gebhart/patrepeval huggingface dataset:
Interaction of Cationic Peptides with Lipoteichoic Acid and Gram-Positive Bacteria (1999)

Compounds with antiendotoxin properties have been extensively studied for their potential as therapeutic agents for sepsis attributable to gram-negative bacteria. However, with the increasing incidence of gram-positive sepsis, there is interest in identifying compounds with a broad spectrum of action against both gram-positive and gram-negative bacteria. A series of synthetic alpha-helical cationic peptides related to bee melittin and silk moth cecropin have previously been shown to bind lipopolysaccharide (LPS) with high affinity, inhibit LPS-induced tumor necrosis factor alpha (TNF-alpha) production in vitro and in vivo, and kill gram-negative bacteria. In this study, we analyzed whether these peptides were active against gram-positive bacteria; whether they could bind to lipoteichoic acid (LTA), the major proinflammatory structure on gram-positive bacteria; and whether they could block the ability of LTA to promote the release of cytokines by the RAW 264.7 murine macrophage cell line. We found that the cationic peptides demonstrated moderate growth-inhibitory activity toward gram-positive bacteria. In addition, the peptides bound LTA with high affinity. This correlated with the ability of the peptides to block LTA-induced production of TNF and interleukin-6 by RAW 264.7 cells but did not correlate with their ability to kill the bacteria. The peptides also effectively inhibited LTA-induced TNF production in a whole human blood assay. The peptides were also able to partly block the ability of heat-killed Staphylococcus aureus, as well as soluble products of live S. aureus, to stimulate cytokine production by macrophages. Our results indicate that these cationic peptides may be useful to prevent sepsis and inflammation caused by both gram-negative and gram-positive bacteria.
Current Balancing Control for Interleaved Half-Bridge Submodules in Modular Multilevel Converters (2022)

This paper presents a closed-loop current balancing control for Modular Multilevel Converters with Interleaved half-bridge Sub-Modules (ISM-MMC). The new control loop solves the well-known problem of proper current balancing among interleaved half-bridge legs in each ISM-MMC submodule while preserving a simple and reliable structure. In addition to that, a novel capacitor voltage balancing strategy for MMCs is developed. The new algorithm contains main advantages of the classical capacitor voltage balancing methods while provides an opportunity to decouple two balancing tasks of ISM-MMC, namely capacitor voltage and interleaved legs current balancing. The proposed control methods feature good dynamic performance and are compliant with a digital processor's operational constraints. The effectiveness of the new balancing methods was verified during extensive numerical simulations and experimental tests on a laboratory prototype by the corresponding system response under the input/output characteristics variation and interleaved current control perturbation.
Molecular contrast optical coherence tomography: SNR comparison of techniques and introduction of ground state recovery pump-probe OCT (2005)

Molecular contrast OCT (MCOCT) is an extension of OCT in which specific molecular species are imaged based on their spectroscopic characteristics. In order to improve the sensitivity and specificity of MCOCT, several techniques have recently been introduced which depend upon coherent detection of inelastically scattered light from molecules of interest in a sample. These techniques include harmonic generation, coherent anti-Stokes Raman scattering, and several different forms of pump-probe spectroscopy. We have developed a theoretical framework to facilitate the comparison of different inelastic scattering-based contrast mechanisms for molecular contrast OCT. This framework is based upon the observation that since the noise floor is defined by the reference arm power in a shot-noise limited heterodyne detection system, the relevant comparison among the techniques is isolated to the available molecular-specific signal power. We have derived the value of the molecular contrast signal power for second harmonic generation OCT (SHOCT) and three different pump-probe OCT (PPOCT) techniques. Motivated by this analysis, we have constructed a preliminary ground state recovery pump-probe OCT system, and demonstrated its performance using rhodamine 6G as the MCOCT contrast agent.
Compact X-ray Tool For Critical-Dimension Metrology (2009)

