gebhart/patrepeval huggingface dataset:
Upper Cretaceous Stratigraphy and Micropaleontology of the Crowsnest Pass - Waterton Area, Southern Alberta Foothills (1977)

ABSTRACT The Upper Cretaceous in the southern Alberta Foothills is represented almost entirely by clastic sediments with a maximum thickness of about 14,000 ft (4270 m). This essentially uninterrupted sequence, in which all stages from the late Cenomanian through the Maestrichtian are represented, consists of alternating phases of marine, littoral or deltaic, and continental deposition. In ascending order, the major rock units consist of the Alberta Group (Blackstone, Cardium and Wapiabi Formations), Belly River, Bearpaw, Blood Reserve, St. Mary River and Willow Creek Formations. Of these units, the Blackstone, Wapiabi and Bearpaw are predominantly shale and marine in origin; the Cardium, Blood Reserve and lower part of the St. Mary River are somewhat arenaceous and represent littoral to deltaic regimes; the Belly River, most of the St. Mary River, and the Willow Creek consist of varying proportions of shale, siltstone and sandstone, and were deposited mainly under continental conditions. A succession of 11 microfaunas is recognized in the Alberta Group and Bearpaw Formation. In order of decreasing age, with indicated environments in parentheses, these are the lower pelagic (outer shelf to upper bathyal) and Pseudoclavulina sp. (nearshore) in the Blackstone Formation; the Trochammina sp. 1 (nearshore), Anomalina (inner shelf), Brachycythere-Bullopora (inner shelf), Anomalinoides henbesti (middle shelf), upper pelagic (middle to outer shelf) and unnamed agglutinated (nearshore) in the Wapiabi Formation; and ostracode (supralittoral), arenaceous foraminiferal (nearshore) and Gavelinella talaria (offshore) in the Bearpaw Formation.
Separation of 1-acylglycerolphosphate acyltransferase and 1-acylglycerolphosphorylcholine acyltransferase of rat liver microsomes. (1975)

1-Acylglycerolphosphate acyltransferase (Ec 2.3.1-) and 1-acylglycerolphosphorylcholine acyltransferase (EC 2.3.1.23) of rat liver microsomes were separated from each other. The separation was achieved by sucrose density gradient centrifugation of the enzyme preparation that was obtained by solubilizing microsomes with a nonionic detergent, Triton X-100, and subjecting the solubilized microsomes to molecular-sieve chromatography. The two acyltransferases are distinguishable from each other also with respect to their stabilities to heat and to Triton X-100. Hence, it is concluded that these acyltransferases are distinct enzymes. These results, together with our previous finding that glycerolphosphate acyltransferase is also a separate enzyme, demonstrate the presence of distinct acyltransferases responsible for the acylation of the different acyl acceptors. Furthermore, the acyl-donor specificities of these acyltransferases provide the enzymatic basis for the nonrandom distribution of fatty acids in naturally occurring glycerolipids.
New Online Biomonitoring System for <i>Gammarus pulex</i> (L.) (Crustacea):  <i>In Situ</i> Test Below a Copper Effluent in South Sweden (1998)

Online biomonitors register biological effects of toxic discharges on selected indicator species and allow for fast, continuous, and ecological relevant water quality control. This paper presents a new online biomonitor based on a quadropole impedance conversion technique that records simultaneously several behavioral parameters of Gammarus pulex, a new biomonitoring test species. The behavior of two different populations of G. pulex was compared; one population originated from an anthropogenically unpolluted stream, and the other population lived at the copper-polluted study site, where the biomonitor was placed. Responses to simulated copper pollution peaks of 70 μg of Cu2+/L were registered in the biomonitor and compared to the natural drift. G. pulex was the most abundant species in the natural drift. A nocturnal drift maximum was found in the natural drift and for both popula tions in the biomonitor. Mortality was high in the biomonitor; the local population survived slightly better than the reference population. The reference population showed significantly less activity than the local population measured as number of active organisms per day and time spent on locomotion and ventilation. Copper pollution pulses provoked increases in number of active organisms and time spent on locomotion in the biomonitor; however, no significant changes in the natural drift were registered.
Plasma concentrations of pemafibrate with co-administered drugs predicted by physiologically based pharmacokinetic modeling in virtual populations with renal/hepatic impairment (2020)

