gebhart/patrepeval huggingface dataset:
Modulation of LTCC Pathways by a Melusin Mimetic Increases Ventricular Contractility During LPS-Induced Cardiomyopathy (2022)

AIM: Sepsis-induced cardiomyopathy is commonplace and carries an increased risk of death. Melusin, a cardiac muscle-specific chaperone, exerts cardioprotective function under varied stressful conditions through activation of the AKT pathway. The objective of this study was to determine the role of melusin in the pathogenesis of lipopolysaccharide (LPS)-induced cardiac dysfunction and to explore its signaling pathway for the identification of putative therapeutic targets. METHODS AND RESULTS: Prospective, randomized, controlled experimental study in a research laboratory. Melusin overexpressing (MelOV) and wild-type (MelWT) mice were used. MelOV and MelWT mice were injected intraperitoneally with LPS. Cardiac function was assessed using trans-thoracic echocardiography. Myocardial expression of L-type calcium channel (LTCC), phospho-Akt and phospho-Gsk3-b were also measured. In separate experiments, wild-type mice were treated post-LPS challenge with the allosteric Akt inhibitor Arq092 and a mimetic peptide (R7W-MP) targeting the LTCC. The impact of these therapies on protein-protein interactions, cardiac function, and survival was assessed. MelOV mice had limited derangement in cardiac function after LPS challenge. Protection was associated with higher Akt and Gsk3-b phosphorylation and restored LTCC density. Pharmacological inhibition of Akt activity reversed melusin-dependent cardiac protection. Treatment with R7W-MP preserved cardiac function in wild-type mice after LPS challenge and significantly improved survival. CONCLUSIONS: This study identifies AKT / Melusin as a key pathway for preserving cardiac function following LPS challenge. The cell-permeable mimetic peptide (R7W-MP) represents a putative therapeutic for sepsis-induced cardiomyopathy.
Template Shape Estimation: Correcting an Asymptotic Bias (2017)

We use tools from geometric statistics to analyze the usual estimation procedure of a template shape. This applies to shapes from landmarks, curves, surfaces, images, etc. We demonstrate the asymptotic bias of template shape estimation using the stratified geometry of the shape space. We give a Taylor expansion of the bias with respect to a parameter $\sigma$ describing the measurement error on the data. We propose two bootstrap procedures that quantify the bias and correct it if needed; they are applicable for any type of shape data. We give a rule of thumb to provide intuition on whether the bias has to be corrected, which reveals the parameters that control the bias' magnitude. We illustrate our results on simulated and real shape data.
Quantum Transport and Field-Induced Insulating States in Bilayer Graphene pnp Junctions (2010)

We perform transport measurements in high quality bilayer graphene pnp junctions with suspended top gates. At a magnetic field B = 0, we demonstrate band gap opening by an applied perpendicular electric field with an On/Off ratio up to 20,000 at 260 mK. Within the band gap, the conductance decreases exponentially by 3 orders of magnitude with increasing electric field and can be accounted for by variable range hopping with a gate-tunable density of states, effective mass, and localization length. At large B, we observe quantum Hall conductance with fractional values, which arise from equilibration of edge states between differentially doped regions, and the presence of an insulating state at filling factor v = 0. Our work underscores the importance of bilayer graphene for both fundamental interest and technological applications.
Perspectives of Nurses and Patients on Call Light Technology (2015)

Call lights are prevalent in inpatient healthcare facilities across the nation. While call light use directly influences the delivery of nursing care, there remain significant gaps both in research and technology that can affect the quality of care and patient satisfaction. This study examines nurse and patient perceptions of the use of a new call communication solution, Eloquence, in the acute care inpatient setting. Eighteen patients were recruited for the study and participated in individual semistructured interviews during their hospital stay. Eighteen nurses were recruited and participated in focus groups for this study. Qualitative descriptive methods were used to analyze the data. Results revealed themes of usability, improved communication, and suggestions for improvement to the alpha prototype design. After a demonstration of the use and capability of Eloquence, nurse and patient participants found Eloquence as a welcomed advancement in nurse call technology that has the potential to improve workflow and patient outcomes. In addition, the participants also proposed ideas on how to further develop the technology to improve its use.
A Sulfoglycolytic Entner-Doudoroff Pathway in Rhizobium leguminosarum bv. trifolii SRDI565 (2020)

