gebhart/patrepeval huggingface dataset:
Taurine chloramine inhibits NO and TNF-α production in zymosan plus interferon-γ activated RAW 264.7 cells. (2011)

Taurine is present abundantly in various tissues, especially in leukocytes embattled to foreign invaders such as microorganisms or oxidants. Taurine-chloramine (Tau-Cl) is produced from taurine at the site of inflammation via the myeloperoxidase-halide pathway in leukocytes induced by oxidants and/or infectious materials. Previously, our data demonstrated that Tau-Cl inhibited nitric oxide (NO) production and TNF-α secretion induced by lipopolysaccharide (LPS), a Toll-like receptor 4 (TLR-4) ligand or lipoarabinomannan (LAM), a TLR-2 ligand plus interferon-γ (IFN-γ) in peritoneal macrophages or RAW 264.7 cells. Zymosan, a β-glucan of yeast cell wall, is a ligand for TLR-2 and dectin-1 and stimulates macrophages to produce proinflammatory mediators such as NO and TNF-α. Based on our previous data, we examined the effect of zymosan and IFN-γ induced production of NO and TNF-α in the absence or presence of Tau-Cl or taurine using RAW 264.7 cells. Production of NO and secretion of TNF-α is increased when zymosan is combined with IFN-γ. Tau-Cl inhibited production of NO and secretion of TNF-α in zymosan plus IFN-γ activated RAW 264.7 cells in a dose-dependent manner (99% vs. 48% using 0.8mM Tau-Cl). Taurine was without effect. Nitric oxide synthase protein (iNOS), induced by zymosan plus IFN-γ, was inhibited by Tau-Cl (0.8mM) as measured using western blot analysis. NOS mRNA was inhibited by Tau-Cl at four, eight and 16 hours post activation, but not at 24 hours. TNF-α mRNA was inhibited at four hours and eight hours, but not at 16 and 24 hours. These data suggest that expression of both iNOS and TNF-α mRNAs are inhibited by treatment with Tau-Cl within four and eight hours, but not at later time points. Transient suppression of activation of RAW 264.7 cells induced by zymosan may play a critical physiological role for taurine in protecting against tissue injury from initial overt inflammation. This study indicates that tropical treatment of taurine may ameliorate inflammatory dermatoses caused by an environmental yeast or abnormal immune function.
2,3-Diaminopyridine Bradykinin B1 Receptor Antagonists (2004)

Bradykinin B1 receptor antagonists embody a potentially novel approach for the treatment of chronic pain and inflammation. A series of 2,3-diaminopyridine B1 antagonists was optimized to have sub-nanomolar affinity and good pharmacokinetic properties. Lead compounds were shown to exhibit good efficacy in rabbit in vivo models of pain and inflammation.
Run Time Approximation of Non-blocking Service Rates for Streaming Systems (2015)

Stream processing is a compute paradigm that promises safe and efficient parallelism. Modern big-data problems are often well suited for stream processing's throughput-oriented nature. Realization of efficient stream processing requires monitoring and optimization of multiple communications links. Most techniques to optimize these links use queueing network models or network flow models, which require some idea of the actual execution rate of each independent compute kernel within the system. What we want to know is how fast can each kernel process data independent of other communicating kernels. This is known as the "service rate" of the kernel within the queueing literature. Current approaches to divining service rates are static. Modern workloads, however, are often dynamic. Shared cloud systems also present applications with highly dynamic execution environments (multiple users, hardware migration, etc.). It is therefore desirable to continuously re-tune an application during run time (online) in response to changing conditions. Our approach enables online service rate monitoring under most conditions, obviating the need for reliance on steady state predictions for what are probably non-steady state phenomena. First, some of the difficulties associated with online service rate determination are examined. Second, the algorithm to approximate the online non-blocking service rate is described. Lastly, the algorithm is implemented within the open source RaftLib framework for validation using a simple microbenchmark as well as two full streaming applications.
Supplementary Figure Legend from KEAP1-Dependent Synthetic Lethality Induced by AKT and TXNRD1 Inhibitors in Lung Cancer (2023)

&lt;p&gt;PDF file, 23K.&lt;/p&gt;
Ribozymes, the first 20 years (2002)

