gebhart/patrepeval huggingface dataset:
Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially processed plant derived carbon (2017)

Abstract Background The transformation of plant photosynthate into soil organic carbon and its recycling to CO 2 by soil microorganisms is one of the central components of the terrestrial carbon cycle. There are currently large knowledge gaps related to which soil-associated microorganisms take up plant carbon in the rhizosphere and the fate of that carbon. Results We conducted an experiment in which common wild oats ( Avena fatua) were grown in a 13 CO 2 atmosphere and the rhizosphere and non-rhizosphere soil was sampled for genomic analyses. Density gradient centrifugation of DNA extracted from soil samples enabled distinction of microbes that did and did not incorporate the 13 C into their DNA. A 1.45 Mbp genome of a Saccharibacteria (TM7) was identified and, despite the microbial complexity of rhizosphere soil, curated to completion. The genome lacks many biosynthetic pathways, including genes required to synthesize DNA de novo . Rather, it requires externally-derived nucleotides for DNA and RNA synthesis. Given this, we conclude that rhizosphere-associated Saccharibacteria recycle DNA from bacteria that live off plant exudates and/or phage that acquired 13 C because they preyed upon these bacteria and/or directly from the labelled plant DNA. Isotopic labeling indicates that the population was replicating during the six-week period of plant growth. Interestingly, the genome is ~30% larger than other complete Saccharibacteria genomes from non-soil environments, largely due to more genes for complex carbon utilization and amino acid metabolism. Given the ability to degrade cellulose, hemicellulose, pectin, starch and 1,3-β-glucan, we predict that this Saccharibacteria generates energy by fermentation of soil necromass and plant root exudates to acetate or lactate. The genome encodes a linear electron transport chain featuring a terminal oxidase, suggesting that this Saccharibacteria may respire aerobically. The genome encodes a hydrolase that could breakdown salicylic acid, a plant defense signaling molecule, and genes to make a variety of isoprenoids, including the plant hormone zeatin. Conclusions Rhizosphere Saccharibacteria likely depend on other bacteria for basic cellular building blocks. We propose that isotopically labeled CO 2 is incorporated into plant-derived carbon and then into the DNA of rhizosphere organisms capable of nucleotide synthesis, and the nucleotides are recycled into Saccharibacterial genomes.
Selective Delivery of PEGylated Compounds to Tumor Cells by Anti-PEG Hybrid Antibodies (2015)

Polyethylene glycol (PEG) is attached to many peptides, proteins, liposomes, and nanoparticles to reduce their immunogenicity and improve their pharmacokinetic and therapeutic properties. Here, we describe hybrid antibodies that can selectively deliver PEGylated medicines, imaging agents, or nanomedicines to target cells. Human IgG1 hybrid antibodies αPEG:αHER2 and αPEG:αCD19 were shown by ELISA, FACS, and plasmon resonance to bind to both PEG and HER2 receptors on SK-BR-3 breast adenocarcinoma and BT-474 breast ductal carcinoma cells or CD19 receptors on Ramos and Raji Burkitt's lymphoma cells. In addition, αPEG:αHER2 specifically targeted PEGylated proteins, liposomes, and nanoparticles to SK-BR-3 cells that overexpressed HER2, but not to HER2-negative MCF-7 breast adenocarcinoma cells. Endocytosis of PEGylated nanoparticles into SK-BR-3 cells was induced specifically by the αPEG:αHER2 hybrid antibody, as observed by confocal imaging of the accumulation of Qdots inside SK-BR-3 cells. Treatment of HER2(+) SK-BR-3 and BT-474 cancer cells with αPEG:αHER2 and the clinically used chemotherapeutic agent PEGylated liposomal doxorubicin for 3 hours enhanced the in vitro effectiveness of PEGylated liposomal doxorubicin by over two orders of magnitude. Hybrid anti-PEG antibodies offer a versatile and simple method to deliver PEGylated compounds to cellular locations and can potentially enhance the therapeutic efficacy of PEGylated medicines.
Inhibition of G Protein-Activated Inwardly Rectifying K+ Channels by Phencyclidine (2011)

