gebhart/patrepeval huggingface dataset:
Quantum Chemical Study of Carbohydrate–Phospholipid Interactions (2011)

Carbohydrates on host membranes are fundamental to many important biological processes. Here, we seek a basic understanding of the nature of the interactions between carbohydrates and phospholipids to dissect their roles in molecular recognition. A hybrid quantum mechanics/quantum mechanics (QM/QM) scheme with two different levels of treatment was used to explore the conformations and energetics of carbohydrate-phospholipid complexes. We investigate the interactions of two phospholipids (POPC and DOPC) with mannose using density functional theory. Carbohydrate-phospholipid interactions are probed with respect to competing interactions with water. Our hybrid QM/QM approach demonstrates that mannose interactions with phospholipids can result in alterations in charge distributions and conformations of phospholipids. The results clearly reveal the interplay between conventional and nonconventional hydrogen bonding; moreover, nonpolar interactions are shown to be crucial in the recognition and further stabilization of carbohydrate-phospholipid complexes. The influence of the acyl chain on phospholipid headgroup orientation is clearly evident in our investigation. The significance of the conventional OH···O and nonconventional CH···O and CH···C interactions in the stabilization of the intermolecular complexes is deduced from the molecular electron density topology using Bader's atoms-in-molecules theory. Finally, we have compared the QM energies with molecular mechanics energies for the same interactions to aid in the refinement of the all-atom lipid-carbohydrate force fields.
Changes in Blood Flow, Temperature and Muscle Endurance in Association with Cryotherapy (2010)

[Purpose] Sustained isometric muscle actions induce fatigue which manifests as a decline in force. This decline has well known physiological correlates that are often assessed using EMG signal frequency changes, changes in blood flow and muscle temperature. The purpose of this study was to investigate how cooling influences recovery following isometric muscle fatigue. [Methods] Eight healthy volunteers performed isometric elbow flexion to fatigue on two occasions, with 10 minutes of rest with no cooling, 2 minutes and 10 minutes cooling. The surface EMG (median frequency), deep muscle temperature and circulating blood flow were assessed during and after each endurance task. [Results] The 10-minute cooling condition extended endurance in the isometric contraction task. No changes to median frequency EMG signals were detected and the deep temperature and blood flow was most profoundly affected with the extended period of cooling compared to rest and 2 minutes. [Conclusion] This exercise task was enough to induce fatigue in this study. It was shown that 10 minutes cooling for fatigued muscles will extend the duration of subsequent exercise. Indeed, the results of this study suggest the effects of muscle fatigue recovery by cooling are instantaneous.
Hydrothermal synthesis of lithium silicate from waste glass. A preliminary study (2015)

Current environmental directives to conserve resources and to divert waste streams have generated significant interest in mineral recycling. In this respect, this preliminary study has demonstrated that lithium metasilicate can be prepared by hydrothermal reaction between waste container glass and lithium hydroxide solutions at 100 °C. Minor proportions of calcium hydroxide, calcite, lithium carbonate and tobermorite were also produced during the reaction. Percentage crystallinity and proportion of lithium metasilicate in the reaction product were found to increase as functions of lithium hydroxide concentration (between 1 and 4 M). This research has also shown that the lithium metasilicate phase can take up 6.4 mmol/g of Zn2+ ions after 24 h during batch sorption. Further work to optimise the yield and to appraise the antimicrobial properties of Zn2+-bearing lithium metasilicate is now warranted.
Design of Compact and Efficient Superdirective Array with Parasitic Elements (2019)

International audience
Overexpression of Exosomal Cardioprotective miRNAs Mitigates Hypoxia-Induced H9c2 Cells Apoptosis (2017)

