gebhart/patrepeval huggingface dataset:
Activities of Quinolones Against Obligately Anaerobic Bacteria (2007)

Quinolones are of clinical and scientific interest since their discovery based on the nalidixic acid in the early 1960s. They are based on two types of ring structures, the quinolone nucleus and the naphthyridone nucleus. Nalidixic acid as the first discovered agent is a naphthyridone and has only a moderate activity against Gram-negative rods. The modification of the quinolone and naphthyridone structures resulted in increasing activities of the quinolones against Gram-negative, Gram-positive, atypical and obligately anaerobic bacteria and mycobacteria. The quinolones are now divided into four groups due to their different spectrum of activity. The first and second group of quinolones i.e. norfloxacin, ciprofloxacin or ofloxacin have no or only little activity against obligately anaerobic bacteria. In contrast, the newer quinolones like sitafloxacin, clinafloxacin, trovafloxacin, moxifloxacin, gatifloxacin, garenoxacin and others like i.e. WCK 771 and ATB-492 have significant improved activities against anaerobes. Thus, these quinolones have been considered for the treatment of anaerobe and mixed infections. The present review provides an overview of the activities of quinolones against obligately anaerobic bacteria as described by in vitro as well as in vivo studies. Keywords: Quinolones, naphthyridones, anaerobes, aerobe/anaerobe mixed infections
Specific and photostable rhodamine-based tracker for 3D video imaging of single acidic organelles (2014)

Three-dimensional video imaging has emerged as an indispensable tool for real-time monitoring of dynamic acidic organelles. However, the limitation of video imaging is the absence of a specific stain for acidic organelle trackers. The aim of this work was to investigate the applicability of a potential acidic organelle tracker, Lyso-R, in three-dimensional video imaging in live cells. In a close examination of three differently designed rhodamine dyes, Lyso-R outperformed the other two with a suitable pKa value and higher membrane permeability. The uninterrupted fluorescence of Lyso-R towards macromolecules, e.g. lecithin and proteins, led to higher specificity and signal-to-background ratio than LysoTracker DND 189 and DND 99 for imaging acidic organelles. In addition, Lyso-R was photostable, and MTT assays confirmed its low toxicity towards cells. Inspired by these facts, three-dimensional tracking of a single acidic organelle in a live cell was obtained by staining with Lyso-R under confocal microscopy. The measurement of this organelle demonstrated that the distance change of the organelle centroid on XY plane was sharper than its depth change. The usage of Lyso-R was further extended with two-dimensional video imaging of acidic organelles during various cell metabolisms. All of these results demonstrate the potential applicability of Lyso-R as a three-dimensional imaging tracker of acidic organelles.
Characterization of minor constituents in commercial oleic acid (1982)

Abstract Minor constituents were isolated from a mixture of commercial oleic acid manufactured from beef tallow by 10 different companies. Silicic acid was used as an adsorbent to isolate the minor constituents. They were first separated into acidic and nonacidic fractions. Each fraction was then separated into numerous subfractions by stepwise gradient elution liquid chromatography, using silicic acid as the adsorbent. The subfractions which had an adverse effect on the color stability of oleic acid during heating were characterized with functional group analysis, elemental analysis and IR spectrophotometry. The minor constituents amounted to ca. 1.18% of the commercial oleic acid. They were complex mixtures with multiple functional groups. Some of the subfractions contained 2\s‐3 times as much oxygen in the molecule as oleic acid. They had molecular weights ranging from 308 to 830 which are from monomers to trimers of oxidized oleic acid. These minor components contained carbonyl, ester and hydroxyl groups and double bonds. Some of the nonacidic minor constituents may contain amide groups. Most of the acidic subfractions were dark red, viscous liquids and the nonacidic subfractions were dark green or greenish‐brown, semisolid substances. A relationship was established that the greater the polarity of the minor constituents, the greater is its adverse effect on the color stability of oleic acid during heating.
Gain-of-Function Mutations inRARBCause Intellectual Disability with Progressive Motor Impairment (2016)