Addictive drugs, such as opioids, ethanol, cocaine, amphetamine, and phencyclidine (PCP), affect many functions of the nervous system and peripheral organs, resulting in severe health problems. G protein-activated inwardly rectifying K(+) (GIRK, Kir3) channels play an important role in regulating neuronal excitability through activation of various Gi/o protein-coupled receptors including opioid and CB(1) cannabinoid receptors. Furthermore, the channels are directly activated by ethanol and inhibited by cocaine at toxic levels, but not affected by methylphenidate, methamphetamine, and 3,4-methylenedioxymethamphetamine (MDMA) at toxic levels. The primary pharmacological action of PCP is blockade of N-methyl-D-aspartate (NMDA) receptor channels that are associated with its psychotomimetic effects. PCP also interacts with several receptors and channels at relatively high concentrations. However, the molecular mechanisms underlying the various effects of PCP remain to be clarified. Here, we investigated the effects of PCP on GIRK channels using the Xenopus oocyte expression system. PCP weakly but significantly inhibited GIRK channels at micromolar concentrations, but not Kir1.1 and Kir2.1 channels. The PCP concentrations effective in inhibiting GIRK channels overlap clinically relevant brain concentrations in severe intoxication. The results suggest that partial inhibition of GIRK channels by PCP may contribute to some of the toxic effects after overdose.
Phylogenetic analysis and identification of different serovars of Mycobacterium intracellulare at the molecular level (1990)

Comparative 16S rRNA sequencing was used to infer the phylogenetic relationship among different serovars of the Mycobacterium avium-M. intracellulare complex as well as to define signature nucleotides characteristic for different serovars. In general, the groups defined by rRNA sequencing reflect the classification obtained with sensitin tests and pathogenicity examinations in chickens. Unique 16S rRNA sequence patterns could be defined for (1) M. avium, (2) M. intracellulare serovars 4, 5, 6, 8, 9, 10 and 11, (3) M. intracellulare serovars 12, 13, 14, 15, 17, 19 and 20, (4) M. intracellulare serovar 7 and (5) M. intracellulare serovar 18. Phylogenetically, groups 1 and 2 on one hand and groups 3, 4 and 5 on the other hand each share a common ancestor. M. paratuberculosis was indistinguishable from M. intracellulare serovars 4, 5, 6, 8, 9, 10 and 11 by this kind of analysis.
CW Upconversion Lasing at Blue, Green and Red Wavelengths In An Infrared-Pumped Pr3+-Doped Fluoride Fibre At Room Temperature (1991)

We report an upconversion laser, in the form of a fluoride fibre doped with praseodymium, which oscillates at five wavelengths, in the blue, green and red spectral regions. The threshold powers and pump wavelengths, at 1.01 μm and 0.83 μm suggest that diode-pumped operation should be easily achievable. This offers the prospect of a simple, efficient and reliable source.
Developmental Pattern of Estrogen Receptor Expression in Female Mouse Genital Tracts (1989)

The distribution of the estrogen receptor (ER) was investigated in neonatal female genital tracts (uterus, oviduct, cervix, and vagina) from days 1-22 after birth, using immunohistochemistry employing an anti-ER monoclonal antibody. In uteri, the ER in epithelial cells began to be observed by day 4. The number of positive epithelial cells and the staining intensity gradually increased until day 22 of age. On the other hand, uterine stroma cells gave a strong ER immunostaining even on day 1. The staining intensity reached a maximum by days 4-7 and then slightly decreased with age. In the oviduct, cervix, and vagina, epithelial cells showed positive ER immunostaining on day 1, and the intensity increased gradually until day 22. ER immunostaining in stroma cells was almost constant during the development period. The ER in both epithelial and stroma cells from these younger animals showed similar biochemical properties, i.e. an increased affinity for nuclei and resistance to extraction with PBS. Thus, during neonatal development of the female reproductive tract, ER is present not only in stroma cells but also in epithelial cells. This ER protein exhibits properties and characteristics similar to those of adult mice. The presence of ER suggests that some of the estrogen actions of cell proliferation, differentiation, and tissue abnormalities resulting from prenatal and postnatal estrogen administration may be mediated by receptor interactions.
Quasi-bound states determination using a perturbed wavenumbers method in a large quantum box (1997)

A perturbed wavenumbers method (PWM) is presented that is capable of determining the quasi-bound-state eigenenergies and their lifetimes for quantum heterostructures having arbitrary potential profiles. The numerical method presented solves the single-band effective-mass Schrodinger equation without using complex energies. It is applicable to quantum structures that are symmetric, asymmetric, unbiased, or biased. For multiple quantum heterostructures, extensive comparisons of this numerical method with other currently used techniques are included. In addition, a modified density of states formulation is presented and applied to these example cases.
Platelet-activating factor and its receptor mediate melanoma progression by regulating expression of MMP-2, MT1-MMP and MCAM/MUC18 (2007)

