gebhart/patrepeval huggingface dataset:
ZIKA-001: Safety and Immunogenicity of an Engineered DNA Vaccine Against ZIKA virus infection (2017)

Abstract Background While Zika virus (ZIKV) infection is typically self-limited, congenital birth defects and Guillain-Barré syndrome are well-described. There are no therapies or vaccines against ZIKV infection. Methods ZIKA-001 is a phase I, open label, clinical trial designed to evaluate the safety, side effect profile, and immunogenicity of a synthetic, DNA vaccine (GLS-5700) targeting the pre-membrane+envelope proteins (prME) of the virus. Two groups of 20 participants received GLS-5700 at one of two dose levels: 1 mg or 2 mg DNA/dose at 0, 4, and 12 weeks. Vaccine was administered as 0.1 or 0.2 ml (1 or 2 mg) intradermal (ID) injection followed by electroporation (EP) with the CELLECTRA®-3P device Results The median age of the 40 participants was 38 (IQR 30–54) years; 60% were female 30% Latino and 78% white. No SAEs have been reported to date. Local minor AEs were injection site pain, redness, swelling and itching that occurred in half of the participants. Systemic adverse events were rare and included headache, myalgias, upper respiratory infections, fatigue/malaise and nausea. Four weeks after the first dose 25% vs. 60% of the participants in the 1 mg and 2 mg dose seroconverted. By week 6, 2 weeks after the second dose, the response was 65 and 84% respectively and 2 weeks after the third dose all participants in both dosing groups developed antibodies. At the end of the vaccination period over 60% of vaccinated person neutralized Zika virus in a vero cell assay and greater than 80% on neuronal cell targets. The protective efficacy of the antibodies generated by the vaccine was evaluated in the lethal IFNAR−/− mouse model. After the intraperitoneal administration of 0.1 ml of either baseline, week 14 serum or PBS the animals were challenged with 106 PFUs of ZIKV PR209 isolate. Whereas animals administered PBS (control) or baseline serum succumbed after a median of 5 days, those pretreated with week 14 serum from study participants survived suggesting that the humoral response generated by the vaccine is protective in this model. Conclusion Our trial shows for the first time in humans the safety and immunogenicity of an engineered DNA encoding consensus viral protein against ZIKV. Future studies will evaluate the effectiveness of the vaccine. Disclosures C. C. Roberts, GeneOne: Member, Salary. S. White, GeneOne: Member, Salary. A. S. Khan, Inovio: Employee and Shareholder, Salary and Stock. J. Boyer, Inovio: Employee and Shareholder, Salary and Stock. Y. K. Park, GeneOne: Board Member, CEO and Employee, Salary and Stock. S. Trottier, Canadian Institutes of Health Research: Investigator, Research grant. C. Remigio, GeneOne: Employee and Shareholder, Salary and Stock. G. P. Kobinger, GeneOne: Grant Investigator and Scientific Advisor, Grant recipient and Research support. D. Weiner, GeneOne: Grant Investigator and Scientific Advisor, Grant recipient, Licensing agreement or royalty and Stock. J. Maslow, GeneOne: Employee, Salary and Stock.
Myocardial Stiffness Evaluation Using Noninvasive Shear Wave Imaging in Healthy and Hypertrophic Cardiomyopathic Adults (2018)

MS was found to increase with age in healthy adults and was significantly higher in HCM-HFpEF patients. Myocardial SWI has the potential to become a clinical tool for the diagnostic of diastolic dysfunction. (Non-invasive Evaluation of Myocardial Stiffness by Elastography [Elasto-Cardio]; NCT02537041).
Effect of Variable Gravity on Evaporation of Binary Fluids in a Capillary Pore Evaporator (1996)

The research project focuses on experimental investigation of the capillary-pumped evaporative heat transfer phenomenon. The objective is to examine whether the heat transfer and stability of a heated meniscus in a capillary pore can be enhanced by adding trace amounts of a non-volatile solute to a solvent and to understand the changes that occur. The experimental setup consists of a single pore evaporator connected to a reservoir which supplies liquid to the evaporator. In addition to the experiments of capillary-pumped evaporation, a parallel experimental study has been conducted to systematically investigate the effects of gravity as well as the effects of bulk composition on the heat transfer characteristics of evaporating binary thin films near the contact line region along an inclined heated surface. To investigate the buoyancy effects on evaporation along an inclined heated surface, the angle of inclination from a horizontal plane was varied fro 15 C to 90 C. An optimum concentration between 0.5% and 1% decane in pentane/decane solutions has been demonstrated at different angles of inclination. Improved heat transfer was found for the geometry with the smallest angle of inclination of 15 degrees. In addition, flow visualization has revealed that at low inclination angles effective heat transfer takes place primarily due to an extension of the thin film near the contact line. At these low inclination angles, the optimum concentration is associated with enhanced wetting characteristics and reduced thermocapillary stresses along the interface.
Synthesis and structure-activity study of protease inhibitors. IV. Amidinonaphthols and related acyl derivatives. (1985)