Pharmacokinetic profiles of pemafibrate with virtual drug and/or disease interactions were assessed by creating a detailed physiologically based pharmacokinetic (PBPK) model.Passive diffusion clearance in liver was experimentally determined as 0.013 mL/min/10<sup>6</sup> human hepatocytes. <i>In vitro</i> intrinsic clearance values for pemafibrate by cytochromes P450 2C8, 2C9, and 3A4 were 54, 26, and 16 μL/min/mg protein, respectively. Values for the effective permeability and the intrinsic clearance of hepatic uptake by organic anion transporting polypeptide (OATP) 1B1 were optimized in a simulator platform.This PBPK model was subsequently validated using reported maximum pemafibrate plasma concentration and area under the curve values in reported interaction studies in healthy subjects co-administered with rifampicin.For subjects with Child-Pugh A and B liver cirrhosis, the intrinsic clearance of hepatic uptake of pemafibrate by OATP1B1 were modeled using 53% and 31% of that of healthy subjects, respectively. Virtual co-administrations of rifampicin and sacubitril (OATP1B inhibitors) in subjects with renal impairment and liver cirrhosis resulted in 11- to 13-folds (rifampicin) and 1.1- to 1.3-folds (sacubitril) increased plasma exposures of pemafibrate.The current PBPK model and simulations revealed different pharmacokinetic profiles for pemafibrate following co-administration of rifampicin or sacubitril in virtual subjects with or without renal/hepatic impairment.
Chromium Supplementation Does Not Improve Glucose Tolerance, Insulin Sensitivity, or Lipid Profile (2005)

Chromium supplements are thought to be the second most commonly taken nutritional supplement, used by an estimated 10 million Americans (1). Chromium is an essential element in humans, and deficiency is associated with the development of diabetes, which was first noted in patients receiving long-term parenteral nutrition before the advent of routine chromium supplementation (2,3). In these patients, diabetes resolved following chromium replacement (2–4).

The dietary requirement for chromium is controversial, with the recommended daily intake in the U.S. being 0.05–0.20 μg (5). Chromium is abundant in the environment; however, aside from the extreme situation of unsupplemented parenteral nutrition, it has proven difficult to ascertain any clinical effects, due solely to chromium deficiency. Despite these difficulties, chromium supplements are widely promoted in the complementary health industries.

There are many studies examining the effects of various forms of chromium supplementation (rev. in 6,7). These studies utilized a variety of chromium formulations, varying doses, and patients with normal glucose tolerance, diabetes, or gestational diabetes. The outcomes have been inconsistent. Some studies showed no benefit, and other studies have shown inconsistent improvements in glucose, insulin resistance, and/or lipids. The paucity of data has prompted the National Institutes of Health to release a program announcement to address the issue: “Chromium as an adjuvant therapy …
Long insert whole genome sequencing for copy number variant and translocation detection (2013)

As next-generation sequencing continues to have an expanding presence in the clinic, the identification of the most cost-effective and robust strategy for identifying copy number changes and translocations in tumor genomes is needed. We hypothesized that performing shallow whole genome sequencing (WGS) of 900-1000-bp inserts (long insert WGS, LI-WGS) improves our ability to detect these events, compared with shallow WGS of 300-400-bp inserts. A priori analyses show that LI-WGS requires less sequencing compared with short insert WGS to achieve a target physical coverage, and that LI-WGS requires less sequence coverage to detect a heterozygous event with a power of 0.99. We thus developed an LI-WGS library preparation protocol based off of Illumina's WGS library preparation protocol and illustrate the feasibility of performing LI-WGS. We additionally applied LI-WGS to three separate tumor/normal DNA pairs collected from patients diagnosed with different cancers to demonstrate our application of LI-WGS on actual patient samples for identification of somatic copy number alterations and translocations. With the evolution of sequencing technologies and bioinformatics analyses, we show that modifications to current approaches may improve our ability to interrogate cancer genomes.
Nonproportional response of LaBr<sub>3</sub>:Ce and LaCl<sub>3</sub>:Ce scintillators to synchrotron x-ray irradiation (2010)