2461 Enzymatic and oxidative degradation of cellular and lipoprotein-associated phosphatidylcholine produces key initial components of an inflammatory response - platelet-activating factor (PAF) and PAF mimetics. These short-lived biologically active phospholipid autocoids act through the specific GPCR-type PAF receptor to activate platelets, inflammatory and endothelial cells. Nevertheless, the functions of PAF/PAFR in tumor cells are largely unknown. We have found that PAF receptor antagonist PCA4248 inhibits growth of experimental A375SM human melanoma lung metastasis in nude mice. In vitro analysis of a panel of melanoma cells demonstrated that all melanoma cell lines express PAF receptor and that stimulation of metastatic melanoma cells with exogenous PAF results in the expression and activation of matrix metalloproteinases MMP-2 and MT1-MMP. This effect was mediated by PAF-induced phosphorylation and activation of transcription factors CREB and ATF-1, which occurred through a PAFR-mediated mechanism that utilized Gα q proteins, adenylate cyclase, p38 MAP kinase and protein kinase A. These results suggest that CREB and ATF-1 may act as molecular sensors to PAF-mediated stimulation. Consequently, the inflammatory tumor microenvironment may control specific transcriptional responses associated with overexpression of CREB and ATF-1, which is known to take place during the acquisition of the metastatic phenotype by melanoma cells. Our further studies indicate that PAF is also involved in constitutive gene expression in melanoma cells. First, we found that several structurally independent PAFR antagonists inhibit the in vitro growth of A375SM melanoma cells, most probably by downregulating their constitutive Cyclin D1 expression. Targeting PAFR expression in A375SM cells with small interfering RNA oligonucleotides confirmed that downregulation of Cyclin D1 expression was mediated via PAFR signaling. Second, PAFR knockdown with siRNA revealed that PAFR mediates constitutive expression of the melanoma cell adhesion protein MCAM/MUC18, a marker of metastatic melanoma as well as melanoma cancer stem cells. Conversely, inhibition of MCAM/MUC18 expression in A375SM cells by means of siRNA or shRNA led to an increase in PAFR expression, suggesting the existence of a feedback loop regulation between PAFR and MCAM/MUC18 expression. Overall, our results demonstrate that PAF acts as a promoter of melanoma metastasis by mediating gene expression in melanoma cells.
Brassinolide-Induced Elongation of Inner Tissues of Segments of Squash (<italic>Cucurbita maxima</italic> Duch.) Hypocotyls (1994)

Brassinolide (BR) stimulated elongation of etiolated squash hypocotyl segments with outer tissues removed, as well as that of unpeeled segments, while IAA has no effect on peeled segments. BR changed the mechanical properties of cell walls of the inner tissue. The inner tissue is probably the target tissue in BR-induced elongation.
Defining Left Ventricular Noncompaction Using Cardiac Computed Tomography (2013)

CT using the standard MRI NC:C ratio cutoff >2.3 accurately characterizes pathologic LVNC.
Scaling Methods of Sediment Bioremediation Processes and Applications (2006)

Abstract Bioremediation has been argued to be one of the most cost‐effective remediation technologies available to reduce soil, sediment, or groundwater contamination, particularly because this approach may allow for the implementation of in‐place strategies. Recent trends have advocated the application of innovative sediment stabilization strategies through placement of (reactive) capping material to allow long‐term biodegradation of contaminants in these complex biogeochemical environments. The potential long‐term risk reduction associated with this approach requires a demonstration of causal relationships between sediment or contaminant stability on the one hand, and microbial reactivity on the other. The spatial analysis needed to fully understand and quantify these correlations requires sensitive probabilistic techniques. Geostatistics has been used for the characterization of multi‐scale spatial patterns for the last few decades, and the analysis of microbial attributes has shown significant spatial structures on microbial abundance and activity. However, there is a dearth of information on the applicability of geostatistics to quantitatively describe the interaction between the microorganisms and their environment. Using the Passaic River (NJ) dioxin data as a model dataset, multiple scaling models were applied to scale and interpolate sampled dioxin data and derive dechlorination signatures in sediments. Unlike conventional geostatistic tools that are based on the point‐to‐point spatial structures, the new multi‐scale model (M‐Scale) introduces a new framework for spatial analysis in which regional values at different scales are anchored by the correlations to each other. Spatial dioxin distributions and microbial dechlorination signatures were used as benchmarks for comparison of M‐Scale to ordinary kriging. The results from cross‐validation and jackknifing approaches applied to these datasets were analyzed and compared using Quantile‐Quantile (Q–Q) plots and reproduction coefficients. These plots indicated that the M‐Scale better preserves the local features of hotspots during data interpolation to a basin‐wide scale. Current efforts focus on mapping microbial abundance and respiratory competence in the Anacostia River, based on measurements at three different scales. The outcomes of this work will be used to develop an uncertainty‐based spatial decision tool for site remediation in this watershed using various capping strategies.
Experimenting with Gnutella Communities (2002)