Rhizobia are nitrogen-fixing bacteria that engage in symbiotic relationships with plant hosts but can also persist as free-living bacteria in the soil and rhizosphere. Here, we show that free-living <i>Rhizobium leguminosarum</i> SRDI565 can grow on the sulfosugar sulfoquinovose (SQ) or the related glycoside SQ-glycerol using a sulfoglycolytic Entner-Doudoroff (sulfo-ED) pathway, resulting in production of sulfolactate (SL) as the major metabolic end product. Comparative proteomics supports the involvement of a sulfo-ED operon encoding an ABC transporter, sulfo-ED enzymes, and an SL exporter. Consistent with an oligotrophic lifestyle, proteomics data revealed little change in expression of the sulfo-ED proteins during growth on SQ versus mannitol, a result confirmed through biochemical assay of sulfoquinovosidase activity in cell lysates. Metabolomics analysis showed that growth on SQ involves gluconeogenesis to satisfy metabolic requirements for glucose-6-phosphate and fructose-6-phosphate. Metabolomics analysis also revealed the unexpected production of small amounts of sulfofructose and 2,3-dihydroxypropanesulfonate, which are proposed to arise from promiscuous activities of the glycolytic enzyme phosphoglucose isomerase and a nonspecific aldehyde reductase, respectively. The discovery of a rhizobium isolate with the ability to degrade SQ builds our knowledge of how these important symbiotic bacteria persist within soil.<b>IMPORTANCE</b> Sulfonate sulfur is a major form of organic sulfur in soils but requires biomineralization before it can be utilized by plants. Very little is known about the biochemical processes used to mobilize sulfonate sulfur. We show that a rhizobial isolate from soil, <i>Rhizobium leguminosarum</i> SRDI565, possesses the ability to degrade the abundant phototroph-derived carbohydrate sulfonate SQ through a sulfoglycolytic Entner-Doudoroff pathway. Proteomics and metabolomics demonstrated the utilization of this pathway during growth on SQ and provided evidence for gluconeogenesis. Unexpectedly, off-cycle sulfoglycolytic species were also detected, pointing to the complexity of metabolic processes within cells under conditions of sulfoglycolysis. Thus, rhizobial metabolism of the abundant sulfosugar SQ may contribute to persistence of the bacteria in the soil and to mobilization of sulfur in the pedosphere.
Increasing the density of passive photonic-integrated circuits via nanophotonic cloaking (2016)

Photonic-integrated devices need to be adequately spaced apart to prevent signal cross-talk. This fundamentally limits their packing density. Here we report the use of nanophotonic cloaking to render neighbouring devices invisible to one another, which allows them to be placed closer together than is otherwise feasible. Specifically, we experimentally demonstrated waveguides that are spaced by a distance of ∼λ<sub>0</sub>/2 and designed waveguides with centre-to-centre spacing as small as 600 nm (<λ<sub>0</sub>/2.5). Our experiments show a transmission efficiency >-2 dB and an extinction ratio >15 dB over a bandwidth larger than 60 nm. This performance can be improved with better design algorithms and industry-standard lithography. The nanophotonic cloak relies on multiple guided-mode resonances, which render such devices very robust to fabrication errors. Our devices are broadly complimentary-metal-oxide-semiconductor compatible, have a minimum pitch of 200 nm and can be fabricated with a single lithography step. The nanophotonic cloaks can be generally applied to all passive integrated photonics.
Regiospecific and Stereoselective Syntheses of (±) Morphine, Codeine, and Thebaine via a Highly Stereocontrolled Intramolecular 4 + 2 Cycloaddition Leading to a Phenanthrofuran System (2009)

Total syntheses of the morphine alkaloids are described that use a direct stereoselective formation of the phenanthrofuran system via an intramolecular 4 + 2 cycloaddition of a diene tethered to the 4-position of a 7-methoxybenzofuran-3-carboxylic acid ester.
Urinary Tract Infection (1992)