Retinoic acid (RA) signaling plays a key role in the development and function of several systems in mammals. We previously discovered that the de novo mutations c.1159C>T (p.Arg387Cys) and c.1159C>A (p.Arg387Ser) in the RA Receptor Beta (RARB) gene cause microphthalmia and diaphragmatic hernia. However, the natural history of affected subjects beyond the prenatal or neonatal period was unknown. Here, we describe nine additional subjects with microphthalmia who have de novo mutations in RARB, including the previously described p.Arg387Cys as well as the novel c.887G>C (p.Gly296Ala) and c.638T>C (p.Leu213Pro). Moreover, we review the information on four previously reported cases. All subjects who survived the neonatal period (n = 10) displayed severe global developmental delay with progressive motor impairment due to spasticity and/or dystonia (with or without chorea). The majority of subjects also showed Chiari type I malformation and severe feeding difficulties. We previously found that p.Arg387Cys and p.Arg387Ser induce a gain-of-function. We show here that the p.Gly296Ala and p.Leu213Pro RARB mutations further promote the RA ligand-induced transcriptional activity by twofold to threefold over the wild-type receptor, also indicating a gain-of-function mechanism. These observations suggest that precise regulation of RA signaling is required for brain development and/or function in humans.
One-Step Regio- and Stereoselective Electrochemical Synthesis of Orexin Receptor Antagonist Oxidative Metabolites (2022)

Synthesis of drug metabolites, which often have complex structures, is an integral step in the evaluation of drug candidate metabolism, pharmacokinetic (PK) properties, and safety profiles. Frequently, such synthetic endeavors entail arduous, multiple-step de novo synthetic routes. Herein, we present the one-step Shono-type electrochemical synthesis of milligrams of chiral α-hydroxyl amide metabolites of two orexin receptor antagonists, MK-8133 and MK-6096, as revealed by a small-scale (pico- to nano-mole level) reaction screening using a lab-built online electrochemistry (EC)/mass spectrometry (MS) (EC/MS) platform. The electrochemical oxidation of MK-8133 and MK-6096 was conducted in aqueous media and found to produce the corresponding α-piperidinols with exclusive regio- and stereoselectivity, as confirmed by high-resolution nuclear magnetic resonance (NMR) characterization of products. Based on density functional theory (DFT) calculations, the exceptional regio- and stereoselectivity for this electrochemical oxidation are governed by more favorable energetics of the transition state, leading to the preferred secondary carbon radical α to the amide group and subsequent steric hindrance associated with the U-shaped conformation of the cation derived from the secondary α-carbon radical, respectively.
Estimating ASME Section III and VIII Heat Exchanger Nozzle Loads (2009)

Heat Exchange Institute (HEI) Standards for Power Plant Heat Exchangers, 4th Edition provides guidance on how to estimate the nozzle loads of cylindrical shells. The procedure covered in one of the appendices of the document relies on WRC Bulletin 107 methodology which uses internal pressure, physical geometry and material properties to estimate external forces and moments. The forces and moments are the limiting loads when the heat exchanger material is taken to yield. The material yield defines the range of possible load combinations that will meet the design criteria. However, for operability, the design criteria sometimes may differ from the yield but usually is based on heat exchanger supplier experience. This paper provides a way to estimate heat exchanger nozzle loads that more closely reflect operating conditions that take into account supplier experience. In this paper, generalized load formulae are developed for the nozzles. The formulae are iteratively solved to meet the stress criteria based on supplier experience. The resultant loads are evaluated using WRC Bulletin 107 to ensure that the loads are bounded by the acceptance criteria. Unbounded loads are rejected and reiterated until the loads are acceptable.
Measuring the subjective response to interior lighting: paired comparisons and semantic differential scaling (2003)

Paired comparisons and semantic differential (SD) scales were used as part of a larger study assessing subjective responses to linear fluorescent direct/indirect lighting systems. Two experiments were performed under identical lighting conditions, one with each technique, yielding independent subjective response data sets for the same light settings. This article compares independent multidimensional scaling solutions from the two datasets and describes an intercorrelation analysis of the SD scaling responses. These analyses highlight strengths and weaknesses of the two psychometric techniques. Guidance is offered for applying paired comparisons and SD scales in future lighting research.
Impaired flow-induced dilation in mesenteric resistance arteries from receptor protein tyrosine phosphatase-μ-deficient mice (2005)