Les réseaux informatique ainsi que les systèmes distribués peuvent être considérés comme des communautés où les composantes - que ce soit des systèmes complets, des programmes ou des usagers - interagissent dans un environnement partagé. Ces communautés sont dynamiques car des éléments peuvent s'y joindre ou quitter en tout temps. L'article présente les résultats d'une suite d'expériences et de mesures faites sur Gnutella, un système peer-to-peer à grande échelle qui opère sans aucun contrôle centralisé. Nous avons remarqué qu'une grande partie des messages échangés sont erronés ou redondants et que les interactions entre n?uds ne durent pas très longtemps. En particulier, des connexions durant plus d'une minute sont des phénomènes rares. Les n?uds passent donc la majorité de leur temps à remplacer les partenaires perdus et, contrairement à l'idée répandue que les réseaux peer-to-peer sont immenses, nous avons noté que les communautés effectives étaient assez limitées. Gnutella est un environnement très dynamique avec peu de stabilité. Par exemple, de 42,000 sites avec lesquels nous avons établi une connexion, il a seulement été possible de re-communiquer de façon régulière avec 57. Dans un tel environnement, la chance joue un rôle important dans la performance observée; mais nous avons élaboré un protocole expérimental permettant de comparer diverses options.
Calculation on 3-Dimensional Propagation of Amplified Spontaneous Emission in a Cassegrain Type 3-Pass Amplifier. (2000)

The multi-pass laser amplifier has been often used as the final power amplification stage in the high peakpower laser systems. The Amplified Spontaneous Emission (ASE) at such a strongly pumped laser generally results in a parasitic oscillation that limits a high gain operation of the amplifier. The three dimensional propagation of the finite-band-width ASE from laser glasses has been calculated for a 30-m long Cassegranian 3-pass disk amplifiers of 35-cm clear aperture. The computational code includes the temporal behavier of flashlamp pumping, the gain reduction in a laser disk due to ASE generation, the long-path back-and-force propagation of ASE between Cassegranian mirrors, and the reduction effect on ASE of spatial filter installed after the amplifier. The ASE energy and its profile have been compared for the on-axis and off-axis arrangement of Cassegranian optics, and also z-pass geometries for three pass configuration. The off-axis alignment of the mirror pairs is very preferable to reduce ASE to one hundredth level than that appeared in the on-axis geometry.
ChemInform Abstract: OCTAMETHYLNAPHTHALENE (IMPROVED SYNTHESIS) AND OCTAMETHYLBIPHENYLENE (1979)

Abstract Tetramethyldehydrobenzol (II), hergestellt aus o‐Dibromtetramethylbenzol (I) und Butyl‐ a lithium, wird durch Pentamethylpyrrol (III) quantitativ zum Addukt (IV) abgefangen, das mit m‐Chlorperbenzoesäure Octamethylnaphthalin (VI) liefert.
Wildfires, complexity, and highly optimized tolerance (2005)

Recent, large fires in the western United States have rekindled debates about fire management and the role of natural fire regimes in the resilience of terrestrial ecosystems. This real-world experience parallels debates involving abstract models of forest fires, a central metaphor in complex systems theory. Both real and modeled fire-prone landscapes exhibit roughly power law statistics in fire size versus frequency. Here, we examine historical fire catalogs and a detailed fire simulation model; both are in agreement with a highly optimized tolerance model. Highly optimized tolerance suggests robustness tradeoffs underlie resilience in different fire-prone ecosystems. Understanding these mechanisms may provide new insights into the structure of ecological systems and be key in evaluating fire management strategies and sensitivities to climate change.
Load Down-Regulates TNF-Alpha Induced Cartilage Degradation in Part Through NF-KB and P38 Pathways (2007)

