gebhart/patrepeval huggingface dataset:
Detoxification of toxins by bacillithiol in Staphylococcus aureus (2012)

Bacillithiol (BSH), an α-anomeric glycoside of l-cysteinyl-d-glucosaminyl-l-malate, is a major low-molecular-mass thiol found in bacteria such as Bacillus sp., Staphylococcus aureus and Deinococcus radiodurans. Like other low-molecular-mass thiols such as glutathione and mycothiol, BSH is likely to be involved in protection against environmental toxins including thiol-reactive antibiotics. We report here a BSH-dependent detoxification mechanism in S. aureus. When S. aureus Newman strain was treated with monobromobimane and monochlorobimane, the cellular BSH was converted to the fluorescent S-conjugate BS-bimane. A bacillithiol conjugate amidase activity acted upon the BS-bimane to produce Cys-bimane, which was then acetylated by an N-acetyltransferase to generate N-acetyl-Cys-bimane, a mercapturic acid. An S. aureus mutant lacking BSH did not produce mercapturic acid when treated with monobromobimane and monochlorobimane, confirming the involvement of bacillithiol. Furthermore, treatment of S. aureus Newman with rifamycin, the parent compound of the first-line anti-tuberculosis drug, rifampicin, indicated that this thiol-reactive antibiotic is also detoxified in a BSH-dependent manner, since mercapturic acids of rifamycin were observed in the culture medium. These data indicate that toxins and thiol-reactive antibiotics are detoxified to less potent mercapturic acids in a BSH-dependent manner and then exported out of the cell in S. aureus.
Octave-Tuning Dual-Core Folded VCO Leveraging a Triple-Mode Switch-Less Tertiary Magnetic Loop (2021)

To satisfy the requirements for multi-standard frequency generation, mode-switching oscillators are developed to increase the frequency tuning range without incurring considerable phase noise penalty. However, this improvement in the tuning range is often limited by the parasitics of the circuitry for mode selection and tuning. To address this challenge, this work presents a dual-core octave-tuning VCO using a switch-less tertiary magnetic coupling loop. The design employs the benefits of transformer-switching without incurring switch loss and quality factor degradation and also the benefits of mode switching without the parasitics from the mode selection and tuning network. The VCO employs a non-constant RC scaling for the capacitors' bank, across the tuning bits, and positive feedback dc-coupled inductive-degenerated output buffer to maximize the tuning range. Implemented in 22 nm fully depleted silicon-on-insulator (FDSOI), the dual-core VCO achieves a 72% tuning at 8-17 GHz and a figure-of-merit-tuning (FoM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> ) of 208.8 dBc/Hz at 11 GHz. The chip operates from a 0.45 V supply with a power consumption of 17-33 mW and a core area of 0.39 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . To the best of our knowledge, the VCO achieves the highest FoM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> and lowest supply for designs over 10 GHz.
Crystal structure of 2,3,5,6-tetrachloro-1’, 3’,3a’,4’,5’,7a’-hexahydrospiro[cyclohexa-2,5- diene-1,1’-benzo[c]furan]-4-one, [C5Cl4O]C[C7H10O] (2000)

Table 1. Data collection and handling.
Opening of mitochondrial K<sub>ATP</sub>channels enhances cardioprotection through the modulation of mitochondrial matrix volume, calcium accumulation, and respiration (2004)