The transmembrane receptor-like protein tyrosine phosphatase-mu (RPTPmu) is thought to play an important role in cell-cell adhesion-mediated processes. We recently showed that RPTPmu is predominantly expressed in the endothelium of arteries and not in veins. Its involvement in the regulation of endothelial adherens junctions and its specific arterial expression suggest that RPTPmu plays a role in controlling arterial endothelial cell function and vascular tone. To test this hypothesis, we analyzed myogenic responsiveness, flow-induced dilation, and functional integrity of mesenteric resistance arteries from RPTPmu-deficient (RPTPmu(-/-)) mice and from wild-type littermates. Here, we show that cannulated mesenteric arteries from RPTPmu(-/-) mice display significantly decreased flow-induced dilation. In contrast, mechanical properties, myogenic responsiveness, responsiveness to the vasoconstrictors phenylephrine or U-46619, and responsiveness to the endothelium-dependent vasodilators methacholine or bradykinin were similar in both groups. Our results imply that RPTPmu is involved in the mechanotransduction or accessory signaling pathways that control shear stress responses in mesenteric resistance arteries.
ChemInform Abstract: Giant Magnetoresistance and Related Properties of Rare‐Earth Manganates and Other Oxide Systems (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Label‐free quantitative analysis of the membrane proteome of Bace1 protease knock‐out zebrafish brains (2013)

The aspartyl protease BACE1 cleaves neuregulin 1 and is involved in myelination and is a candidate drug target for Alzheimer's disease, where it acts as the β-secretase cleaving the amyloid precursor protein. However, little is known about other substrates in vivo. Here, we provide a proteomic workflow for BACE1 substrate identification from whole brains, combining filter-aided sample preparation, strong-anion exchange fractionation, and label-free quantification. We used bace1-deficient zebrafish and quantified differences in protein levels between wild-type and bace1 -/- zebrafish brains. Over 4500 proteins were identified with at least two unique peptides and quantified in both wild-type and bace1 -/- zebrafish brains. The majority of zebrafish membrane proteins did not show altered protein levels, indicating that Bace1 has a restricted substrate specificity. Twenty-four membrane proteins accumulated in the bace1 -/- brains and thus represent candidate Bace1 substrates. They include several known BACE1 substrates, such as the zebrafish homologs of amyloid precursor protein and the cell adhesion protein L1, which validate the proteomic workflow. Additionally, several candidate substrates with a function in neurite outgrowth and axon guidance, such as plexin A3 and glypican-1 were identified, pointing to a function of Bace1 in neurodevelopment. Taken together, our study provides the first proteomic analysis of knock-out zebrafish tissue and demonstrates that combining gene knock-out models in zebrafish with quantitative proteomics is a powerful approach to address biomedical questions.
Elastic constants, internal friction, and piezoelectric coefficient ofα−TeO2 (2004)

We studied the interrelationship of elastic and piezoelectric properties with the lattice structure and crystal physics of paratellurite $(\ensuremath{\alpha}\ensuremath{-}{\mathrm{TeO}}_{2}).$ Tetragonal paratellurite ${(D}_{4}^{4},P422)$ shows six independent elastic constants ${C}_{\mathrm{ijkl}},$ the associated internal friction ${Q}_{\mathrm{ijkl}}^{\ensuremath{-}1},$ and one piezoelectric coefficient ${e}_{14}.$ We determined simultaneously these material coefficients using resonant ultrasound spectroscopy coupled with laser-Doppler interferometry. Mode identification, essential for success, was done by measuring the displacement distributions on a vibrating-specimen surface. Our ${C}_{\mathrm{ijkl}}$ were consistent with reported values measured by conventional methods. Our ${e}_{14}$ exceeds the reported value by 53%. We focus on several unusual elastic properties, including a negative Poisson ratio. Considering a star-shape truss structure on the basal plane consistently explains all of them. Internal friction correlates with the ${C}_{\mathrm{ijkl}}$ temperature derivatives, suggesting phonon-phonon interactions as a dominant cause of the mechanical loss.
Human umbilical vein endothelial cell killing by activated neutrophils. Loss of sensitivity to injury is accompanied by decreased iron content during in vitro culture and is restored with exogenous iron. (1992)

