gebhart/patrepeval huggingface dataset:
Metals removal and recovery from municipal sludge _ (1981)

A fundamental goal of microbial ecology is to accurately determine the species composition in a given microbial ecosystem. In the context of the human microbiome, this is important for establishing links between microbial species and disease states. Here we benchmark the Microba Community Profiler (MCP) against other metagenomic classifiers using 140 moderate to complex <i>in silico</i> microbial communities and a standardized reference genome database. MCP generated accurate relative abundance estimates and made substantially fewer false positive predictions than other classifiers while retaining a high recall rate. We further demonstrated that the accuracy of species classification was substantially increased using the Microba Genome Database, which is more comprehensive than reference datasets used by other classifiers and illustrates the importance of including genomes of uncultured taxa in reference databases. Consequently, MCP classifies appreciably more reads than other classifiers when using their recommended reference databases. These results establish MCP as best-in-class with the ability to produce comprehensive and accurate species profiles of human gastrointestinal samples.
Analysis of the autonomous system network topology (2001)

Mapping the Internet is a major challenge for network researchers. It is the key to building a successful modeling tool able to generate realistic graphs for use in networking simulations. In this paper we provide a detailed analysis of the inter-domain topology of the Internet. The collected data and the resulting analysis began in November 1997 and cover a period of two and a half years. We give results concerning major topology properties (nodes and edges number, average degree and distance, routing policy, etc.) and main distributions (degree, distance, etc.). We also present many results about the trees of this network. The evolution of these properties is reviewed and major trends are highlighted. We propose some empirical laws that match this current evolution. Four new power-laws concerning the number of shortest paths between node pairs and the tree size distribution are provided with their detailed validation.
Increased Membrane Affinity of the C1 Domain of Protein Kinase Cδ Compensates for the Lack of Involvement of Its C2 Domain in Membrane Recruitment (2005)

Protein kinase C (PKC) family members are allosterically activated following membrane recruitment by specific membrane-targeting modules. Conventional PKC isozymes are recruited to membranes by two such modules: a C1 domain, which binds diacylglycerol (DAG), and a C2 domain, which is a Ca2+-triggered phospholipid-binding module. In contrast, novel PKC isozymes respond only to DAG, despite the presence of a C2 domain. Here, we address the molecular mechanism of membrane recruitment of the novel isozyme PKCdelta. We show that PKCdelta and a conventional isozyme, PKCbetaII, bind membranes with comparable affinities. However, dissection of the contribution of individual domains to this binding revealed that, although the C2 domain is a major determinant in driving the interaction of PKCbetaII with membranes, the C2 domain of PKCdelta does not bind membranes. Instead, the C1B domain is the determinant that drives the interaction of PKCdelta with membranes. The C2 domain also does not play any detectable role in the activity or subcellular location of PKCdelta in cells; in vivo imaging studies revealed that deletion of the C2 domain does not affect the stimulus-dependent translocation or activity of PKCdelta. Thus, the increased affinity of the C1 domain of PKCdelta allows this isozyme to respond to DAG alone, whereas conventional PKC isozymes require the coordinated action of Ca2+ binding to the C2 domain and DAG binding to the C1 domain for activation.
Protective ability of acetylsalicylic acid (aspirin) to scavenge radiation induced free radicals in J774A.1 macrophage cells. (1998)

Radiation generates a variety of free radicals during the exposure of biological tissues through radiolysis of water. These free radicals are highly reactive and cause oxidative damage to biological molecules. This study examined the protective ability of aspirin against radiation induced oxidative stress. The study assessed the protective effect of aspirin (0.05 mM, 0.10 mM, 0.50 mM) on the generation of free radicals during exposure of J774A.1 macrophage cells to radiation (13.25 cGy). Approximately a 2.2-fold increase in superoxide anion formation as determined by cytochrome c reduction was observed following exposure of the cells to radiation for 20 one second exposures. Preincubation with aspirin exhibited a dose dependent decrease in free radical production as assessed by chemiluminescence and cytochrome c reduction. Aspirin also produced a concentration dependent reduction in radiation induced DNA damage in the cells. The data indicate that radiation of these cells results in production of reactive oxygen species and DNA damage, and aspirin can decrease these effects in a concentration dependent manner.
The functions of paucimannose N-glycans in Caenorhabditis elegans (2009)