Previously, we have shown that the pharmacological opening of the mitochondrial ATP-sensitive K channels with diazoxide (DZX) enhances the cardioprotection afforded by magnesium-supplemented potassium (K/Mg) cardioplegia. To determine the mechanisms involved in the cardioprotection afforded by K/Mg + DZX cardioplegia, rabbit hearts (n=24) were subjected to isolated Langendorff perfusion. Control hearts were perfused for 75 min. Global ischemia (GI) hearts were subjected to 30 min of equilibrium, 30 min of GI, and 15 min of reperfusion. K/Mg and K/Mg + DZX cardioplegia hearts received either K/Mg or K/Mg + DZX for 5 min before GI and reperfusion. Tissue was harvested for mitochondrial isolation and transmission electron microscopy (TEM). Mitochondrial structure, area, matrix volume, free calcium, and oxygen consumption were determined. TEM demonstrated that GI mitochondria were damaged and that K/Mg and K/Mg + DZX preserved mitochondrial structure. TEM and light scattering demonstrated separately that mitochondrial matrix and cristae area and matrix volume were significantly increased after GI and reperfusion with GI > K/Mg + DZX > K/Mg hearts (P <0.05 vs. control). Mitochondrial free calcium was significantly increased in GI and K/Mg hearts. K/Mg + DZX significantly decreased mitochondrial free calcium accumulation (P <0.05 vs. GI and K/Mg). State 3 oxygen consumption and respiratory control index in malate (complex I substrate)- and succinate (complex II substrate)-energized mitochondria were significantly decreased (P <0.05 vs. control) in the GI and K/Mg + DZX groups. These data indicate that the enhanced cardioprotection afforded by K/Mg + DZX cardioplegia occurs through the preservation of mitochondrial structure and the significant decrease in mitochondrial free calcium accumulation and mitochondrial state 3 oxygen consumption.
Structure and Function of the RedJ Protein, a Thioesterase from the Prodiginine Biosynthetic Pathway in Streptomyces coelicolor (2011)

Prodiginines are a class of red-pigmented natural products with immunosuppressant, anticancer, and antimalarial activities. Recent studies on prodiginine biosynthesis in Streptomyces coelicolor have elucidated the function of many enzymes within the pathway. However, the function of RedJ, which was predicted to be an editing thioesterase based on sequence similarity, is unknown. We report here the genetic, biochemical, and structural characterization of the redJ gene product. Deletion of redJ in S. coelicolor leads to a 75% decrease in prodiginine production, demonstrating its importance for prodiginine biosynthesis. RedJ exhibits thioesterase activity with selectivity for substrates having long acyl chains and lacking a β-carboxyl substituent. The thioesterase has 1000-fold greater catalytic efficiency with substrates linked to an acyl carrier protein (ACP) than with the corresponding CoA thioester substrates. Also, RedJ strongly discriminates against the streptomycete ACP of fatty acid biosynthesis in preference to RedQ, an ACP of the prodiginine pathway. The 2.12 Å resolution crystal structure of RedJ provides insights into the molecular basis for the observed substrate selectivity. A hydrophobic pocket in the active site chamber is positioned to bind long acyl chains, as suggested by a long-chain ligand from the crystallization solution bound in this pocket. The accessibility of the active site is controlled by the position of a highly flexible entrance flap. These data combined with previous studies of prodiginine biosynthesis in S. coelicolor support a novel role for RedJ in facilitating transfer of a dodecanoyl chain from one acyl carrier protein to another en route to the key biosynthetic intermediate 2-undecylpyrrole.
Transcriptional regulation of the interleukin 2 gene by glucocorticoid hormones. Role of steroid receptor and antigen-responsive 5'-flanking sequences. (1990)

Dexamethasone treatment of the Jurkat T77 cell clone inhibited the enhancing effect of 12-O-tetradecanoylporbol-13-acetate (TPA) and the calcium ionophore A23187 on the interleukin 2 (IL2) mRNA levels and gene transcription from intact nuclei. Dexamethasone treatment of Jurkat T77 cells inhibited the TPA/A23187-dependent activation of the transcription from the transfected pIL2CAT, containing 600 base pairs of the genomic sequences upstream of the coding region of IL2 gene, including the TPA/calcium responsive cis-regulatory elements and promoter sequences, driving the expression of the chloramphenicol acetyltransferase (CAT) gene. Transfection of either Jurkat T77 cell clone or glucocorticoid-resistant Jurkat cells with a human glucocorticoid receptor cDNA under the transcriptional control of the Rous sarcoma virus long terminal repeat (LTR) (pRShGR alpha) significantly increased or induced, respectively, the dexamethasone-mediated inhibition of the TPA/A23187-dependent expression of pIL2-CAT as well as the enhancing effect on the expression of the cotransfected CAT gene under the control of the mouse mammary tumor virus LTR, as a marker of glucocorticoid receptor action. This suggests a role for the glucocorticoid receptor in mediating the dexamethasone action on IL2 gene expression. To study the cis-regulatory sequence specificity of the dexamethasone-induced interference with the TPA/A23187-mediated T cell activating signals, we studied the effect of the hormone on the regulatory elements contained in the Rous sarcoma virus and human T lymphotropic virus 1 long terminal repeats and the SV40 promoter, which are known to be transcriptionally enhanced by those activating agents. Dexamethasone was unable to interfere with the TPA/A23187-mediated enhancement of these cis-regulatory elements, suggesting that the hormone effect is specific for IL-2 gene sequences. Our data suggest that the dexamethasone-mediated transcriptional inhibition of the IL2 gene is mediated by an interference with the protein kinase C and calcium-mediated trans-activation of the antigen-responsive and T cell-specific elements lying in the 5'-flanking region of the gene.
Neuropathic itch (2019)