Various amidinonaphthols and their acyl derivatives were synthesized and evaluated for inhibitory activities against trypsin, plasmin, kallikrein, thrombin, Clr and Cls, as well as against in vitro complement-mediated hemolysis. 6-Amidino-2-naphthyl 4-guanidinobenzoate (74, FUT-175) was found to have potent inhibitory activities, particularly against trypsin (IC50 : 0.02 μM), Clr (IC50 : 0.1 μM) and Cls (IC50 : 0.02 μM), and to be highly effective in inhibiting the complement-mediated hemolysis (IC50 : 0.03μM). FUT-175, furthermore, showed considerable effectiveness in the systemic Forssman shock reaction, in which involvement of the complement system as the pathogenetic factor is well established.
N-Heterocyclic Carbenes for the Organocatalytic Ring-Opening Polymerization of ε-Caprolactone (2009)

We report the synthesis of poly(ε-caprolactone) utilizing N-heterocyclic carbene (NHC) organocatalysts. Sterically unencumbered NHCs were found to be highly effective for the living ring-opening polymerization of ε-caprolactone under mild conditions. The NHCs were able to produce poly(ε-caprolactone)s with controlled molecular weights, low polydispersities, and well-defined end groups derived from the alcohol initiator. Star-shaped poly(ε-caprolactone)s with three and four arms were prepared using NHC organocatalysts and characterized by 1H NMR and GPC.
Reporting Results (2008)

This brief guide is ideal for science and engineering students and professionals to help them communicate technical information clearly, accurately, and effectively. The focus is on the most common communication forms, including laboratory reports, research articles, and oral presentations, and on common issues that arise in classroom and professional practice. This book will be especially useful to students in a first chemistry or physics laboratory course. Advanced courses will often use the same formatting as required for submission to technical journals or for technical report writing, which is the focus of this book. Good communication habits are appropriate in all forms of technical communication. This book will help the reader develop effective communication skills. It is also ideal as a reference on stylistic and grammar issues throughout a technical career. Unlike most texts, which concentrate on writing style, this book also treats oral presentations, graphing, and analysis of data.
Obesity-Associated Hepatic Steatosis, Somatotropic Axis Impairment and Ferritin Levels are Strong Predictors of COVID-19 Severity (2023)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Anti-inflammatory potential of saponins derived from cultured wild ginseng roots in lipopolysaccharide-stimulated RAW 264.7 macrophages (2015)

Ginseng, namely the root of Panax ginseng Meyer, is a well-known traditional medicine that has been used in Asian countries for thousands of years. Ginseng saponins have been shown to exert a variety of prominent pharmacological effects in a number of diseases. The aim of the present study was to identify the anti-inflammatory effects of total saponins extracted from cultured wild ginseng roots (TSWG) on lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages. An elevated production of nitric oxide (NO) was detected in the RAW 264.7 cells in response to stimulation with LPS, as shown by NO detection assay using Griess reagent. However, pre-treatment with TSWG inhibited the production of NO through the suppression of inducible NO synthase gene expression. Furthermore, the LPS-induced gene expression and production of tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) were significantly reduced by treatment with TSWG, as shown by ELISA, and western blot analysis and RT-PCR, respectively. In the LPS-stimulated RAW 264.7 cells, nuclear factor-κB (NF-κB) was translocated from the cytosol to the nucleus, while pre-treatment with TSWG induced the sequestration of NF-κB in the cytosol through the inhibition of the inhibitor of κB degradation, as shown by immunofluorescence staining. TSWG also contributed to the downregulation of mitogen-activated protein kinases and Akt in the LPS-stimulated RAW 264.7 cells. Additionally, in the TSWG-treated RAW 264.7 cells, we observed the activation of nuclear factor (erythroid-derived 2)-like 2 and an increase in heme oxygenase-1 expression; these effects were associated with the inhibition of the generation of reactive oxygen species. The results from the present study indicate that TSWG exerts anti-inflammatory and antioxidant effects, suggesting that TSWG may be an effective therapeutic agent for inflammatory diseases and prevent cellular damage induced by oxidative stress.
A Comparison of Strategies for Obtaining High-Resolution NMR Spectra of Quadrupolar Nuclei (1996)