Small Angle X‐ray Scattering (SAXS) is a possible candidate to complement and, in a longer term, to replace existing methods like CD‐SEM and OCD for measurements of CD profiles. Previously reported CD‐SAXS results were very promising; however as obtained using bulky sources as synchrotron, they are most often restricted to research rather than production control. We have designed a pilot set‐up (XCD™) around μ‐focus X‐tube, high‐luminosity focusing mirror‐monochromator and pixilated detector, having in mind that after further optimization of the components, the tool will have a suitable footprint and acceptable throughput. The system operates on MoKα (17.4 keV) beam shining through the wafer, from below. The measurement spot size is 100 μ. The angular resolution allows to measure structures with a pitch 100 nm and below. A software package was developed to simulate and process XCD spectra, taking into account all the components contributing to the instrumental function of the system. A special technique was developed for alignment. For the purpose of the feasibility study a special CD structure was prepared. It consists of Si trenches with 50 nm pitch. It was found that in a relatively short time, pitch and width can be extracted with a precision on the level 1% RSD. The depth of the trenches was measured using another independent X‐ray channel (fast XRR) operating on the CuKα line (8 keV) at the grazing angle, striking normally to the trenches direction.
Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells (2020)

Studying posttranslational modifications classically relies on experimental strategies that oversimplify the complex biosynthetic machineries of living cells. Protein glycosylation contributes to essential biological processes, but correlating glycan structure, underlying protein, and disease-relevant biosynthetic regulation is currently elusive. Here, we engineer living cells to tag glycans with editable chemical functionalities while providing information on biosynthesis, physiological context, and glycan fine structure. We introduce a non-natural substrate biosynthetic pathway and use engineered glycosyltransferases to incorporate chemically tagged sugars into the cell surface glycome of the living cell. We apply the strategy to a particularly redundant yet disease-relevant human glycosyltransferase family, the polypeptide N-acetylgalactosaminyl transferases. This approach bestows a gain-of-chemical-functionality modification on cells, where the products of individual glycosyltransferases can be selectively characterized or manipulated to understand glycan contribution to major physiological processes.
Seamless Multimedia Transmission During Fast Handover in Mobile IPV6 Environment (2006)

In this paper, we propose the seamless video transmission scheme over wireless LANs during fast handover in Mobile IPv6. In fact, a mobile node cannot receive the IP packets during handover. A number of extensions to fast handover for mobile IPv6 have been introduced to recover its weakness. Fast handover algorithm in mobile IPv6 allows the new access router in the adjacent cell to pre-buffer the data packets of a mobile node to prevent packet loss. In a mobile communication environment, however, transmission of multimedia data should consider the realtimeliness of the data. We focus on the multimedia data delivery during fast handover in mobile IPv6 environment
(Invited) Organic Color Center Photoluminescence Modulation for Biomedical Applications (2021)

The modulation of single-walled carbon nanotube (SWCNT) photoluminescence has been under investigation for the unique potential to develop biosensors to detect many classes of analytes. Covalent sp3 defects on SWCNTs, dubbed organic color centers (OCCs), have been explored for their photoluminescent properties, including increasing quantum yield and introducing new chemical sensitivities. The application of OCCs for biomedical applications requires new methods to control SWCNT surface chemistry and the resulting biological interactions/biocompatibility via supramolecular interactions with polymers and other excipients. We have found specific utilities of OCCs for the detection of chemical phenomena where SWCNT photoluminescence is normally relatively insensitive, such as pH changes in the physiologic range of 4.5 - 8. We developed OCC-based sensors to measure pH in live cells and in vivo, as well as other emerging applications. We believe that OCCs will facilitate the development of biosensors for disease detection and biomedical research.
Opioid peptides. Pharmacological activity and lipophilic character of dermorphin oligopeptides. IV. (1983)