Recent evidence suggests that hypoxia caused by acute myocardial infarction can induce cardiomyocyte apoptosis. Exosomes are signalling mediators that contribute to intercellular communication by transporting cytosolic components including miRNAs, mRNAs, and proteins. However, the systemic regulation and function of exosomal miRNAs in hypoxic cardiomyocytes are currently not well understood. Here, we used small RNA sequencing to investigate the effects of hypoxia stress on miRNAome of rat cardiomyoblast cells (H9c2) and corresponding exosomes. We identified 92 and 62 miRNAs in cells and exosomes, respectively, that were differentially expressed between hypoxia and normoxia. Hypoxia strongly modulated expression of hypoxia-associated miRNAs in H9c2 cells, and altered the miRNAome of H9c2 cells-derived exosomes. Functional enrichment analysis revealed extensive roles of differentially expressed exosomal miRNAs in the HIF-1 signalling pathway and in apoptosis-related pathways including the TNF, MAPK, and mTOR pathways. Furthermore, gain- and loss-of-function analysis demonstrated potential anti-apoptotic effects of the hypoxia-induced exosomal miRNAs, including miR-21-5p, miR-378-3p, miR-152-3p, and let-7i-5p; luciferase reporter assay confirmed that <i>Atg12</i> and <i>Faslg</i> are targets of miR-152-3p and let-7i-5p, respectively. To summarize, this study revealed that hypoxia-induced exosomes derived from H9c2 cells loaded cardioprotective miRNAs, which mitigate hypoxia-induced H9c2 cells apoptosis.
ChemInform Abstract: Simplex Optimization of Electroreduction of Oxygen Mediated by Methyl Viologen Supported on Zeolite‐Modified Carbon Paste Electrode. (1988)

Abstract Incorporation of zeolite Y into a carbon paste electrode is shown to improve the efficiency of mediated electroreduction of oxygen by methyl viologen (MV) cation radical.
The financial derivatives reader (1992)

Introduction - financial derivatives and financial engineering. Part 1 Derivative instruments: theory and pricing forwards and futures options options on futures Swaps. Part 2 Equity market applications: equity derivatives and the crash debt market applications foreign exchange applications.
Novosibirsk Project of Gas-Dynamic Multiple-Mirror Trap (2013)

Development of a new linear device for confinement of fusion plasmas is under way in the Budker Institute of Nuclear Physics, Novosibirsk. The new device combines features of existing GOL-3 and GDT traps, namely, the central GDT-like cell with sloshing ions produced by intense neutral beam injection, and the multiple-mirror end sections for suppression of axial plasma losses. It is designed as a prototype of an energy-efficient neutron source and a testbed for development of mirror-based fusion reactors.
Genetic diversity of cultured and wild populations of the giant freshwater prawnMacrobrachium rosenbergii(de Man, 1879) based on microsatellite analysis (2012)

Freshwater prawn (Macrobrachium rosenbergii) culture in the Western Hemisphere is primarily, if not entirely, derived from 36 individual prawns originally introduced to Hawaii from Malaysia in 1965 and 1966. Little information is available regarding genetic variation within and among cultured prawn stocks worldwide. The goal of the current study was to characterize genetic diversity in various prawn populations with emphasis on those cultured in North America. Five microsatellite loci were screened to estimate genetic diversity in two wild (Myanmar and India-wild) and seven cultured (Hawaii-1, Hawaii-2, India-cultured, Israel, Kentucky, Mississippi and Texas) populations. Average allelic richness ranged from 3.96 (Israel) to 20.45 (Myanmar). Average expected heterozygosity ranged from 0.580 (Israel) to 0.935 (Myanmar). Many of the cultured populations exhibited reduced genetic diversity when compared with the Myanmar and the India-cultured populations. Significant deficiency in heterozygotes was detected in the India-cultured, Mississippi and Kentucky populations (overall Fis estimated of 0.053, 0.067 and 0.108 respectively) reflecting moderate levels of inbreeding. Overall estimate of fixation index (Fst = 0.1569) revealed moderately high levels of differentiation among the populations. Outcome of this study provide a baseline assessment of genetic diversity in some available strains that will be useful for the development of breeding programmes.
Author response: The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture (2017)

Surprising connections between gene architecture and splicing kinetics are illuminated using short, progressive metabolic labeling/RNA sequencing and novel computational modeling approaches in Drosophila cells.
Quality of Life Enjoyment and Satisfaction Questionnaire: a new measure. (1993)

The Quality of Life Enjoyment and Satisfaction Questionnaire (Q-LES-Q) is a self-report measure designed to enable investigators to easily obtain sensitive measures of the degree of enjoyment and satisfaction experienced by subjects in various areas of daily functioning. The summary scores were found to be reliable and valid measures of these dimensions in a group of depressed outpatients. The Q-LES-Q measures were related to, but not redundant with, measures of overall severity of illness or severity of depression within this sample. These findings suggest that the Q-LES-Q measures may be sensitive to important differences among depressed patients that are not detected by the measures usually employed.
Head-Coupled Kinematic Template Matching for Target Selection in Hangry Piggos (2020)