線虫には約 150 種類の N 型糖鎖の存在が判明している。本稿では，無脊椎動物に多く存在し，脊椎動物にないパウチマンノース型 N-グリカンの合成と機能について考察する。線虫の糖鎖はフコシル化とホスフォリルコリン付加により，多様性を呈しており，ホスフォリルコリンは多くの病原菌において抗原決定基として知られている。パウチマンノース型 N-グリカンの合成には，UDP-GlcNAc:α3-D-マンノシド β1,2-N-アセチルグルコサミン転移酵素（GnTI, Mgat1 遺伝子によってコードされる）反応が先行する。線虫では，GnTI に 3 つのアイソザイム（GLY-12, GLY-13, GLY-14）がある。それぞれのアイソザイムは標的蛋白質が異なっており，線虫の病原菌に対する防御において異なった機能を持つ。線虫における GnTI 標的蛋白質の同定により，無脊椎動物及び脊椎動物の感染防御における GnTI 標的糖蛋白質の機能が明らかになるものと期待される。
Suicide enzyme inactivators (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSuicide enzyme inactivatorsRobert H. Abeles and Alan L. MaycockCite this: Acc. Chem. Res. 1976, 9, 9, 313–319Publication Date (Print):September 1, 1976Publication History Published online1 May 2002Published inissue 1 September 1976https://pubs.acs.org/doi/10.1021/ar50105a001https://doi.org/10.1021/ar50105a001research-articleACS PublicationsRequest reuse permissionsArticle Views767Altmetric-Citations302LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Characteristics of toothbrushes (1983)

A bstract — Most of the manual toothbrushes available on the Australian market during 1980–81 were purchased and examined in the light of the revised Australian Standard for Toothbrushes (AS 1032). The Standard deals only with nylon monofilament brushes and does not cover powered brushes, natural bristle brushes or the single use devices often distributed through vending machines. The problems arising from natural bristle brushes and the single use devices are discussed. The dimensional characteristics of the brushes have been determined and the various styles compared. Particular attention has been given to the classification of textural stiffness of the brushes and the extent to which claims of end rounded monofilaments are valid. Few brushes for which end‐rounding is claimed comply with the Standard requirement that at least 50 per cent of monofilaments shall be rounded.
GRK2 in the Heart: A GPCR Kinase and Beyond (2014)

The newly identified characteristics of GRK2, including the S-nitrosylation of GRK2 and the localization of GRK2 on mitochondria, merit further investigation. They may contribute to it being a pro-death kinase and result in HF under stressed conditions through regulation of intracellular signaling, including cardiac reduction-oxidation (redox) balance. A thorough understanding of the functions of GRK2 in the heart is necessary in order to finalize it as a candidate for drug development.
Superantigenicity of streptococcal M protein. (1990)

M proteins that define the serotypes of group A streptococci are powerful blastogens for human T lymphocytes. The mechanism by which they activate T cells was investigated and compared with the conventional T cell mitogen phytohemagglutinin, and the known superantigen staphylococcal enterotoxin B. Although major histocompatibility complex (MHC) class II molecules are required for presentation, there is no MHC restriction, since allogeneic class II molecules presented the bacterial protein to human T cells. Type 5 M protein appears to bind class II molecules on the antigen-presenting cells and stimulate T cells bearing V beta 8 sequences. Our results indicate that this streptococcal M protein is a superantigen and suggest a possible mechanism of its role in the pathogenesis of the postinfectious autoimmune sequelae.
Lignin oxidation and depolymerisation in ionic liquids (2015)

The depolymerisation of lignin directly in the black liquor was studied, comparing two ionic liquids as extracting solvents (butylimidazolium hydrogen sulphate and triethylammonium hydrogen sulphate), under oxidising conditions.
Magnetic barrier--A new concept in magnetic separation (1976)