In 1982 we reported the first catalytic RNA or ribozyme: the self-splicing intron of the Tetrahymena pre-rRNA. Additional examples of natural ribozymes were soon found, and research in the field focused on their enzymic mechanism and secondary and tertiary structure. Ribozymes identified through in vitro selection extended the repertoire of RNA catalysis. Two directions of current and future interest are the determination of atomic-resolution structures of large ribozymes by X-ray crystallography and the structural and mechanistic analysis of complexes of ribozymes with protein facilitators of their activity.
Epithelin/Granulin Precursor Expression in Human Breast Carcinoma (1999)

Abstract : Breast cancer is a major cause of morbidity and mortality in women worldwide. Breast tumors are initially estrogen-dependent but eventually become estrogen-independent and refractory to anti-estrogen therapy. Thus, it is very important to develop new insights into breast cancer. Our approach has been to analyze the cellular changes associated with highly tumorigenic properties. We have characterized a novel growth factor, PC-cell derived growth factor (PCDGF) (epithelin/granulin precursor) in human breast carcinoma cells. This application investigates the role of PCDGF in the proliferation of human breast cancer cells. In estrogen-receptor positive cells, PCDGF expression was stimulated in a dose and time-dependent fashion by estradiol and inhibited by tamoxifen. In estrogen-receptor negative cells, PCDGF was constitutively overexpressed. PCDGF acted as an autocrine growth factor both for ER(+) and ER(-) cells. Most importantly, inhibition of PCDGF expression by anti sense PCDGF cDNA transfection in ER(-) breast carcinoma led to a 90% inhibition of tumor incidence and size. These characteristics make PCDGF an important factor involved in the tumorigenicity of breast carcinoma. Future goals are to further investigate PCDGF role on the proliferation of breast cancer cells and examine PCDGF expression in human breast cancer biopsies at different stages of the disease.
Active Site Engineering of the Epoxide Hydrolase from Agrobacterium radiobacter AD1 to Enhance Aerobic Mineralization of cis-1,2-Dichloroethylene in Cells Expressing an Evolved Toluene ortho-Monooxygenase (2004)

Chlorinated ethenes are the most prevalent ground-water pollutants, and the toxic epoxides generated during their aerobic biodegradation limit the extent of transformation. Hydrolysis of the toxic epoxide by epoxide hydrolases represents the major biological detoxification strategy; however, chlorinated epoxyethanes are not accepted by known bacterial epoxide hydrolases. Here, the epoxide hydrolase from Agrobacterium radiobacter AD1 (EchA), which enables growth on epichlorohydrin, was tuned to accept cis-1,2-dichloroepoxyethane as a substrate by accumulating beneficial mutations from three rounds of saturation mutagenesis at three selected active site residues, Phe-108, Ile-219, and Cys-248 (no beneficial mutations were found at position Ile-111). The EchA F108L/I219L/C248I variant coexpressed with a DNA-shuffled toluene ortho-monooxygenase, which initiates attack on the chlorinated ethene, enhanced the degradation of cis-dichloroethylene (cis-DCE) an infinite extent compared with wild-type EchA at low concentrations (6.8 microm) and up to 10-fold at high concentrations (540 microm). EchA variants with single mutations (F108L, I219F, or C248I) enhanced cis-DCE mineralization 2.5-fold (540 microm), and EchA variants with double mutations, I219L/C248I and F108L/C248I, increased cis-DCE mineralization 4- and 7-fold, respectively (540 microm). For complete degradation of cis-DCE to chloride ions, the apparent Vmax/Km for the Escherichia coli strain expressing recombinant the EchA F108L/I219L/C248I variant was increased over 5-fold as a result of the evolution of EchA. The EchA F108L/I219L/C248I variant also had enhanced activity for 1,2-epoxyhexane (2-fold) and the natural substrate epichlorohydrin (6-fold).
Supplementary table 5 from Low Cancer Stem Cell Marker Expression and Low Hypoxia Identify Good Prognosis Subgroups in HPV(−) HNSCC after Postoperative Radiochemotherapy: A Multicenter Study of the DKTK-ROG (2023)