We demonstrate Head-Coupled Kinematic Template Matching (HC-KTM) - a new technique to predict a ray pointer's landing position (end-position and angle) for selection movements in virtual reality (VR) environments. The technique adapts and extends a prior 2D kinematic template matching method to VR environments where ray pointers are used for selection. It builds on the insight that the kinematics of a controller and Head-Mounted Display (HMD) can be used to predict the ray's final landing position and angle. In our VR game, Hangry Piggos, we leverage HC-KTM to generate target predictions within a scene, and we apply pointing visualization techniques on top of them to accelerate a player's selection.
C781, a β-Arrestin Biased Antagonist at Protease-Activated Receptor-2 (PAR2), Displays in vivo Efficacy Against Protease-Induced Pain in Mice (2022)

Given the limited options and often harmful side effects of current analgesics and the suffering caused by the opioid crisis, new classes of pain therapeutics are needed. Protease-activated receptors (PARs), particularly PAR2, are implicated in a variety of pathologies, including pain. Since the discovery of the role of PAR2 in pain, development of potent and specific antagonists has been slow. In this study, we describe the in vivo characterization of a novel small molecule/peptidomimetic hybrid compound, C781, as a β-arrestin-biased PAR2 antagonist. In vivo behavioral studies were done in mice using von Frey filaments and the Mouse Grimace Scale. Pharmacokinetic studies were done to assess pharmacokinetic/pharmacodynamic relationship in vivo. We used both prevention and reversal paradigms with protease treatment to determine whether C781 could attenuate protease-evoked pain. C781 effectively prevented and reversed mechanical and spontaneous nociceptive behaviors in response to small molecule PAR2 agonists, mast cell activators, and neutrophil elastase. The ED<sub>50</sub> of C781 (intraperitoneal dosing) for inhibition of PAR2 agonist (20.9 ng 2-AT)-evoked nociception was 6.3 mg/kg. C781 was not efficacious in the carrageenan inflammation model. Pharmacokinetic studies indicated limited long-term systemic bioavailability for C781 suggesting that optimizing pharmacokinetic properties could improve in vivo efficacy. Our work demonstrates in vivo efficacy of a biased PAR2 antagonist that selectively inhibits β-arrestin/MAPK signaling downstream of PAR2. Given the importance of this signaling pathway in PAR2-evoked nociception, C781 exemplifies a key pharmacophore for PAR2 that can be optimized for clinical development. PERSPECTIVE: Our work provides evidence that PAR2 antagonists that only block certain aspects of signaling by the receptor can be effective for blocking protease-evoked pain in mice. This is important because it creates a rationale for developing safer PAR2-targeting approaches for pain treatment.
Botzilla (2010)

Hosts infected with malicious software, so called malware, are ubiquitous in today's computer networks. The means whereby malware can infiltrate a network are manifold and range from exploiting of software vulnerabilities to tricking a user into executing malicious code. Monitoring and detection of all possible infection vectors is intractable in practice. Hence, we approach the problem of detecting malicious software at a later point when it initiates contact with its maintainer; a process referred to as "phoning home". In particular, we introduce Botzilla, a method for detection of malware communication, which proceeds by repetitively recording network traffic of malware in a controlled environment and generating network signatures from invariant content patterns. Experiments conducted at a large university network demonstrate the ability of Botzilla to accurately identify malware communication in network traffic with very low false-positive rates.
Ruthenium-Mediated Regio- and Stereoselective Alkenylation of Pyridine (2003)