Particles can be separated according to their mass magnetic susceptibilities by using a magnetic energy gradient barrier. When a stream of particles with different magnetic susceptibilities is fed to the barrier at an angle, a continuous separation can be obtained. The particles having susceptibilities higher than a predetermined value are deflected and guided by the magnetic barrier to a releasing region, where they pass through the barrier. Particles with lower susceptibilities which penetrate the barrier follow a different path from the more magnetic fraction and are separately collected.
Development and validation of genetic algorithm-based facility layout a case study in the pharmaceutical industry (1999)

In the layout design of pharmaceutical factories, several important objectives often need to be considered, such as operation cost, maintenance cost, material handing cost, throughput rate, etc. Most of the existing algorithms for facility layout design were developed based on pre-determined single objectives; namely, the distance-based objectives or the adjacency-based objectives. In this paper, we propose a genetic algorithm approach with an embedded simulation model which allows the user to select the objectives that are important in each particular layout design in the pharmaceutical industry. To verify the feasibility of the proposed method, the layout designs of two pharmaceutical plants for solid dosage forms were used as a test bed. One represents a typical small-size pharmaceutical plant and the other represents a medium-size plant. The objectives are to maximize throughput rate and to minimize travelling time per trip. A simulation model was developed, and the efficiency of the layouts generated by human designers CORELAP, CRAFT, and BLOCPLAN, is compared. The comparison indicates that the proposed genetic algorithm method significantly outperforms human designers and other computer algorithms in minimizing travelling time per trip under the same throughput rate.
Nano-LiFePO[sub 4]∕MWCNT Cathode Materials Prepared by Room-Temperature Solid-State Reaction and Microwave Heating (2007)

The precursors of were prepared by room-temperature solid-state reaction using , , as raw materials. Citric acid was added to reduce the particle size of , and multiwalled carbon nanotubes (MWCNTs) were adopted to improve the electrical conductivity. The samples were synthesized for a few minutes by microwave heating. X-ray diffraction and transmission electron microscope were used to characterize their structures and morphologies. The results showed that all samples had the same olivine phase structure. When both citric acid and MWCNTs were added, nanoparticles of homogeneously coated on the MWCNTs. An electrochemical test showed that , with both citric acid and MWCNTs addition, demonstrated an excellent electrochemical capacity of at C/2 and stable cycle ability. Citric acid expansion reduced the particle size, thus reducing the length of diffusion or improving the reversibility of the lithium ion intercalation/deintercalation. MWCNTs functioned as a lead to connect the particles and enabled active materials to transport lithium ions and electrons at fast rates.
The Effects of Mastoparan on the Carrot Cell Plasma Membrane Polyphosphoinositide Phospholipase C (1995)

When [3H]inositol-labeled carrot (Daucus carota L.) cells were treated with 10 or 25 microM wasp venom peptide mastoparan or the active analog Mas-7 there was a rapid loss of more than 70% of [3H]phosphatidylinositol-4-monophosphate (PIP) and [3H]phosphatidylinositol-4,5-bisphosphate (PIP2) and a 3- and 4-fold increase in [3H]inositol-1,4-P2 and [3H]inositol-1,4,5-P3, respectively. The identity of [3H]inositol-1,4,5-P3 was confirmed by phosphorylation with inositol-1,4,5-P3 3-kinase and co-migration with inositol-1,3,4,5-P4. The changes in phosphoinositides were evident within 1 min. The loss of [3H]PIP was evident only when cells were treated with the higher concentrations (10 and 25 microM) of mastoparan or Mas-7. At 1 microM Mas-7, [3H]PIP increased. The inactive mastoparan analog Mas-17 had little or no effect on [3H]PIP or [3H]PIP2 hydrolysis in vivo. Neomycin (100 microM) inhibited the uptake of Mas-7 and thereby inhibited the Mas-7-stimulated hydrolysis of [3H]PIP and [3H]PIP2. Plasma membranes isolated from mastoparan-treated cells had increased PIP-phospholipase C (PLC) activity. However, when Mas-7 was added to isolated plasma membranes from control cells, it had no effect on PIP-PLC activity at low concentrations and inhibited PIP-PLC at concentrations greater than 10 microM. In addition, guanosine-5'-O-(3-thiotriphosphate) had no effect on the PIP-PLC activity when added to plasma membranes isolated from either the Mas-7-treated or control cells. The fact that Mas-7 did not stimulate PIP-PLC activity in vitro indicated that the Mas-7-induced increase in PIP-PLC in vivo required a factor that was lost from the membrane during isolation.
Pump-mediated inhomogeneous effects in EDFAs and their impact on gain spectral modeling (2002)