The nonproportional scintillation response of LaBr(3) doped with 5% Ce(3+) and of LaCl(3) doped with 10% Ce(3+) was measured using highly monochromatic synchrotron irradiation. To estimate the photon response, pulse height spectra at many finely spaced energy values between 9 and 100 keV were measured. The experiment was carried out at the X-1 beamline at the Hamburger Synhrotronstrahlungslabor (HASYLAB) synchrotron radiation facility in Hamburg, Germany. Special attention was paid to the x-ray fluorescence escape peaks as they provide us with additional information about photon response in the range 1.2-14.5 keV for LaBr(3):Ce and 2.0-11.6 keV for LaCl(3):Ce. A rapid variation of the photon response curve is observed near the lanthanum K-electron binding energy for both scintillators. A dense sampling of data was performed around this energy and those data are used to apply a method, which we call K-dip spectroscopy. This method allows us to derive the electron response curves of LaBr(3):Ce and LaCl(3):Ce down to energies as low as 0.1 keV.
Negative Capacitance in a Ferroelectric Capacitor (2014)

The Boltzmann distribution of electrons poses a fundamental barrier to lowering energy dissipation in conventional electronics, often termed as Boltzmann Tyranny. Negative capacitance in ferroelectric materials, which stems from the stored energy of phase transition, could provide a solution, but a direct measurement of negative capacitance has so far been elusive. Here we report the observation of negative capacitance in a thin, epitaxial ferroelectric film. When a voltage pulse is applied, the voltage across the ferroelectric capacitor is found to be decreasing with time-in exactly the opposite direction to which voltage for a regular capacitor should change. Analysis of this inductance-like behavior from a capacitor presents an unprecedented insight into the intrinsic energy profile of the ferroelectric material and could pave the way for completely new applications.
High Performance Composites Research at NASA-Langley (1988)

<div class="htmlview paragraph">Barriers to the more extensive use of advanced composites in heavily loaded structure on commercial transports are discussed from a materials viewpoint. NASA-Langley matrix development activities designed to overcome these barriers are presented. These include the synthesis of processable, tough, durable matrices, the development of resin property/composite property relationships which help guide the synthesis program, and the exploitation of new processing technology to effectively combine reinforcement filament with polymer matrices. Examples of five classes of polymers being investigated as matrix resins at NASA-Langley will be presented, including amorphous and semi-crystalline thermoplastics, lightly crosslinked thermoplastics, semi-interpenetrating networks and toughened thermosets. Relationships between neat resin modulus, resin fracture energy, interlaminar fracture energy, composite compression strength, and post-impact compression strength will be shown. Powder and slurry processing techniques will be discussed.</div>
Identification of Comamonas testosteroni as an androgen degrader in sewage (2016)

Numerous studies have reported the masculinization of freshwater wildlife exposed to androgens in polluted rivers. Microbial degradation is a crucial mechanism for eliminating steroid hormones from contaminated ecosystems. The aerobic degradation of testosterone was observed in various bacterial isolates. However, the ecophysiological relevance of androgen-degrading microorganisms in the environment is unclear. Here, we investigated the biochemical mechanisms and corresponding microorganisms of androgen degradation in aerobic sewage. Sewage samples collected from the Dihua Sewage Treatment Plant (Taipei, Taiwan) were aerobically incubated with testosterone (1 mM). Androgen metabolite analysis revealed that bacteria adopt the 9, 10-seco pathway to degrade testosterone. A metagenomic analysis indicated the apparent enrichment of Comamonas spp. (mainly C. testosteroni) and Pseudomonas spp. in sewage incubated with testosterone. We used the degenerate primers derived from the meta-cleavage dioxygenase gene (tesB) of various proteobacteria to track this essential catabolic gene in the sewage. The amplified sequences showed the highest similarity (87-96%) to tesB of C. testosteroni. Using quantitative PCR, we detected a remarkable increase of the 16S rRNA and catabolic genes of C. testosteroni in the testosterone-treated sewage. Together, our data suggest that C. testosteroni, the model microorganism for aerobic testosterone degradation, plays a role in androgen biodegradation in aerobic sewage.
N6-Methyladenine DNA modification in Xanthomonas oryzae pv. oryzicola genome (2018)