No AccessJournal of Urology1 Oct 1992Urinary Tract Infection Anthony J. SchaefferM.D. Anthony J. SchaefferAnthony J. Schaeffer More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)36911-2AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail © 1992 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 148Issue 4October 1992Page: 1370-1372 Advertisement Copyright & Permissions© 1992 by The American Urological Association Education and Research, Inc.MetricsAuthor Information Anthony J. Schaeffer More articles by this author Expand All Advertisement PDF downloadLoading ...
Analysis of radiation from two separate axisymmetric horns using the method of moments (2003)

A method of moments (MoM) technique is described for analyzing the radiation from two parallel axisymmetric horns whose apertures are non-coplanar. Using the equivalence principle and appropriate boundary conditions, a set of integral equations is obtained with currents on the horn surfaces as the unknowns. These integral equations are solved by the MoM to yield the surface currents. The radiation patterns of the two horns as well as the coupling between them are calculated from these surface currents. Numerical results are presented for a pair of axisymmetric horns.
Analysis of radiophotoluminescence center formation mechanism in Ag-doped phosphate glasses (2018)

Ag-doped phosphate glasses have widely been used as radiophotoluminescence (RPL) dosimeters. However, the RPL center formation process is not fully understood. In this study, we investigated the RPL center formation process in Ag-doped Na–Al phosphate glasses. We observed that two RPL centers (Ag0 and Ag2+) were formed at temperatures higher than 100 and 250 K, respectively. In addition, activation energies of their formation were estimated to be 20 and 267 meV, respectively. These results suggest that the electron transfer process is not a simple thermally activated process.
Quantitative Kinetic Analyses of Histone Turnover Using Imaging and Flow Cytometry (2020)

Dynamic histone changes occur as a central part of chromatin regulation. Deposition of histone variants and post-translational modifications of histones are strongly associated with properties of chromatin status. Characterizing the kinetics of histone variants allows important insights into transcription regulation, chromatin maintenance and other chromatin properties. Here we provide a protocol of quantitative and sensitive approaches to test the timing of incorporation and dissociation of histones using a two-color SNAP-labeling system, labelling pre-existing and newly-incorporated histones distinctly. Together with cell cycle synchronization methods and cell cycle markers, this approach enables a pulse-chase analysis to determine the turnover of histone variants during the cell cycle, detected using imaging or flow cytometry methods at single cell resolution. As well as testing global histone turnover, cell cycle-dependent cellular localization of histone variants can be also addressed using imaging approaches.
Extracting health-related causality from twitter messages using natural language processing (2019)

Twitter messages (tweets) contain various types of topics in our daily life, which include health-related topics. Analysis of health-related tweets would help us understand health conditions and concerns encountered in our daily lives. In this paper we evaluate an approach to extracting causalities from tweets using natural language processing (NLP) techniques. Lexico-syntactic patterns based on dependency parser outputs are used for causality extraction. We focused on three health-related topics: “stress”, “insomnia”, and “headache.” A large dataset consisting of 24 million tweets are used. The results show the proposed approach achieved an average precision between 74.59 to 92.27% in comparisons with human annotations. Manual analysis on extracted causalities in tweets reveals interesting findings about expressions on health-related topic posted by Twitter users.
Safety evaluation of the food enzyme with β‐glucanase and β‐xylanase activities from the Trichoderma reesei strain DP‐Nya67 (2020)

Abstract The food enzyme with β‐glucanase and β‐xylanase (4‐β‐d‐xylan xylanohydrolase, EC 3.2.1.8) activities is produced with the non‐genetically modified Trichoderma reesei (strain DP‐Nya67) by DuPont. The food enzyme is intended to be used in brewing processes, grain treatment for the production of starch and gluten fractions, and distilled alcohol production. Since residual amounts of the food enzyme are removed by distillation and during grain treatment, dietary exposure was only calculated for brewing processes. Based on the maximum recommended use levels for brewing processes, dietary exposure to the food enzyme–Total Organic Solids (TOS) was estimated to be up to 4.585 mg TOS/kg body weight (bw) per day. Since the compositional data provided was insufficient to characterise the food enzyme batches used for toxicological testing, their suitability for use in the toxicological tests could not be established. As result, the toxicological studies provided were not further considered by the Panel. Similarities of the amino acid sequences to those of known allergens were searched and no matches were found. The Panel considered that, under the intended conditions of use, the risk of allergic sensitisation and elicitation reactions by dietary exposure cannot be excluded, but the likelihood to occur is considered to be low. In the absence of compositional data sufficient to characterise the food enzyme batches used for toxicological testing, the Panel is unable to complete its assessment of the safety of the food enzyme.
Transitioning from micro to nano-photonics with Photonic Crystal Fibers (2009)