Neuropathic itch is clinically important but has received much less attention as compared to neuropathic pain. In the past decade, itch-specific pathways have been characterized on a cellular and molecular level, but their exact role in the pathophysiology of neuropathic itch is still unclear. Traditionally, mutually exclusive theories for itch such as labeled line, temporal/spatial pattern, or intensity theory have been proposed, and experimental studies in mice mainly favor the specificity theory of itch. By contrast, results in humans also suggest a role for spatial and temporal patterns in neuropathic itch. Rarefication of skin innervation in neuropathy could provide a "spatial contrast" discharge pattern, and axotomy could induce de novo expression of the itch-specific spinal neuropeptide, gastrin-releasing peptide, in primary afferent nociceptors, thereby modulating itch processing in the dorsal horn. Thus, clinical neuropathy may generate itch by changes in the spatial and temporal discharge patterns of nociceptors, hijacking the labeled line processing of itch and abandoning the canonical scheme of mutual exclusive itch theories. Moreover, the overlap between itch and pain symptoms in neuropathy patients complicates direct translation from animal experiments and, on a clinical level, necessitates collaboration between medical specialities, such as dermatologists, anesthesiologists, and neurologists.
Evaluation of acoustic radiation force impulse elastography for fibrosis staging of chronic liver disease: a pilot study (2009)

Ultrasonic ARFI elastography is a novel, non-invasive and reliable method for the assessment of liver fibrosis in patients with chronic liver disease.
A Comparative Study of the Tensile, Fatigue, and Creep Properties of Sintered (SNW-1000 &amp; GS-44) and Hiped (PY-6) Silicon Nitride Ceramics (2008)

Significant progress has been made in understanding the mechanical properties of two differently processed, namely hot isostatically pressed (HIPed) (GTE-PY6) and sintered silicon nitrides (SNW-1000 and GS-44). Experiments showed that as the temperature increased from room to 1000°C the tensile strengths of sintered SNW-1000 and GS-44, and HIPed PY-6 dropped by 10%, 15%, and more than 26% respectively. At higher temperatures, strength of SNW-1000 dropped much faster than those of GS-44 and PY-6. This is due to the difference in the amount and types of densification aids and the processing of the sintered and the HIPed materials. S-N curves show that endurance limits of SNW-1000 is higher than those of GS-44 at temperatures 1000°C and 1100°C. But at 1200°C the endurance limit of GS 44 is higher than that of SNW-1000. From the results of the creep tests a stress exponent ‘n’ of 9.36 was obtained for PY-6, while SNW-1000 exhibited a stress exponent of 4.32 at 1200°C. The ‘n’ for GS-44 is found to be unity at lower temperatures such as 1100°C, implying that the creep is diffusional. It increased to 2 and above at temperatures 1200°C and 12750C indicating a change in the creep mechanism. In contrast to PY-6, the as-received SNW-1000 and GS-44 revealed amorphous phases at multi-grain junctions and grain boundaries. TEM observations(GS-44) revealed that dislocation density and the number of strain whorls in samples tested at 1000°C is much less than the specimens tested at 12750C under the same stress level.
Трансгенные животные в экспериментальной фармакологии: фокус на рецепторах следовых аминов (2019)

Trace Amine-Associated Receptors (TAARs), discovered twenty years ago, have led to the identification of new treatments for neuropsychiatric disorders. An important fact was that shortly after the discovery of the receptors, a line of transgenic animals with a knockout of the TAAR1 receptor gene was created. The data obtained with the help of transgenic animals made it possible to understand not only the function of receptors, but also the mechanisms of action of psychotropic substances, the interactions of neurotransmitters with trace amines and pathological mechanisms in which trace amines play an important role. This brief review will examine the functions of trace amine receptors and the role of transgenic animals in their study.
Waste Photovoltaic Panels for Ultrapure Silicon and Hydrogen through the Low-Temperature Magnesium Silicide (2017)