A novel alkenylation reaction of pyridine is developed. Heating a cationic ruthenium vinylidene complex [CpRu(=C=CHR)(PPh(3))(2)]PF(6) in pyridine at 100-125 degrees C for 24 h affords (E)-2-alkenylpyridine. Initially, pyridine coordinates to ruthenium by displacement of one of the phosphine ligands. Then, [2 + 2] heterocycloaddition occurs to form a four-membered ruthenacyclic complex. Deprotonation of the beta-hydrogen affords a neutral pi-azaallyl complex. Protonolysis furnishes the product. As a result, a vinylidene group is inserted into the alpha C-H bond of pyridine. The alkenylation reaction is made catalytic in ruthenium by the use of (alkyn-1-yl)silane as the vinylidene source. Treatment of (alkyn-1-yl)trimethylsilane with pyridine in the presence of a cationic ruthenium complex [CpRu(PPh(3))(2)]PF(6) affords the corresponding (E)-2-alkenylpyridine in good yield in a regio- and stereoselective manner.
Machine-learning-based biochemical characterization of atherosclerotic plaques in intravascular optical coherence tomography–fluorescence lifetime imaging (2021)

Intravascular optical coherence tomography-fluorescence lifetime imaging (OCT-FLIm) provides co-registered structural and biochemical information of atherosclerotic plaques in a label-free manner. For intuitive image interpretation of OCT-FLIm, herein, we present a machine learning classifier where key biochemical components (lipids, lipids+macrophages, macrophages, fibrotic, and normal) related to plaque destabilization are characterized based on the combination of multispectral FLIm parameters and convolutional OCT features. Using dataset from in vivo atheromatous swine models, the classification accuracy was &gt;92% for each plaque component according the five-fold cross validation. This highly translatable imaging strategy will open a new avenue for clinical intracoronary assessment of high-risk plaques.
Photooxidative Degradation of Beer Bittering Principles:  A Key Step on the Route to Lightstruck Flavor Formation in Beer (2005)

Isohumulones, dihydroisohumulones, tetrahydroisohumulones, and humulinones, important hop-derived bittering compounds in beer, were shown to give rise to reactive triacylmethyl radicals on interaction with triplet-excited riboflavin after spin trapping by 5,5-dimethyl-1-pyrroline N-oxide or 2-methyl-2-nitrosopropane, followed by electron paramagentic resonance spectroscopy combined with spectral simulation. Electron abstraction from the ionized beta-tricarbonyl chromophore, which is common to all five-membered ring hop derivatives, is the initial event on photoinduced degradation. Radicaloid decomposition of isohumulones leads to precursors for 3-methylbut-2-ene-1-thiol, the lightstruck constituent in beer. Interaction of reduced derivatives of isohumulones with triplet-excited riboflavin furnished radical precursors of volatile aldehydes, which may lead to the development of unpleasant stale or cardboard flavors.
Measuring surface slope error on precision aspheres (2007)

Optical designers are becoming increasingly aware of the importance of specifying and tolerancing slope errors on optical surfaces, especially aspheric surfaces. Slope errors can degrade system optical performance - in some cases even if the peak to valley surface figure errors meets the optical design tolerance analysis. With this awareness, more optical engineers are putting requirements for peak surface slope on optical element drawings. This puts pressure on optical fabricators to understand slope specifications and react to these requirements, and use the appropriate metrology instrumentation to ensure final system performance. This paper will discuss appropriate ways to specify slope errors, and the challenges and limitations of measuring slope errors with commercial interferometers. The optical designer should be aware of how slope errors are measured on Fizeau interferometers and should specify the spatial intervals of interest when tolerancing aspheric elements. Peak slope error measurement is prone to erroneous measurement errors due to surface contamination, environmental errors, and pupil focus. Finally, filtering has a strong influence on surface slope calculations. Practical examples of slope specifications and experimental results will be presented.
Rerouting of the lignin biosynthetic pathway by inhibition of cytosolic shikimate recycling in transgenic hybrid aspen (2022)