The preliminary pharmacological activity pattern in guinea pig ileum and mouse vas deferens bioassays of five dermorphin related tetrapeptides is reported. The biological activities of the compounds under examination appear to be correlated in a statistically significant way to the lipophilic character of the C-terminal substituents.
Synergistic Enzyme Cocktail to Enhance Hydrolysis of Steam Exploded Wheat Straw at Pilot Scale (2018)

Multiple enzymes are required for efficient saccharification of lignocellulosic biomass and no wild type organism is capable of producing all enzymes in desired levels. In this study, steam explosion of wheat straw was carried out at pilot scale and a synthetic enzyme mixture (EnzMix) was developed by partially replacing the cellulase with critical dosages of commercially available accessory enzymes (β-glucosidase, xylanase and laccase) through central composite design. Highest degree of synergism (DS) was observed with β-glucosidase (1.68) followed by xylanase (1.36). Finally, benchmarking of EnzMix (Celluclast, β-glucosidase and xylanase in a protein ratio of 20.40: 38.43: 41.16, respectively) and other leading commercial enzymes was carried out. Interestingly, saccharification improved by 75% at 6h and 30% at 24h, respectively in comparison of control. By this approach, 25% reduction in enzyme dosage was observed for obtaining the same saccharification yield. Thus development of enzyme cocktail is an effective and sustainable approach for high saccharification efficiency.
Optical control of coherent lattice vibrations in tellurium (2004)

We present femtosecond time-resolved measurements of the dielectric tensor of tellurium under single and double pulse excitation. We demonstrate the ability to both enhance and cancel coherent lattice vibrations for large lattice shifts under near-damage threshold excitation. The excitation conditions for which cancellation is achieved in tellurium reveal a departure from the low-excitation strength behavior of similar materials.
Optics and photonics education in central Florida (2003)

We will describe several education programs that serve the growing optics industry in the Central Florida region, including the School of Optics' graduate programs and two-year and four-year programs in Photonics Technology taught by collaboration between the University of Central Florida and local community colleges.
Annulation of Tetrathiafulvalene to the Bay Region of Perylenediimide: Fast Electron-Transfer Processes in Polar and Nonpolar Solvents (2011)

A tetrathiafulvalene donor has been annulated to the bay region of perylenediimide through a 1H-benzo[d]pyrrolo[1,2-a]imidazol-1-one spacer affording an extended π-conjugated molecular dyad (TTF−PDI). To gain insight into its ground- and excited-state electronic properties, the reference compound Ph-PDI has been prepared via a direct Schiff-base condensation of N,N′-bis(1-octylnonyl)benzoperylene-1′,2′:3,4:9,10-hexacarboxylic-1′,2′-anhydride-3,4:9,10-bis(imide) with benzene-1,2-diamine. Both the experimental and the computational (DFT) results indicate that TTF−PDI exhibits significant intramolecular electronic interactions giving rise to an efficient photoinduced charge-separation process. Free-energy calculations verify that the light-induced process from TTF to the singlet-excited state of PDI is exothermic in both polar and nonpolar solvents. Fast adiabatic electron-transfer processes of a compactly fused, π-conjugated TTF−PDI dyad in benzonitrile, 2-methyltetrahydrofuran, anisole and toluene were observed by femtosecond transient absorption spectral measurements. The lifetimes of radical-ion pairs slightly increase with decreasing the solvent polarities, suggesting that the charge-recombination occurs in the Marcus inverted region. By utilizing the nanosecond transient absorption technique, the intermolecular electron-transfer process in a mixture of TTF-diamine/Ph-PDI has been observed via the triplet excited PDI for the first time.
Reconstructing a metazoan genetic pathway with transcriptome-wide epistasis measurements (2017)