DNA N6-methyladenine (6mA) modifications expand the information capacity of DNA and have long been known to exist in bacterial genomes. Xanthomonas oryzae pv. Oryzicola (Xoc) is the causative agent of bacterial leaf streak, an emerging and destructive disease in rice worldwide. However, the genome-wide distribution patterns and potential functions of 6mA in Xoc are largely unknown. In this study, we analyzed the levels and global distribution patterns of 6mA modification in genomic DNA of seven Xoc strains (BLS256, BLS279, CFBP2286, CFBP7331, CFBP7341, L8 and RS105). The 6mA modification was found to be widely distributed across the seven Xoc genomes, accounting for percent of 3.80, 3.10, 3.70, 4.20, 3.40, 2.10, and 3.10 of the total adenines in BLS256, BLS279, CFBP2286, CFBP7331, CFBP7341, L8, and RS105, respectively. Notably, more than 82% of 6mA sites were located within gene bodies in all seven strains. Two specific motifs for 6 mA modification, ARGT and AVCG, were prevalent in all seven strains. Comparison of putative DNA methylation motifs from the seven strains reveals that Xoc have a specific DNA methylation system. Furthermore, the 6 mA modification of rpfC dramatically decreased during Xoc infection indicates the important role for Xoc adaption to environment.
Large‐scale mammalian cell culture: Design and use of an economical batch suspension system (1982)

Abstract Large‐scale mammalian cell culture in the absence of antibiotics requires stringent conditions of sterility for all vessels, procedure, and systems used. Application of existing fermentation technology suffers from the differences between mammalian and bacterial cultures. Relatively simple and inexpensive 100‐L vessels have been designed specifically for medium storage and antibiotic‐free mammalian cell culture. These vessels are portable and sterilized in a 2 × 3 × 5 ft conventional or VACUMATIC autoclave. They consist of 30‐gal 316 stainless‐steel sanitary process drums whose heads have been modified to meet the rapid pressure changes that occur during autoclaving. The vessels incorporate systems for aseptic introduction and removal of both liquids and gases required for inoculation, growth, and harvesting of cell suspensions. A two‐disk vibromixer is used for agitation with inoculation at a laminar flow hood and incubation in a warm room. These vessels have been used for culture of one rat and eight human tumor lines for over 2 × 10 5 L of suspension.
TRPM2 mediates ischemic kidney injury and oxidant stress through RAC1 (2014)

Ischemia is a leading cause of acute kidney injury. Kidney ischemia is associated with loss of cellular ion homeostasis; however, the pathways that underlie ion homeostasis dysfunction are poorly understood. Here, we evaluated the nonselective cation channel transient receptor potential melastatin 2 (TRPM2) in a murine model of kidney ischemia/reperfusion (I/R) injury. TRPM2-deficient mice were resistant to ischemic injury, as reflected by improved kidney function, reduced histologic damage, suppression of proapoptotic pathways, and reduced inflammation. Moreover, pharmacologic TRPM2 inhibition was also protective against I/R injury. TRPM2 was localized mainly in kidney proximal tubule epithelial cells, and studies in chimeric mice indicated that the effects of TRPM2 are due to expression in parenchymal cells rather than hematopoietic cells. TRPM2-deficient mice had less oxidative stress and lower levels of NADPH oxidase activity after ischemia. While RAC1 is a component of the NADPH oxidase complex, its relation to TRPM2 and kidney ischemic injury is unknown. Following kidney ischemia, TRPM2 promoted RAC1 activation, with active RAC1 physically interacting with TRPM2 and increasing TRPM2 expression at the cell membrane. Finally, inhibition of RAC1 reduced oxidant stress and ischemic injury in vivo. These results demonstrate that TRPM2-dependent RAC1 activation increases oxidant stress and suggest that therapeutic approaches targeting TRPM2 and/or RAC1 may be effective in reducing ischemic kidney injury.
A Unique β1,3-Galactosyltransferase Is Indispensable for the Biosynthesis of <i>N</i>-Glycans Containing Lewis a Structures in <i>Arabidopsis thaliana</i> (2007)