Lignin is a phenolic polymer deposited in the plant cell wall, and is mainly polymerized from three canonical monomers (monolignols), i.e. p-coumaryl, coniferyl and sinapyl alcohols. After polymerization, these alcohols form different lignin substructures. In dicotyledons, monolignols are biosynthesized from phenylalanine, an aromatic amino acid. Shikimate acts at two positions in the route to the lignin building blocks. It is part of the shikimate pathway that provides the precursor for the biosynthesis of phenylalanine, and is involved in the transesterification of p-coumaroyl-CoA to p-coumaroyl shikimate, one of the key steps in the biosynthesis of coniferyl and sinapyl alcohols. The shikimate residue in p-coumaroyl shikimate is released in later steps, and the resulting shikimate becomes available again for the biosynthesis of new p-coumaroyl shikimate molecules. In this study, we inhibited cytosolic shikimate recycling in transgenic hybrid aspen by accelerated phosphorylation of shikimate in the cytosol through expression of a bacterial shikimate kinase (SK). This expression elicited an increase in p-hydroxyphenyl units of lignin and, by contrast, a decrease in guaiacyl and syringyl units. Transgenic plants with high SK activity produced a lignin content comparable to that in wild-type plants, and had an increased processability via enzymatic saccharification. Although expression of many genes was altered in the transgenic plants, elevated SK activity did not exert a significant effect on the expression of the majority of genes responsible for lignin biosynthesis. The present results indicate that cytosolic shikimate recycling is crucial to the monomeric composition of lignin rather than for lignin content.
Role of Intraoperative Insulin Monitoring in Surgical Management of Insulinoma (2001)

Background and Purpose: Precise localization and surgical excision is the therapeutic strategy for insulinomas. However, it is often difficult to localize the insulinomas, because of their small size. Surgeons may not localize and remove all of them together, particularly in patients with multiple insulinomas. We reviewed our experience to confirm the efficacy of blood glucose and intraoperative immunoreactive insulin (IRI) monitoring for surgical management of insulinomas. Patients and Methods: Thirty-nine patients with insulinoma were surgically treated in our department. Perioperative blood glucose monitoring was performed in 14 patients, intraoperative quick IRI assay of the peripheral blood in 10 patients, and assay of a portal sample in 4 patients by an IMX analyzer. Results: Rebound response of blood glucose to insulinoma removal was not always noted (8/14; 57%). Seven of ten patients showed a decrease of peripheral serum IRI levels within 15 minutes after removal of the insulinoma. The other two patients showed a rebound response of peripheral blood glucose or portal IRI. All the patients who had intraoperative monitoring of peripheral blood and peripheral and portal IRI had no recurrent insulinoma syndrome after surgical removal of their insulinomas. Conclusion: Combined monitoring of peripheral blood glucose and peripheral and portal IRI are helpful in the surgical management of insulinomas, as they can indicate that no insulinoma remains.
Non-invasive brain stimulation and neuroenhancement (2022)

Attempts to enhance human memory and learning ability have a long tradition in science. This topic has recently gained substantial attention because of the increasing percentage of older individuals worldwide and the predicted rise of age-associated cognitive decline in brain functions. Transcranial brain stimulation methods, such as transcranial magnetic (TMS) and transcranial electric (tES) stimulation, have been extensively used in an effort to improve cognitive functions in humans. Here we summarize the available data on low-intensity tES for this purpose, in comparison to repetitive TMS and some pharmacological agents, such as caffeine and nicotine. There is no single area in the brain stimulation field in which only positive outcomes have been reported. For self-directed tES devices, how to restrict variability with regard to efficacy is an essential aspect of device design and function. As with any technique, reproducible outcomes depend on the equipment and how well this is matched to the experience and skill of the operator. For self-administered non-invasive brain stimulation, this requires device designs that rigorously incorporate human operator factors. The wide parameter space of non-invasive brain stimulation, including dose (e.g., duration, intensity (current density), number of repetitions), inclusion/exclusion (e.g., subject's age), and homeostatic effects, administration of tasks before and during stimulation, and, most importantly, placebo or nocebo effects, have to be taken into account. The outcomes of stimulation are expected to depend on these parameters and should be strictly controlled. The consensus among experts is that low-intensity tES is safe as long as tested and accepted protocols (including, for example, dose, inclusion/exclusion) are followed and devices are used which follow established engineering risk-management procedures. Devices and protocols that allow stimulation outside these parameters cannot claim to be "safe" where they are applying stimulation beyond that examined in published studies that also investigated potential side effects. Brain stimulation devices marketed for consumer use are distinct from medical devices because they do not make medical claims and are therefore not necessarily subject to the same level of regulation as medical devices (i.e., by government agencies tasked with regulating medical devices). Manufacturers must follow ethical and best practices in marketing tES stimulators, including not misleading users by referencing effects from human trials using devices and protocols not similar to theirs.