Summary form only given. Recently it has been shown that small changes in pump wavelength within the 980-nm pump band change the shape of the gain spectrum of erbium-doped fiber amplifiers (EDFAs). These gain variations can be as large as 3 dB in a typical line amplifier and cannot be explained by the well known homogeneous model for EDFAs. Pump-induced gain changes must be accounted for in multiwavelength amplifiers and systems operating over the pump-wavelength-sensitive short-wavelength portion of the erbium gain band. In this paper, we compare the impact of pump-mediated inhomogeneities on the gain spectra of EDFAs pumped in the 1480- and 980-nm pump bands. We find that the shape of the EDFA gain spectrum is less affected by changes in pump wavelength in the 1480-nm band, and show that in both cases the dynamic gain tilt function (DGTF) is relatively insensitive to changes in pump wavelength. The latter indicates that inversion-induced gain changes can be predicted from a (measured) DGTF despite pump band and some signal band inhomogeneities. We present fluorescence line narrowing measurements that explain these results and suggest a physical mechanism for 980-nm band pump-mediated inhomogeneities.
Extracorporeal membrane oxygenation support of donor abdominal organs in non‐heart‐beating donors (2000)

Both family consent and legal consent were required for organ/tissue donation from non-heart-beating donors (NHBD) in Taiwan. A district attorney had to come to the bedside to confirm the donor's asystole, confirm the family consent, and complete some legal documents before a legal consent was issued for organ donation. The resultant warm ischemic time would be unpredictably long and in fact precluded the organ donation from NHBD in Taiwan. We developed a method of using extracorporeal membrane oxygenation (ECMO) to maintain NHBD for a longer time and prevent warm ischemic injury of the donor abdominal organs. After ventilator disconnection in NHBD, phentolamine and heparin were injected and mannitol infusion was given. After the donor's asystole was confirmed by the electrocardiogram (EKG) strip recording, the ECMO support was set up through the right femoral veno-arterial route, an occlusion balloon catheter was inserted through the left femoral artery to occlude the thoracic aorta, and bilateral femoral arteries were ligated. Usually, the ECMO could begin within 10 min after the donor's asystole. The ECMO, combined with a cooler, provided cold oxygenated blood to the abdominal visceral organs, and prevented their warm ischemic injuries. Under the ECMO support (range: 45-70 min), eight renal grafts were procured from 4 NHBD. With the exception of the first two renal grafts with delayed function, all others had immediate function postoperatively and dialysis was no longer needed. In conclusion, by our ECMO technique, NHBD could be maintained for a longer time and the renal grafts had better immediate postoperative function than those reported by other methods.
Natural quality variable-rate spectral speech coding below 3.0 kbps (2002)

We propose new techniques for natural quality variable rate spectral speech coding at an average rate of 2.2 kbps for dialog speech and 2.8 kbps for monolog speech. The coder models the Fourier spectrum of each frame and it builds on recent enhancements to the classical multiband excitation (MBE) approach. New techniques for robust pitch estimation and tracking, for efficient quantization of voiced and unvoiced spectra and encoding of partial phase information are the key features that result in improved quality over earlier spectral vocoders. Subjective performance results are reported which show that the coder is very close in quality to the ITU-T G.723.1 algorithm at 5.3 kbps.
Pharmacotherapy of Attention-deficit/Hyperactivity Disorder Reduces Risk for Substance Use Disorder (1999)

Consistent with findings in untreated ADHD in adults, untreated ADHD was a significant risk factor for SUD in adolescence. In contrast, pharmacotherapy was associated with an 85% reduction in risk for SUD in ADHD youth.
Identification of a monocyte receptor on herpesvirus-infected endothelial cells. (1991)