&lt;p&gt;Univariate analyses of CSC markers. HR = hazard ratio; 95% CI = 95 percent confidence interval.&lt;/p&gt;
Multi-input transient fuel control with auto-calibration (2007)

Most engine transient fuel control methods use the mass of injected fuel to drive the compensator dynamics. This works well in conventional engines because several other main factors that affect the fuel puddle, such as mass air-flow and manifold air pressure (MAP), are coupled closely with the injected fuel. In variable cam timing (VCT) engines, MAP and mass of injected fuel are decoupled to the point that they may move in opposite directions under certain conditions. To circumvent this problem we propose using MAP as the second input to compensate for fuel puddle dynamics. The structure of the new compensator is derived from a detailed model of the puddle dynamics. Further, we provide a method to automatically fit the new model and compensator parameters from dynamometer data. The model and compensator performance is illustrated by simulations and experiments.
Surface and Bulk Diffusion of H218O on Single-Crystal H216O Ice Multilayers (1996)

The surface and bulk diffusion of H218O on single-crystal H216O ice multilayers grown epitaxially on Ru(001) were measured using laser-induced thermal desorption (LITD) techniques. Low-energy electron diffraction studies confirmed that the ice multilayers on Ru(001) were crystalline to thicknesses of at least 105 bilayers (i.e., ∼385 Å). Measurements of H218O surface diffusion on the crystalline ice multilayers were performed using a scanning LITD method with mass spectrometric detection. Using a mask, one bilayer of isotopically-labeled H218O was deposited on half of a crystalline H216O ice multilayer. LITD measurements were then used to scan the coverage profile as a function of diffusion time at 140 K. No H218O LITD signals were observed on the masked half of the crystal for diffusion times as long as 60 min. These measurements were consistent with an upper limit for H218O surface diffusion of DS ≤ 5 × 10-9 cm2/s at 140 K. The lack of measurable surface diffusion may indicate that H218O is diffusing into the underlying ice multilayer. H2O bulk diffusion was investigated with a novel technique utilizing a combination of isothermal desorption/depth profiling and LITD probing. In this new method, a single bilayer of H218O was deposited on a crystalline H216O multilayer. Isothermal desorption with zero-order desorption kinetics was then employed to depth profile the ice multilayer. LITD was concurrently used to monitor the isotopes remaining in the multilayer versus time. If the ice film desorbs in a layer-by-layer fashion with zero-order desorption kinetics and no interlayer mixing, the bilayer of H218O should desorb from the ice surface in ∼7 s at 160 K. However, H218O was monitored during the desorption of the entire H216O ice multilayer. This behavior indicates that H218O is diffusing readily into the underlying ice multilayer. The bulk diffusion coefficient of H218O into crystalline ice multilayers of various thicknesses was determined to be DB = 1.5(±0.5) × 10-15 cm2/s at 160 K. Sandwich experiments with stacked multilayers confirmed that H218O was diffusing into the ice bulk with no influence from a possible “liquid-like” layer on the ice surface. An Arrhenius analysis of the temperature-dependent bulk diffusion coefficients yielded an activation energy of EB = 16.7 ± 1.6 kcal/mol and a preexponential of D0 = 9.7(±0.5) × 107 cm2/s. This diffusion activation energy is within the experimental error of some of the previous measurements at higher temperatures close to the ice melting point. When the Arrhenius diffusion parameters are extended to the stratospheric temperature range of 180−210 K, the residence time τ of a H2O molecule on the ice surface ranges from 5.4 × 10-3 s to 6.8 × 10-6 s, respectively, before diffusion into the underlying ice bulk. These diffusion measurements indicate very dynamic ice surfaces at stratospheric temperatures that may facilitate the incorporation of reactants into stratospheric clouds.
Transceiver optimization for interference MIMO relay systems using the structure of relay matrix (2015)

In this paper, we study the transceiver design problem for amplify-and-forward interference multiple-input multiple-output (MIMO) relay communication systems, where multiple transmitter-receiver pairs communicate simultaneously with the aid of a relay node. We aim at minimizing the mean-squared error (MSE) of the signal waveform estimation at the receivers subjecting to transmission power constraints at the transmitters and the relay node. Since the transceiver optimization problem is nonconvex with matrix variables, the globally optimal solution is intractable to obtain. To overcome the challenge, we propose an iterative transceiver design algorithm where the transmitter, relay, and receiver matrices are optimized iteratively by exploiting the optimal structure of the relay precoding matrix. Simulation results show that the proposed algorithm performs better than the existing technique in terms of both MSE and bit-error-rate.
Positron Emission Tomography and Neuropsychological Studies in Dementia (2020)