First passage human umbilical vein endothelial cells (HUVECs) were sensitive to killing by activated neutrophils and reagent hydrogen peroxide (H2O2). Catalase and deferoxamine prevented killing whereas soybean trypsin inhibitor and superoxide dismutase did not. In these regards, HUVECs are similar to previously characterized endothelial cells from bovine and rat. Although first passage HUVECs were killed by activated neutrophils, sensitivity fell off rapidly as the cells were maintained in culture. At passage 2 (four population doublings), and beyond, HUVECs were highly resistant. The cells also became resistant to killing by reagent H2O2. The acquisition of resistance to killing was not accompanied by a failure to up-regulate neutrophil adhesion molecules or to support neutrophil adhesion. Levels of intracellular anti-oxidants (total thiols, though not glutathione, glutathione peroxidase or catalase activity) increased as a function of passage in culture. However, levels of glutathione and total thiols in late passage (resistant) HUVECs were similar to levels in late passage rat pulmonary artery endothelial cells, that were sensitive to killing by activated neutrophils. Cell-associated iron in HUVECs fell as a function of time in culture. By passage 2, the amount of total iron measurable with the Ferrozine reagent was only about 30% of the amount recovered from first passage HUVECs. The loss of iron from the cells may underlie much of the concomitant resistance to killing because when the cells were pretreated with iron under conditions in which it could be taken up, sensitivity to killing by activated neutrophils and by H2O2 was restored.
Theranostic Nanoparticles and Their Spectrum in Cancer (2019)

Nanoparticles offer a lot of advantageous backgrounds for many applications due to their physical, chemical and biological properties. Their different composition (metals, lipids, polymers, peptides) and shapes (spheres, rods, pyramids, flowers and so on) are influenced by the synthesis methods and functionalization procedures. However, in the medical field, researchers focus on the biocompatibility and biodegradability of the nanoparticles in their attempts for a targeted therapy in which the nanocarriers need to bypass certain biological barriers. Moreover, the increased interest in molecular imaging has brought nanoparticles in the spotlight for their applications in two distinct directions: therapy and diagnosis. Furthermore, recent advances in nanoparticle designs have introduced novel nano-objects suitable as both detection and delivery systems at the same time, thus providing theranostic applications.
Integrated Pilot Plant for a Large Cold Crucible Induction Melter (2002)

COGEMA has been vitrifying high-level liquid waste produced during nuclear fuel reprocessing on an industrial scale for over 20 years, with two main objectives: containment of the long lived fission products and reduction of the final volume of waste. Research performed by the French Atomic Energy Commission (CEA) in the 1950s led to the selection of borosilicate glass as the most suitable containment matrix for waste from spent nuclear fuel and to the development of the induction melter technology. This was followed by the commissioning of the Marcoule Vitrification Facility (AVM) in 1978. The process was implemented at a larger scale in the late 1980s in the R7 and T7 facilities of the La Hague reprocessing plant. COGEMA facilities have produced more than 11,000 high level glass canisters, representing more than 4,500 metric tons of glass and 4.5 billion curies. To further improve the performance of the vitrification lines in the R7 and T7 facilities, the CEA and COGEMA have been developing the Cold Crucible Melter (CCM) technology since the 1980s. This technology benefits from the 20 years of COGEMA HLW vitrification experience and ensures a virtually unlimited equipment service life and extensive flexibility in dealing with different types of waste. The high specific power directly transferred by induction to the melt allows high operating temperatures without any impact on the process equipment. In addition, the mechanical stirring of the melter significantly reduces operating constraints. COGEMA is already providing the CCM technology to international customers for nuclear and non-nuclear applications and plans to implement it in the La Hague vitrification plant for the vitrification of highly concentrated and corrosive solutions produced by uranium/molybdenum fuel reprocessing. The paper presents the CCM project that led to the building and start-up of this evolutionary and flexible pilot plant. It also describes the plant's technical characteristics and reports commissioning results.
Two-dimensional materials for low power and high frequency devices (2015)