In plants, the only known outer-chain elongation of complex N-glycans is the formation of Lewis a [Fuc alpha1-4(Gal beta1-3)GlcNAc-R] structures. This process involves the sequential attachment of beta1,3-galactose and alpha1,4-fucose residues by beta1,3-galactosyltransferase and alpha1,4-fucosyltransferase. However, the exact mechanism underlying the formation of Lewis a epitopes in plants is poorly understood, largely because one of the involved enzymes, beta1,3-galactosyltransferase, has not yet been identified and characterized. Here, we report the identification of an Arabidopsis thaliana beta1,3-galactosyltransferase involved in the biosynthesis of the Lewis a epitope using an expression cloning strategy. Overexpression of various candidates led to the identification of a single gene (named GALACTOSYLTRANSFERASE1 [GALT1]) that increased the originally very low Lewis a epitope levels in planta. Recombinant GALT1 protein produced in insect cells was capable of transferring beta1,3-linked galactose residues to various N-glycan acceptor substrates, and subsequent treatment of the reaction products with alpha1,4-fucosyltransferase resulted in the generation of Lewis a structures. Furthermore, transgenic Arabidopsis plants lacking a functional GALT1 mRNA did not show any detectable amounts of Lewis a epitopes on endogenous glycoproteins. Taken together, our results demonstrate that GALT1 is both sufficient and essential for the addition of beta1,3-linked galactose residues to N-glycans and thus is required for the biosynthesis of Lewis a structures in Arabidopsis. Moreover, cell biological characterization of a transiently expressed GALT1-fluorescent protein fusion using confocal laser scanning microscopy revealed the exclusive location of GALT1 within the Golgi apparatus, which is in good agreement with the proposed physiological action of the enzyme.
Improving on saddleback search (2010)

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Urine Proteome Scans Uncover Total Urinary Protease, Prostaglandin D Synthase, Serum Amyloid P, and Superoxide Dismutase as Potential Markers of Lupus Nephritis (2010)

To identify potential biomarkers in immune-mediated nephritis, urine from mice subjected to an augmented passive model of anti-glomerular basement membrane (GBM)-induced experimental nephritis was resolved using two-dimensional gels. The urinary proteome in these diseased mice was comprised of at least 71 different proteins. Using orthogonal assays, several of these molecules, including serum amyloid P (SAP), PG D synthase, superoxide dismutase, renin, and total protease were validated to be elevated in the urine and kidneys of mice during anti-GBM disease, as well as in mice with spontaneously arising lupus nephritis. Among these, urinary protease was the only marker that appeared to be exclusively renal in origin, whereas the others were partly serum-derived. Longitudinal studies in murine lupus demonstrated that total urinary protease had better predictive value for histologically active nephritis (r = 0.78) compared with proteinuria (r = -0.04), azotemia (r = 0.28), or the other markers examined, whereas urine SAP emerged as the single most predictive marker of histological glomerulonephritis. Collectively, these studies uncover total urinary protease, PG D synthase, SAP, and superoxide dismutase as novel biomarkers of anti-GBM disease and lupus nephritis, with stronger correlation to renal disease compared with currently employed biomarkers. These findings could have important diagnostic and prognostic ramifications in the management of these renal diatheses.
Well plate-based perfusion culture device for tissue and tumor microenvironment replication (2015)

There are significant challenges in developing in vitro human tissue and tumor models that can be used to support new drug development and evaluate personalized therapeutics. The challenges include: (1) working with primary cells which are often difficult to maintain ex vivo, (2) mimicking native microenvironments from which primary cells are harvested, and (3) the lack of culture devices that can support these microenvironments to evaluate drug responses in a high-throughput manner. Here we report a versatile well plate-based perfusion culture device that was designed, fabricated and used to: (1) ascertain the role of perfusion in facilitating the expansion of human multiple myeloma cells and evaluate drug response of the cells, (2) preserve the physiological phenotype of primary murine osteocytes by reconstructing the 3D cellular network of osteocytes, and (3) circulate primary murine T cells through a layer of primary murine intestine epithelial cells to recapitulate the interaction of the immune cells with the epithelial cells. Through these diverse case studies, we demonstrate the device's design features to support: (1) the convenient and spatiotemporal placement of cells and biomaterials into the culture wells of the device; (2) the replication of tissues and tumor microenvironments using perfusion, stromal cells, and/or biomaterials; (3) the circulation of non-adherent cells through the culture chambers; and (4) conventional tissue and cell characterization by plate reading, histology, and flow cytometry. Future challenges are identified and discussed from the perspective of manufacturing the device and making its operation for routine and wide use.
Symbols Units Nomenclature How to represent a cube corner (1983)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text W. H. Steel, "Symbols Units Nomenclature How to represent a cube corner," Appl. Opt. 22, 761-761 (1983) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article