The adhesion of circulating blood cells to vascular endothelium may be an initial step in atherosclerosis, inflammation, and wound healing. One mechanism for promoting cell-cell adhesion involves the expression of adhesion molecules on the surface of the target cell. Herpes simplex virus infection of endothelium induces arterial injury and has been implicated in the development of human atherosclerosis. We now demonstrate that HSV-infected endothelial cells express the adhesion molecule GMP140 and that this requires cell surface expression of HSV glycoprotein C and local thrombin generation. Monocyte adhesion to HSV-infected endothelial cells was completely inhibited by anti-GMP140 antibodies but not by antibodies to other adhesion molecules such as VCAM and ELAM-1. The induction of GMP140 expression on HSV-infected endothelium may be an important pathophysiological mechanism in virus-induced cell injury and inflammation.
Dose effects of LPS on neutrophils‐ in a whole blood flow cytometric assay of phagocytosis and oxidative burst (1992)

Whole blood phagocytosis (P) and oxidative burst (OB), a rapid and sensitive flow cytometric method for quantifying neutrophil activation, was modified for single laser systems by using propidium iodide labeled Staphylococcus aureus and 2',7' dichlorofluorescein diacetate. The purpose of the present study was to characterize this assay with respect to the stimulatory activity of bacterial lipopolysaccharide (LPS) on phagocytosis. Blood from healthy donors was preincubated with log doses of bacterial LPS B (0.1-1,000 ng/ml) or sterile pyrogen-free saline at 37 degrees C from 0-120 minutes. LPS increased both P and OB in a dose-dependent manner (up to 62 and 121%, respectively) at all time points tested, and this effect on P and OB could be detected even with no preincubation. This LPS-induced phagocytic activity could be blocked by the addition of polymyxin B (10 micrograms/ml) during preincubation. The priming effect of LPS was maximal at 45 min. P and OB were inhibited by preincubation with EDTA at doses greater than 2 mM (60 and 80% inhibition, respectively). These observations are consistent with the exquisite sensitivity of the neutrophil to endotoxin. This method can evaluate neutrophil response to immunomodulatory and chemotherapeutic agents in a physiological milieu. These findings re-emphasize the necessity of using pyrogen-free reagents in any study of neutrophil function.
Using a new Intelligent Well Technology Completions Strategy to Increase Thermal EOR Recoveries–SAGD Field Trial (2012)

Abstract Well segmentation and instrumentation have been used to improve steam injection and production conformance in a completions strategy for a thermal-enhanced oil recovery (EOR) project by using intelligent well technology and interval control valves (ICVs). The initial field trial is ongoing in the injector of a Northern Alberta steam-assisted gravity drainage (SAGD) well pair. The development of the completion technology suitable for thermal conditions, initial field trial results and the plans for further development are described in this paper. The application modeling shows that, depending on the level of heterogeneity present in the reservoir, a 45% reduction in the steam-oil ratio and an almost 70% increase in recovery can be achieved in a SAGD process when both improved injection conformance and producer differential steam-trap control can be applied in a segmented horizontal well pair. A cost-effective, intelligent-well completion solution to achieve this segmentation and control has the potential to add substantial value to field developments through improved steam conformance. This will result in increased energy efficiency and oil recovery. The method under development is also applicable to a wide range of other thermal EOR processes such as cyclic steam stimulation (CSS), steam drive, and variations, including, for example, those involving solvent additives. The initial field deployment in the injector well was initiated to prove the technology, to demonstrate the feasibility of modifying the steam distribution, and to obtain best practices for future developments. A successful installation and commissioning of the intelligent completion has validated the technology. Lessons learned are highlighted. Early injection test results and data show a significant increase in the understanding of the injection and production behavior in the well pair. A test program to optimize the distribution of the steam injection in the well is underway, and the results are discussed. The intelligent completion technology under trial and proposed further developments should enable more extensive use of downhole measurement and control in thermal EOR projects than has been possible to date.
Shuttle Vector System for <i>Methanococcus maripaludis</i> with Improved Transformation Efficiency (2011)

We have identified an open reading frame and DNA element that are sufficient to maintain shuttle vectors in Methanococcus maripaludis. Strain S0001, containing ORF1 from pURB500 integrated into the M. maripaludis genome, supports a significantly smaller shuttle vector, pAW42, and a 7,000-fold increase in transformation efficiency for pURB500-based vectors.