Circulation technology of waste photovoltaic panels for production of ultrapure silicon and energy in the form of hydrogen storage was designed and verified. Preparation of magnesium silicide from waste photovoltaic panel’s silicon and partially oxidized magnesium was thoroughly studied. Work was focused on process optimization, thus, three groups of reactors were tested, namely the continuously evacuated open reactor, pre-evacuated batch reactor and semiopened reactors. The influence of reaction temperature was evaluated in the range of 330–630 °C for various reaction atmospheres; argon and/or air at pressures of 5, 33, and 100 kPa; and vacuum in the range of 5–30 Pa. The effect of nitrogen and oxygen presence in the atmosphere on the resulted reaction and reaction rate was also thoroughly studied. The minimum reaction time guaranteeing the total conversion of silicon for two purities of used magnesium was also determined. The produced materials were analyzed by dispersive Raman spectroscopy, scanning electron microscopy with energy dispersive X-ray spectroscopy, and X-ray diffraction. Finally, the reactor filling, which significantly influenced the formation of magnesium silicide, was tested and established minimally at 30% of reactoŕs volume. Hydrolysis of obtained magnesium silicide by diluted acid for silicon hydrides’ (silanes) production and their subsequent thermal decomposition into the ultrapure silicon and hydrogen were successfully verified.
Improving Reproducibility to Meet Minimal Information for Studies of Extracellular Vesicles 2018 Guidelines in Nanoparticle Tracking Analysis (2021)

Nanoparticle tracking analysis (NTA) has been one of several characterization methods used for extracellular vesicle (EV) research since 2006. Many consider that NTA instruments and their software packages can be easily utilized following minimal training and that size calibration is feasible in-house. As both NTA acquisition and software analysis constitute EV characterization, they are addressed in Minimal Information for Studies of Extracellular Vesicles 2018 (MISEV2018). In addition, they have been monitored by Transparent Reporting and Centralizing Knowledge in Extracellular Vesicle Research (EV-TRACK) to improve the robustness of EV experiments (e.g., minimize experimental variation due to uncontrolled factors). Despite efforts to encourage the reporting of methods and controls, many published research papers fail to report critical settings needed to reproduce the original NTA observations. Few papers report the NTA characterization of negative controls or diluents, evidently assuming that commercially available products, such as phosphate-buffered saline or ultrapure distilled water, are particulate-free. Similarly, positive controls or size standards are seldom reported by researchers to verify particle sizing. The Stokes-Einstein equation incorporates sample viscosity and temperature variables to determine particle displacement. Reporting the stable laser chamber temperature during the entire sample video collection is, therefore, an essential control measure for accurate replication. The filtration of samples or diluents is also not routinely reported, and if so, the specifics of the filter (manufacturer, membrane material, pore size) and storage conditions are seldom included. The International Society for Extracellular Vesicle (ISEV)'s minimal standards of acceptable experimental detail should include a well-documented NTA protocol for the characterization of EVs. The following experiment provides evidence that an NTA analysis protocol needs to be established by the individual researcher and included in the methods of publications that use NTA characterization as one of the options to fulfill MISEV2018 requirements for single vesicle characterization.
Probing spin-orbit interaction via Fano interference (2018)

We experimentally investigate the behavior of the Fano-like plasmonic resonance lineshape in a simple plasmonic system comprising a subwavelength hole or a particle illuminated by a tightly focused Gaussian beam. We observe that for a small lateral displacement of the scatterer, the k-space distribution of the plasmonic wave exhibits a strong spin-dependent azimuthal variation. We attribute this phenomenon to the sensitive light-plasmon coupling conditions arising due to the specific phase matching requirements. This effect is qualitatively described by a Fano-like interference with a complex coupling factor.
Evaluation of the early effect of local irradiation on normal rodent bone marrow metabolism using FDG: preclinical PET studies. (2000)