Abstract A comparison of high-resolution NMR methods for quadrupolar nuclei is presented. The samples studied are pure and modified boron oxide glasses, and the boron NMR spectra are recorded using three different experiments capable of high resolution: Double Rotation, Dynamic Angle Spinning, and Multiple-Quantum Magic Angle Spinning. Resolution of the similar ring and nonring boron sites in these glasses, in the presence of disorder, provides a realistic study of the strengths and limitations of these experiments. Conclusions about the relative applicability of these experiments in different situations are presented.
Image Mosaic Method Based on SIFT Features of Line Segment (2014)

This paper proposes a novel image mosaic method based on SIFT (Scale Invariant Feature Transform) feature of line segment, aiming to resolve incident scaling, rotation, changes in lighting condition, and so on between two images in the panoramic image mosaic process. This method firstly uses Harris corner detection operator to detect key points. Secondly, it constructs directed line segments, describes them with SIFT feature, and matches those directed segments to acquire rough point matching. Finally, Ransac method is used to eliminate wrong pairs in order to accomplish image mosaic. The results from experiment based on four pairs of images show that our method has strong robustness for resolution, lighting, rotation, and scaling.
Structural Mimicry of the α-Helix in Aqueous Solution with an Isoatomic α/β/γ-Peptide Backbone (2011)

Artificial mimicry of α-helices offers a basis for development of protein-protein interaction antagonists. Here we report a new type of unnatural peptidic backbone, containing α-, β-, and γ-amino acid residues in an αγααβα repeat pattern, for this purpose. This unnatural hexad has the same number of backbone atoms as a heptad of α residues. Two-dimensional NMR data clearly establish the formation of an α-helix-like conformation in aqueous solution. The helix formed by our 12-mer α/β/γ-peptide is considerably more stable than the α-helix formed by an analogous 14-mer α-peptide, presumably because of the preorganized β and γ residues employed.
Non-Hermitian gyroscopes: Can exceptional points increase sensor precision? (2022)

We show that exceptional points in conservatively coupled systems can increase the quantum-limited precision of laser gyroscopes as a result of gain saturation, but that this requires recovery of the beat note by interference with an auxiliary mode, with consequences for the quantum and classical noise that depend on the particular recovery scheme.
Quantifying PON1 on HDL with nanoparticle-gated electrokinetic membrane sensor for accurate cardiovascular risk assessment (2023)

Cardiovascular disease-related deaths (one-third of global deaths) can be reduced with a simple screening test for better biomarkers than the current lipid and lipoprotein profiles. We propose using a highly atheroprotective subset of HDL with colocalized PON1 (PON1-HDL) for superior cardiovascular risk assessment. However, direct quantification of HDL proteomic subclasses are complicated by the peroxides/antioxidants associated with HDL interfering with redox reactions in enzymatic calorimetric and electrochemical immunoassays. Hence, we developed an enzyme-free Nanoparticle-Gated Electrokinetic Membrane Sensor (NGEMS) platform for quantification of PON1-HDL in plasma within 60 min, with a sub-picomolar limit of detection, 3-4 log dynamic range and without needing sample pretreatment or individual-sample calibration. Using NGEMS, we report our study on human plasma PON1-HDL as a cardiovascular risk marker with AUC~0.99 significantly outperforming others (AUC~0.6-0.8), including cholesterol/triglycerides tests. Validation for a larger cohort can establish PON1-HDL as a biomarker that can potentially reshape cardiovascular landscape.
Experimental and Numerical Investigations on Flow Losses of a U-Bend and Return Channel System for Centrifugal Compressor (2019)

Abstract The flow losses in a U-bend and return channel system of an inter stage has an important influence on the stage performance. To study the flow characteristics in such system, a pseudo-stage which consists of pseudo guide vanes, U-bend and return channel, combined with a normal stage, was designed and its performance curves were measured at different machine Mach numbers. Simultaneously, the numerical simulations, in which different data processing methods of CFD post process were adopted, were performed and the prediction accuracy was verified by comparison with the experimental results. The results indicated that the design of pseudo guide vanes provides an approximately constant flow direction at the inlet of U-bend with the variation of inlet Reynolds number, which matches the blade metal angle of the return channel well. The further analyses on the measured and numerical results showed that the loss characteristics vary with the inlet Reynolds number. When the Reynolds number is greater than a critical Reynolds number, the loss coefficient in the U-bend and return channel keeps nearly constant. The non-uniformity of flow angle and total pressure at the outlet of return channel were also illustrated and discussed.
Not Typing but Writing: Eye-based Text Entry Using Letter-like Gestures (2007)