Abstract RNA-seq is commonly used to identify genetic modules that respond to perturbations. In single cells, transcriptomes have been used as phenotypes, but this concept has not been applied to whole-organism RNA-seq. Linear models can quantify expression effects of individual mutants and identify epistatic effects in double mutants. To make interpretation of these high-dimensional measurements intuitive, we developed a single coefficient to quantify transcriptome-wide epistasis that accurately reflects the underlying interactions. To demonstrate our approach, we sequenced four single and two double mutants of Caenorhabditis elegans . From these mutants, we reconstructed the known hypoxia pathway. In addition, we uncovered a class of 56 genes that have opposing changes in expression in egl-9(lf) compared to vhl-1(lf) but the egl-9(lf); vhl-1(lf) mutant has the same phenotype as egl-9(lf) . This class violates the classical model of HIF-1 regulation, but can be explained by postulating a role of hydroxylated HIF-1 in transcriptional control. Significance Statement Transcriptome profiling is a way to quickly and quantitatively measure gene expression level. Because of their quantitative nature, there is widespread interest in using transcriptomic profiles as a phenotype for genetic analysis. However, a source of major concern is that whole-animal transcriptomic profiles mix the expression signatures of multiple cellular states, making it hard to accurately reconstruct genetic interactions. Additionally, it has been difficult to quantify epistasis, the signature of genetic interaction between two genes, in these molecular phenotypes. Here, we show that it is possible to accurately reconstruct genetic interactions between genes using whole-animal RNA sequencing, and we demonstrate a powerful new way to measure and understand epistasis arising from these measurements. This suggests that whole-organism RNA-seq can be a powerful tool with which to understand genetic interactions in entire organisms and not only in isolated cells. With the advent of genome engineering tools, generating mutants has become easier and faster for many organisms. As mutants become easier to create, phenotyping them has become a major bottleneck in understanding the biological functions of the genes in question. Our work presents a possible solution to this problem, because transcriptome profiling is fast and sensitive to genetic perturbations regardless of the context they operate in.
영지 포자분 열수 추출물에 의한 U937 인체백혈병세포의 Apoptosis 유발 (2010)

The mushroom Ganoderma lucidum, a lamellaless basidio-mycetous fungus belonging to the family Polyporaceae, is widely distributed in Korea, Japan and China, and has been used as a medicinal material for allergy, arthritis, bronchitis, gastric ulcer, hyperglycemia, hypertension, chronic hepatitis, he...
Lack of Drug-Drug Interaction Between ATI-5923, a Novel Vitamin K Epoxide Reductase Inhibitor, and Amiodarone, in Beagle Dog (2008)

Abstract ATI-5923 is a novel oral anticoagulant that is being developed to prevent thromboembolic events associated with atrial fibrillation, prosthetic heart valves, and deep venous thrombosis. Like warfarin, it is a vitamin K epoxide reductase inhibitor. Unlike warfarin, which is metabolized by CYP2C9 and CYP3A4, ATI-5923 is metabolized by carboxylesterases. Our hypothesis is that ATI 5923 will lead to superior INR (international normalized ratio) control compared to warfarin as it will not be subject to pharmacokinetic interactions observed with many of the drugs that affect warfarin metabolism, leading to either excessive or suboptimal anticoagulation resulting in bleeding or thrombotic complications, respectively. These studies compared the efficacy of ATI-5923 to that of warfarin, when administered either intravenously (IV) or once a day orally, to produce stable anticoagulation in beagle dogs. The drug-drug interaction potential was assessed using co-administration with amiodarone, an inhibitor of CYP3A4 and CYP2C9, with either ATI-5923 or warfarin. Effects on coagulation were assessed by measuring Factor VII and X levels and prothrombin times (PT). Continuous IV infusions (5 to 9 days per dose) and oral administration of ATI 5923 and warfarin (5 to 10 days per dose) caused a dose-dependent decrease in plasma concentrations of Factor VII and Factor X, and an associated increase in PT. On a dose basis, ATI 5923 was a more potent anticoagulant than warfarin. Intravenous fresh frozen canine plasma or subcutaneous vitamin K1 treatment reversed the anticoagulant effects of orally-administered ATI-5923 in adult beagle dogs. Co-administration of amiodarone (40mg/kg for 2 days, 20mg/kg for 6 days) significantly increased the plasma levels and anticoagulation effect of warfarin (0.25mg/kg) in beagle dogs, as measured by increase PT and decrease in factor VII and X. In contrast, amiodarone had no effect on the anticoagulation parameters and plasma levels of ATI-5923 (0.3mg/kg). We conclude that ATI-5923, via a vitamin K-dependent mechanism, causes changes in key parameters of hemostasis in beagle dogs that are consistent with effective anticoagulation but without the important drug-drug interaction commonly observed with amiodarone in warfarin-treated patients.
Supplementary Methods from Danger Signaling Protein HMGB1 Induces a Distinct Form of Cell Death Accompanied by Formation of Giant Mitochondria (2023)