In the past 10 years Photonic Crystal Fibers (PCFs) made a rapid transition from the novelty research item into the commercially available product. Unlike standard optical fibers, PCFs feature very complex transverse geometries that contain a large number of microand nano-sized voids or layers. It is the complexity of the fiber crossection that allows to design the fiber very unusual optical properties. Proposed applications of the PCFs are numerous and among others include: photonic bandgap fibers for transmission of high power mid-IR light [1], bio-compatible and bio-degradable microstructured fibers for medical applications [2,3], high numerical aperture microstructured fibers for efficient light collection [4], high bit rate data communication [5], photonic bandgap fibers for esthetic illumination and photonic textiles [6,7,8], subwavelength microstructured fibers for low-loss transmission of the mid-IR and THz light [9], as well as metallized and photonic bandgap fibers for resonant sensing applications [10,11].
Analyzing Engineered Nanoparticles using Photothermal Infrared Spectroscopy (2016)

Nanoparticles, particles having one or more dimensions smaller than 100 nm, show novel properties and functions that differ significantly from those of their corresponding bulk counterpart. Due to their small size and large surface to volume ratio they can e.g. diffuse easily and be highly reactive. To facilitate occupational safety and health there is a need to develop instruments to monitor and analyze nanoparticles in the industry, research and urban environments. The aim of this Ph.D. project was to develop new sensors that can analyze engineered nanoparticles. Two sensors were studied: (i) a miniaturized toxicity sensor based on electrochemistry and (ii) a photothermal spectrometer based on tensile-stressed mechanical resonators (string resonators). Miniaturization of toxicity sensor targeting engineered nanoparticles was explored. This concept was based on the results of the biodurability test using redox activity measurements. With a new setup adapted to miniaturization, stable pH was achieved, platinum was found to be more suitable than gold for open circuit potential-time measurements, miniaturized platinum working electrodes and quasi silver/silver chloride reference electrodes were fabricated, and Gambles solution with dispersed iron oxide nanoparticles showed lowered potential as expected. Despite the potential of this concept instability and lack of reproducibility continued to be an unneglectable issue. The concept of utilizing string resonators for photothermal spectroscopy was, for the first time, studied in details both theoretically and experimentally. The string-based photothermal spectrometer consists of a string resonator on which an analyte is collected. Wavelength-dependent absorption by the analyte leads to heating of the string which is reflected in its resonance frequency. This setup allows for spectroscopic measurement of the analyte. An analytical model describing the resonance frequency of a string resonator locally heated was developed. The developed model was in agreement with FEM simulations and experimental results. Theoretical and experimental work lead to a set of design rules for the responsivity of the string-based photothermal spectrometer. Responsivity is maximized for a thin, narrow and long string irradiated by high power radiation. Various types of nanoparticles and binary mixtures of them were successfully detected and analyzed. Detection of copper-chelation of the antidiabetic drug metformin was demonstrated as well. The estimated detection limit for the developed system is an analyte with a mass of ∼150 ag (1 ag = 10-18 g). In short, it has been demonstrated that the string-based photothermal spectrometer is a promising technique for nanoparticle detection and analysis.
TAFIM: Targeted Adversarial Attacks against Facial Image Manipulations (2021)