September 3-4, 2007 Leicester, UK Not Typing but Writing: Eye-based Text Entry Using Letter-like Gestures Jacob O. Wobbrock, James Rubinstein, Michael Sawyer, and Andrew T. Duchowski The Information School University of Washington Seattle, WA 98195 USA wobbrock@u.washington.edu Department of Psychology Department of Industrial Engineering School of Computing Clemson University Clemson, SC USA 29634 {jrubins, msawyer, andrewd}@clemson.edu
Stem Cells as Tools for Studying the Genetics of Inherited Retinal Degenerations (2014)

The ability to provide early clinical intervention for inherited disorders is heavily dependent on knowledge of a patient's disease-causing mutations and the resultant pathophysiologic mechanism(s). Without knowing a patient's disease-causing gene, and how gene mutations alter the health and functionality of affected cells, it would be difficult to develop and deliver patient-specific molecular or small molecule therapies. Many believe that the field of stem cell biology holds the keys to the future development of disease-, patient-, and cell-specific therapies. In the case of the eye, which is susceptible to an extremely common late-onset degenerative disease known as age-related macular degeneration, stem cell-based therapies could increase the quality of life for millions of patients worldwide. Furthermore, autologous, patient-specific induced pluripotent stem cells could be a viable source to treat rare Mendelian retinal degenerative diseases such as retinitis pigmentosa, Stargardt disease, and Best disease, to name a few.
External cavity multiwavelength semiconductor hybrid mode-locked laser intracavity gain dynamics (2006)

The intracavity gain dynamics of an external cavity semiconductor hybrid mode-locked laser is measured under multiwavelength operation. The results show a temporal skew between pulses corresponding to different wavelength channels. A measurement of the temporal evolution of the gain reveals a slow gain depletion, avoiding carrier heating and carrier cooling, and decreasing self-phase modulation effects and gain competition between wavelength channels, making multiwavelength operation possible.
An optical deflectometer for the quantitative analysis of turbulent structures (2002)

The optical deflectometer is proposed to make turbulence measurements. The instrument, which is based on the schlieren principle, is nonintrusive and has a practically unlimited frequency response. Its novelty also lies in the fact that it produces a real image of the flowfield under study, in which optical probes may be positioned precisely. This instrument has been successfully applied in studying the turbulent mixing layers of both a low-speed CO/sub 2/ jet and highly compressible Mach 3 airjet. The results are shown to be consistent over a broad range of knife-edge cutoff settings, and are comparable to turbulence data obtained by other more standard turbulence instruments. The major limitation of the optical deflectometer, in its present embodiment, is the fact that it integrates fluctuations across the flow.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Figure 3 from Extracellular Vesicles Modulate the Glioblastoma Microenvironment via a Tumor Suppression Signaling Network Directed by miR-1 (2023)

&lt;p&gt;PDF file - 154K, FIGURE S3 related to FIGURE 4. Characterization of GBM-derived EVs.&lt;/p&gt;
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients (2022)

The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.
Optical scatter imaging of resected breast tumor structures matches the patterns of micro-computed tomography (2022)

Re-excision procedures are frequent in breast-conserving surgery due to residual tumor left behind after initial resection. Projection radiography and volumetric X-ray imaging are used to assess margin adequacy, but X-ray imaging lacks contrast between healthy, abnormal benign, and malignant fibrous tissues important for surgical decision making. The purpose of this study was to compare micro-CT and optical scatter imagery of surgical breast specimens and to demonstrate enhanced contrast to intra-tumoral morphologies and tumor boundary features revealed by optical scatter imaging. Results suggest that optical scatter imaging reveals additional tissue features that could improve margin assessment over X-ray imaging alone.
Experiences applying game theory to system design (2004)

We applied techniques from game theory to help formulate and analyze solutions to two systems problems: discouraging selfishness in multi-hop wireless networks and enabling cooperation among ISPs in the Internet. It proved difficult to do so. This paper reports on our experiences and explains the issues that we encountered. It describes the ways in which the straightforward use of results from traditional game theory did not fit well with the requirements of our problems. It also identifies an important characteristic of the solutions we did eventually adopt that distinguishes them from those available using game theoretic approaches. We hope that this discussion will help to highlight formulations of game theory which are well-suited for problems involving computer systems.