This chapter reviews Positron Emission Tomography (PET) studies of the normal brain as well as Alzheimer’s Disease (AD) in relationship to neuropsychological functions. We will examine a pattern analysis of PET AD scans and demonstrate how these PET AD scans show a characteristic profile in comparison to other types of dementias. Dramatic improvements in our ability to image the human brain in vivo have expanded researchers’ skills in the early diagnosis of AD. One of these techniques, PET, has yielded new significant neurophysiological and cognitive data that shows a distinctive profile for assisting in a diagnosis of AD. PET scanners recently emerged through the integration of several fields of science. Physicists and nuclear engineers developed the essential hardware to measure radioactivity. Physiologists, chemists and statisticians developed models to measure the uptake and decay of radionuclides in brain tissues. Medical doctors and neuropsychologists then developed scanning procedures, experimental design and interpretation of the obtained neurophysiological and neuropsychological data.
Aberration free refocusing for high numerical aperture microscopy (2008)

In this paper, we present a novel technique that permits sectioning microscopes to refocus and acquire images from a large range of specimen depths without introducing movements near the specimen. In contrast to other such remote focusing methods, this technique avoids systematic aberrations that degrade image quality when imaging planes away from the optimal focal plane. Furthermore, the specific geometry that is employed in this work enables refocusing to be carried out at high speed and hence permits, for the first time, a number of dynamical biological processes to be observed. Although this technique can be applied to any optical imaging system, it is particularly suited to the case of high numerical aperture microscope systems. To demonstrate this we present results from two prototype systems built in our laboratory based on a slit scanning confocal fluorescence microscope and a two photon fluorescence microscope.
Competitive Hydrodeoxygenation and Hydrodenitrogenation Reactions in the Hydrotreatment of Fatty Acid and Amine Mixtures (2023)

Abstract Understanding how hydrotreating oxygen-containing compounds together with nitrogen-containing compounds affects the reactivity and selectivity is relevant for processing renewable feedstocks. In this work, competitive hydrodeoxygenation (HDO) and hydrodenitrogenation (HDN) reactions were studied by co-hydrotreating palmitic acid (C16 acid) and tetradecylamine (C14 amine) over a Pt/ZrO 2 catalyst in a batch reactor. HDO proceeded faster than HDN in the studied system, and the deoxygenation reactions were found to have an inhibitory effect on HDN. Co-hydrotreating the C16 acid and the C14 amine expanded the reaction network from the individual HDO and HDN networks and changed the prevailing reaction pathways, initially in favor of oxygen removal. The formation of heavy secondary amides and amines through condensation reactions became increasingly favored as the share of C16 acid in the feed increased. For a given conversion level, the condensation product selectivity was observed to increase as the reaction temperature was decreased, whereas increasing the reaction temperature promoted the formation of the desired paraffins. This work described the ease of HDO compared to HDN, the role of condensation reactions in the co-hydrotreating reaction network, and the inhibitory effect on HDN thereof.
VEGF-C induced angiogenesis preferentially occurs at a distance from lymphangiogenesis (2007)

These results both demonstrate a dependence of VEGF-C-mediated angiogenesis on lymphatic vascular networks and indicate that the mechanism of VEGF-C-mediated lymphangiogenesis is different from that of classical angiogenic mechanisms.
Lignin-based Hydrogel for Water Retention in Silt Loam Soil (2021)