Supplementary Methods from Danger Signaling Protein HMGB1 Induces a Distinct Form of Cell Death Accompanied by Formation of Giant Mitochondria
Effect of temperature and strain-rate on the stress-optic law of cellulose acetate. (1985)

光塑性実験のモデル材料にアセテートを用いた場合の適用性について検討するため雰囲気温度と変形速度の影響を考慮した単軸引張り試験を行い, 応力-ひずみ, 応力-しま次数, ひずみ-しま次数の関係が同時かつ連続的に測定された. これらの実験結果を無次元表示することにより, 雰囲気温度, 変形速度に無関係な式で, それぞれの関係が一義的に表示され, これによりアセテートの光塑性モデル実験が可能であることがわかった.
Phonological and episodic buffer contribution to short-term memory in deaf signers (2009)

Phonological and episodic buffer contribution to short-term memory in deaf signers Elizabeth Hirshorn University of Rochester Nina Fernandez University of Rochester, Boston University Daphne Bavelier University of Rochester Abstract: Deaf individuals who are native users of American Sign Language have been shown to have lower short- term memory (STM) spans than their hearing peers in tasks requiring serial recall of linguistic stimuli. Does this result reflect worse STM skills, or rather different processing biases in the way temporal information is encoded? Temporal information can be maintained through ordered phonological representations in the phonological loop, and through spatio-temporal marking in episodic memory. By systematically removing certain cues (e.g. verbal or spatial), we show that hearing speakers rely more on ordered phonological representations, whereas deaf signers rely more on spatio-temporal marking. Greater reliance on episodic memory in deaf signers is being further examined. This view predicts a greater role for semantic information in STM in deaf signers. Together, these studies indicate different processing biases in how deaf signers and hearing speakers encode information in STM.
Data from Targeting the MYC and PI3K Pathways Eliminates Leukemia-Initiating Cells in T-cell Acute Lymphoblastic Leukemia (2023)

&lt;div&gt;Abstract&lt;p&gt;Disease relapse remains the major clinical challenge in treating T-cell acute lymphoblastic leukemia (T-ALL), particularly those with PTEN loss. We hypothesized that leukemia-initiating cells (LIC) are responsible for T-ALL development and treatment relapse. In this study, we used a genetically engineered mouse model of &lt;i&gt;Pten&lt;/i&gt;&lt;sup&gt;−/−&lt;/sup&gt; T-ALL with defined blast and LIC-enriched cell populations to demonstrate that LICs are responsible for therapeutic resistance. Unlike acute and chronic myelogenous leukemia, LICs in T-ALL were actively cycling, were distinct biologically, and responded differently to targeted therapies in comparison with their differentiated blast cell progeny. Notably, we found that T-ALL LICs could be eliminated by cotargeting the deregulated pathways driven by PI3K and Myc, which are altered commonly in human T-ALL and are associated with LIC formation. Our findings define critical events that may be targeted to eliminate LICs in T-ALL as a new strategy to treat the most aggressive relapsed forms of this disease. &lt;i&gt;Cancer Res; 74(23); 7048–59. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;