with yeast‐ and bacterial‐expressed paramyosin from the bovine lungworm Dictyocaulus viviparus (2015)

Previously, vaccination of cattle with Escherichia coli-expressed bovine lungworm paramyosin (EcPMY) adjuvanted with Quil A resulted in considerable reduction in worm burden and larvae shedding (Strube et al., 2015). To further evaluate the protective potential of PMY, cattle vaccination trials were performed using either E. coli- (EcPMY) or Pichia pastoris-expressed PMY (PpPMY) with different adjuvants (Matrix-Q(™) or Quil A). Combinations EcPMY+Matrix-Q(™) (trial 1), PpPMY+Matrix-Q(™) (trial 2) and PpPMY+Quil A (trial 3) were tested against challenge infections with 2000 Dictyocaulus viviparus larvae. Even though GM worm burden and larvae shedding was lower in almost all vaccinated groups, there were high variations between individuals hampering significant differences. However, in all vaccinated groups, lungworms were significantly shorter compared with those in controls. In vitro stimulation of peripheral blood mononuclear cells (PBMC) with recombinant (r)PMY revealed no significant proliferation following vaccinations or challenge infection. All vaccinated cattle showed a significant rise in specific antibodies, particularly IgG and its subclass IgG1, and detected the native lungworm PMY in immunoblots starting 2 weeks after the first vaccination. The use of a different rPMY-adjuvant combination or combined vaccination with additional recombinant antigens might be a promising future approach towards a new vaccine against lungworms in cattle.