In this paper, we present an overview of the current state-of-the-art in two-dimensional materials beyond graphene, and summarize device performance reported to-date. There is promise for these layered materials to be the foundation of a new area in low power and high frequency electronics, with early reports indicating 10s of gigahertz (GHz) operation without significant optimization of parasitic resistances or capacitances. In addition, we discuss the synthesis of transition metal dichalcogenides and the integration of as-grown material into heterostructures and electronic devices. Finally, we discuss the impact of surface preparation on the integration of dielectrics with MoS<sub>2</sub> required to achieve GHz performance.
Specific Binding of Estrogen to Nuclei from Japanese Quail Kidney Cells (1978)

The binding properties of estrogen to Japanese quail kidney cell nuclei were evaluated by 3H-17 beta-estradiol exchange. Kidney cell nuclei from estrogenized male, as well as laying female quail, had a single class of saturable (0.1-0.2 pmol/mg DNA), high affinity (Kd = 1-2 x 10-10M) nuclear binding sites for 17 beta-estradiol. High affinity estrogen binding sites were not found in kidney cell nuclei from untreated males. Various non-radioactive estrogens (17 beta-estradiol, estrone, estriol and diethylstilbestrol) competed effectively with 3H-17 beta-estradiol for the high affinity binding sites, whereas nonestrogens (testosterone and progesterone) did not complete. It is concluded that the 3H-estradiol binding characteristics of kidney cell nuclei provides strong evidence for a nuclear estrogen receptor in the avian kidney.
The dependence of Schottky junction (I–V) characteristics on the metal probe size in nano metal–semiconductor contacts (2018)

We have studied the dependence of Schottky junction (I–V) characteristics on the metal contact size in metal–semiconductor (M–S) junctions using different metal nanoprobe sizes. The results show strong dependence of (I–V) characteristics on the nanoprobe size when it is in contact with a semiconductor substrate. The results show the evolution from sub-10 nm reversed Schottky diode behavior to the normal diode behavior at 100 nm. These results also indicate the direct correlation between the electric field at the M–S interface and the Schottky rectification behavior. The effect of the metal contact size on nano-Schottky diode structure is clearly demonstrated, which would help in designing a new type of nano-devices at sub-10 nm scale.
Centrifugation does not remove bacteria from the fat fraction of human milk (2021)

Analysis of the human milk microbiome is complicated by the presence of a variable quantity of fat. The fat fraction of human milk is typically discarded prior to analysis. It is assumed that all cells are pelleted out of human milk by high speed centrifugation; however, studies of bovine milk have reported that bacteria may remain trapped within the fat fraction. Here, the bacterial DNA profiles of the fat fraction and cell pellet of human milk (n = 10) were analysed. Human and bacterial DNA was consistently recovered from the fat fraction of human milk (average of 12.4% and 32.7%, respectively). Staphylococcus epidermidis was significantly more abundant in the cell pellet compared to the fat fraction (P = 0.038), and three low-abundance species (< 5% relative abundance) were recovered from one fraction only. However, inclusion of fat reduced the efficiency of DNA extraction by 39%. Culture-based methods were used to quantify the distribution of an exogenously added strain of Staphylococcus aureus in human milk fractions. S. aureus was consistently recovered from the fat fraction (average 28.9%). Bacterial DNA profiles generated from skim milk or cell pellets are not representative of the entire human milk microbiome. These data have critical implications for the design of future work in this field.
Treatment of Complex Regional Pain Syndrome (CRPS) Using Low Dose Naltrexone (LDN) (2013)

Complex Regional Pain Syndrome (CRPS) is a neuropathic pain syndrome, which involves glial activation and central sensitization in the central nervous system. Here, we describe positive outcomes of two CRPS patients, after they were treated with low-dose naltrexone (a glial attenuator), in combination with other CRPS therapies. Prominent CRPS symptoms remitted in these two patients, including dystonic spasms and fixed dystonia (respectively), following treatment with low-dose naltrexone (LDN). LDN, which is known to antagonize the Toll-like Receptor 4 pathway and attenuate activated microglia, was utilized in these patients after conventional CRPS pharmacotherapy failed to suppress their recalcitrant CRPS symptoms.