In this experimental system, normal marrow uptake of FDG transiently rose, then fell, and ultimately returned to baseline after external beam irradiation. Knowledge of this biphasic early irradiation effect on normal bone marrow may be important when the efficacy of radiation therapy on bone metastasis is evaluated using FDG PET after irradiation.
Evaluation of European Union aid to African, Caribbean and Pacific countries. Synthesis report (1998)

This report is based on the findinRS of an evaluation process which included a desk
<i>In vitro</i>Antiviral Diterpenes from the Brazilian Brown Alga<i>Dictyota pfaffii</i> (2004)

Specimens of Dictyota pfaffii from Atol das Rocas, Northeast Brazil, afforded the rare dolabellane diterpene 10,18-diacetoxy-8-hydroxy-2, 6-dolabelladiene (1) and the new 10-acetoxy-8,18-di-hydroxy-2,6-dolabelladiene (2). Reduction of 1 yielded 8,10,18-trihydroxy-2,6-dolabelladiene (3), also present in the crude ex-tract of D. pfaffii. All three structures were assigned by 1D and 2D NMR spectral data. These substances showed strong anti-HSV-1 activity in vitro but only 3 inhibited the reverse transcriptase enzyme of HIV-1.
Determination of paclitaxel and its analogues in the needles of <i>Taxus</i> species by using negative pressure cavitation extraction followed by HPLC‐MS‐MS (2009)

A new separation method, negative pressure cavitation (NPC) extraction followed by HPLC-MS-MS for the determination of paclitaxel and its analogues in the needles of Taxus species is described in this study. Compared with three conventional extraction methods, NPC is a more effective, economical, and facile method for the separation of nature compounds from herbal plants. In contrast to high-temperature extraction, NPC at low temperature can minimize undesirable reactions such as thermal decomposition or degradation. In addition, the extraction mechanism of NPC was also illuminated. The effects of vacuum degree, extraction solvent, ratio of solid to liquid, time, and times extraction were studied and optimized. The optimum extraction conditions were as follows: vacuum degree -0.03 MPa, solvent 80% v/v alcohol, ratio of material to liquid 1:15 (g/mL), extraction time 60 min, extraction (x3). Using these conditions, the recoveries of 10-deacetyl-7-xylosylpaclitaxel, 10-deacetylpaclitaxel, cephalomannine, and paclitaxel were higher than 95.88, 95.82, 94.85, and 96.18%, respectively. The contents of paclitaxel, 10-deacetyl-7-xylosylpaclitaxel, 10-deacetylpaclitaxel, and cephalomannine for Taxus chinensis were 0.0053, 0.0467, 0.0132, and 0.0076%, and 0.0067, 0.0153, 0.0047, and 0.0064% for Taxus cuspidata, respectively. Furthermore, a comparison of SEM images observed the morphological changes of microstructures and cellular damage in yew needles.
Commentary on “The Effects of Musical Fit On Choice Between Competing Pairs of Cultural Products” (2009)

ABSTRACT: Yeoh and North (2009) believe their findings are a clear indication that musical fit can influence product choice among a non-Western sample; pieces of Indian and Malay music primed the selection of one corresponding type of product over another, while when there was no music played the choices indicated no reliable preference for either Indian or Malay items. However, a closer look at their methods of sampling, stimuli, procedures, and results, makes it clear that these conclusions are unfounded.
Supplementary Tables 1-4 from Changes in CpG Islands Promoter Methylation Patterns during Ductal Breast Carcinoma Progression (2023)

Supplementary Tables 1-4 from Changes in CpG Islands Promoter Methylation Patterns during Ductal Breast Carcinoma Progression
Hierarchical Superstructures: Superstructured Biomaterials Formed by Exchange Dynamics and Host–Guest Interactions in Supramolecular Polymers (Adv. Sci. 8/2021) (2021)

Dynamic and reversible assembly of molecules is ubiquitous in the hierarchical superstructures of living systems and plays a key role in cellular functions. In article number 2004042 by Samuel I. Stupp and co‐workers, host ‐guest interactions between b‐cyclodextrin and adamantane‐functionalized peptide amphiphiles led to analogous superstructure formation among nanofibers. The cover displays this hierarchical superstructure formation of fluorescently labelled peptide amphiphile nanofibers captured by confocal microscopy. [Image: see text]