Face manipulation methods can be misused to affect an individual's privacy or to spread disinformation. To this end, we introduce a novel data-driven approach that produces image-specific perturbations which are embedded in the original images. The key idea is that these protected images prevent face manipulation by causing the manipulation model to produce a predefined manipulation target (uniformly colored output image in our case) instead of the actual manipulation. In addition, we propose to leverage differentiable compression approximation, hence making generated perturbations robust to common image compression. In order to prevent against multiple manipulation methods simultaneously, we further propose a novel attention-based fusion of manipulation-specific perturbations. Compared to traditional adversarial attacks that optimize noise patterns for each image individually, our generalized model only needs a single forward pass, thus running orders of magnitude faster and allowing for easy integration in image processing stacks, even on resource-constrained devices like smartphones.
The Role of Driver Assistance Systems in a Future Traffic Scenario (2006)

It is shown in how far driver assistance systems can contribute to enhance the overall traffic safety. Thereby it must be considered as a goal to increase the performance of active safety systems in the scope of an integrated approach, allowing to realize a variety of interactions between the three elements involved in a traffic scenario, say the driver, the vehicle and the driving environment. Focus is pointed on the related technology, the inherent system complexity and aspects of customer acceptance.
Oncolytic virotherapy for small-cell lung cancer induces immune infiltration and prolongs survival (2019)

Oncolytic virotherapy has been proposed as an ablative and immunostimulatory treatment strategy for solid tumors that are resistant to immunotherapy alone; however, there is a need to optimize host immune activation using preclinical immunocompetent models in previously untested common adult tumors. We studied a modified oncolytic myxoma virus (MYXV) that shows high efficiency for tumor-specific cytotoxicity in small-cell lung cancer (SCLC), a neuroendocrine carcinoma with high mortality and modest response rates to immune checkpoint inhibitors. Using an immunocompetent SCLC mouse model, we demonstrated the safety of intrapulmonary MYXV delivery with efficient tumor-specific viral replication and cytotoxicity associated with induction of immune cell infiltration. We observed increased SCLC survival following intrapulmonary MYXV that was enhanced by combined low-dose cisplatin. We also tested intratumoral MYXV delivery and observed immune cell infiltration associated with tumor necrosis and growth inhibition in syngeneic murine allograft tumors. Freshly collected primary human SCLC tumor cells were permissive to MYXV and intratumoral delivery into patient-derived xenografts resulted in extensive tumor necrosis. We confirmed MYXV cytotoxicity in classic and variant SCLC subtypes as well as cisplatin-resistant cells. Data from 26 SCLC human patients showed negligible immune cell infiltration, supporting testing MYXV as an ablative and immune-enhancing therapy.
Supplementary Table S5 from Bacterial-Driven Inflammation and Mutant &lt;i&gt;BRAF&lt;/i&gt; Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy (2023)

&lt;p&gt;Differential expression (DESeq2) tables of RNAseq analysis for tumors collected from PDL1 treatment experiment.&lt;/p&gt;
Investigation of static and quasi-static fields inherent to the pulsed FDTD method (2002)

Demonstrates that trailing dc offsets, which can affect E- or H-fields in finite-difference time-domain simulations, are physically correct static solutions of Maxwell's equations instead of being numerically induced artifacts. It is shown that they are present on the grid when sources are used, which generates nondecaying charges. Static solutions are investigated by exciting electric and magnetic dipoles models with suitable waveforms.
IBM’s Next Generation POWER Processor (2019)

This article consists of a collection of slides from the author's conference presentation.
Transient Turbine Engine Modeling with Hardware-in-the-Loop Power Extraction (PREPRINT) (2008)

Abstract : Increasingly high aircraft power demands require that the interactions between an aircraft's electrical subsystem and the engine subsystem be considered in dynamic, system-level tests. Traditionally, system-level dynamics have only been captured in completely assembled aircraft systems. Component-level or subsystem-level optimization is no longer appropriate because highly interdependent dynamics between subsystems only become apparent during system-level analysis. In an effort to mitigate program risk, enable system-level optimization, and reduce the high cost of testing integrated power and propulsion systems in an altitude-simulating wind tunnel, alternatives such as modeling and simulation can be utilized. Synchronizing and coupling simulations of vastly different time scales is possible; however, the resulting system simulation usually runs very slowly. For this reason, hardware-in-the-loop (HIL) is an ideal test platform where simulations and hardware components can be integrated for system-level testing when time scales are drastically different or actual hardware prototype components are available.