<b><sc>Abstract.</sc></b> Superabsorbent polymers (hydrogels) have been proposed as soil amendments to increase plant available water in soil. Synthetic hydrogels have been widely investigated for use in agriculture. Due to increasing environmental concerns related to synthetic hydrogels, hydrogels from natural sources which are more degradable and biocompatible compared to synthetic hydrogels are being developed. Here, a lignin-based hydrogel was synthesized. The swelling properties of the hydrogel were determined in different aqueous solutions and in soil. Fourier Transform Infrared (FTIR) spectroscopy was used to characterize the hydrogel. Using the hanging water column and the pressure plate method, the soil water retention curve was measured from a soil water pressure head range of -3 cm to the permanent wilting point i.e -15,000 cm for a silt loam soil. For this purpose, the soil was amended with the lignin-based hydrogel at rates of 0, 0.1 and 0.3% (w/w) concentration. Results of the swelling properties of the lignin-based hydrogel show a maximum swelling ratio of 2030% of the hydrogel‘s original mass in deionized water, 1092% in tap water, and 825% in the 0.9% NaCl solution. FTIR spectra of the hydrogel show the presence of O-H bonds which come from the lignin structure and render the hydrogel reactive to water molecules causing swelling as a result. Lignin hydrogel treatment significantly increased water retention near saturation compared to a control treatment of soil with no added lignin hydrogel.
Hypothalamically induced emotional behavior and immunological changes in the cat (2001)

Numerous animal studies on the correlation between stress and immunity have been performed but few such studies have been made concerning the relationship between various kinds of stress-related emotional behavior and immunological changes. Electrical stimulation of the hypothalamus in cats elicits various emotional behaviors such as restlessness, defensive attack, defensive retreat and quiet biting attack. We examined changes in the lymphocyte proliferative responses and plasma cortisol level which accompanied such emotional behavior. A significant increase in plasma cortisol was observed in the restlessness, defensive attack and defensive retreat groups, but not in the quiet biting attack or non-response (control) groups. A significant increase in the lymphocyte proliferative responses to phytohemagglutinin (PHA) was observed in the restlessness and defensive attack groups but not in the defensive retreat, quiet biting attack or non-response groups. These results suggest that various kinds of emotional behavior appear to be differentially correlated with the lymphocyte proliferative responses, while also being differentially correlated with the plasma cortisol concentration. Because the changes in lymphocyte responses and plasma cortisol did not always completely correlate with one another, the changes in the lymphocyte responses are not considered to be influenced by plasma cortisol alone.
Local small airway epithelial injury induces global smooth muscle contraction and airway constriction (2011)

Small airway epithelial cells form a continuous sheet lining the conducting airways, which serves many functions including a physical barrier to protect the underlying tissue. In asthma, injury to epithelial cells can occur during bronchoconstriction, which may exacerbate airway hyperreactivity. To investigate the role of epithelial cell rupture in airway constriction, laser ablation was used to precisely rupture individual airway epithelial cells of small airways (<300-μm diameter) in rat lung slices (∼250-μm thick). Laser ablation of single epithelial cells using a femtosecond laser reproducibly induced airway contraction to ∼70% of the original cross-sectional area within several seconds, and the contraction lasted for up to 40 s. The airway constriction could be mimicked by mechanical rupture of a single epithelial cell using a sharp glass micropipette but not with a blunt glass pipette. These results suggest that soluble mediators released from the wounded epithelial cell induce global airway contraction. To confirm this hypothesis, the lysate of primary human small airway epithelial cells stimulated a similar airway contraction. Laser ablation of single epithelial cells triggered a single instantaneous Ca(2+) wave in the epithelium, and multiple Ca(2+) waves in smooth muscle cells, which were delayed by several seconds. Removal of extracellular Ca(2+) or decreasing intracellular Ca(2+) both blocked laser-induced airway contraction. We conclude that local epithelial cell rupture induces rapid and global airway constriction through release of soluble mediators and subsequent Ca(2+)-dependent smooth muscle shortening.
Wearable Subtitles (2020)

Mobile solutions can help transform speech and sound into visual representations for people who are deaf or hard-of-hearing (DHH). However, where handheld phones present challenges, head-worn displays (HWDs) could further communication through privately transcribed text, hands-free use, improved mobility, and socially acceptable interactions.
Broadband dispersion compensating hole-assisted fibers (2007)

A novel design of a broadband dispersion compensating hole-assisted fiber is demonstrated numerically. The proposed structure exhibits the largest negative dispersion of -552 ps/nm/km at 1550 nm with matched RDS. Further, its Raman amplification properties are investigated. (2 pages)