Pro-inflammatory cytokines, such as interleukin-1 (IL-1) and tumor necrosis factor (TNF), can induce cartilage degradation after acute injury or in inflammatory diseases [1,2,3,7]. The degradative events are coordinated through the elevation and activation of two classes of enzymes, namely matrix metalloproteinases (MMPs) and aggrecanases (ADAMTS-4 and −5) [1,6]. Prior studies suggested that pro-inflammatory responses induced by IL-1β can be inhibited by tensile load [2] and more recently by cyclic compression [8]. It is, however, not clear whether load affects other cytokines, such as TNF-α. TNF-α is known to bind its receptor (TNFR1) to cause a cascade that ends with degradation of an inhibitor, IκBα, and release of the transcription factor NF-κB [3]. The actions of TNF-α are also known to be affected by at least three NF-κB independent pathways including the p38, ERK, and JNK pathways [4]. The objective of this study was to determine whether cyclic compression could affect TNF-α induced cartilage degradation and to determine the roles of p38, ERK, and JNK pathways in TNF-induced cartilage degradation. We hypothesized that cyclic loading would inhibit the degradative effects caused by TNF-α.
Synthesis and biological activities of 4-thiazolidinones and dihydro-3-(2h)-thiophenones. (1988)

2-Amino pyridine was converted into Schiff bases which were reacted with thioglycollic acid to yield the corresponding thiazolidinones. Under similar conditions, thioglycollic acid when reacted with chalkones, dihydro-3-(2H)-Thiophen-ones were obtained. The antibacterial activities of both the type of compounds were studied and compared.
SURFACE SHEAR STRESS ENHANCEMENT UNDER MR FLUID DEFORMATION (2002)

The effect of a regular surface micro topography on a magnitude of surface shear stress in a normal magnetic field under MR fluid deformation between two magnetic plates has been experimentally investigated. It was revealed that the static yield stress was increased by a factor of 2.8 for radially grooved plates as against smooth ones. The effect was most conspicuous at small iron particles volume fractions and strong magnetic fields. It is assumed that grooves create a magneto mechanical barrier that prevents the slip of particle aggregates against the wall.
Esters of 6-dimethylaminohexanoic acid as skin penetration enhancers. (2000)

We prepared a series of five esters of 6-dimethylaminohexanoic acid, and characterised the compounds by their NMR and IR spectra. Their ability to function as transdermal penetration enhancers was subsequently evaluated using excised human skin as a membrane, modified Franz diffusion cells, and theophylline as a model permeant. The penetration-enhancing efficiency of esters 1-5 was studied in the donor media of propylene glycol and isopropyl myristate, and expressed as the corresponding enhancement factors (EF). All the esters increased the penetration of theophylline through the skin. The enhancement factor for the most active substance, undecyl 6-dimethylaminohexanoate, was 118.5 (+/- 19) from propylene glycol.
Role of Quaternary Ammonium Compounds and ATMP on Biocidal Effect and Corrosion Inhibition of Mild Steel and Copper (2005)

Article Role of Quaternary Ammonium Compounds and ATMP on Biocidal Effect and Corrosion Inhibition of Mild Steel and Copper was published on December 1, 2005 in the journal Corrosion Reviews (volume 23, issue 4-5-6).
A QoS-adaptive framework for screen sharing over Internet (2016)

In this paper, we present a QoS-adaptive framework for screen sharing over heterogeneous networks. Basic requirements and important issues of a screen sharing system are described. For determining optimal video coding parameters, adaptation trajectory is used as the hints in making decisions. Further, experiments are carried out to investigate the trade-off between video bitrate and the buffering delay in time-varying networks.
Optimal point estimates for multi-target states based on kernel distances (2012)

Almost all multi-target tracking systems have to generate point estimates for the targets, e.g., for displaying the tracks. The novel idea in this paper is to consider point estimates for multi-target states that are optimal according to a kernel distance measure. Because the kernel distance is a metric on point sets and ignores the target labels, shortcomings of Minimum Mean Squared Error (MMSE) estimates for multi-target states can be avoided. We show how the calculation of these point estimates can be casted as an optimization problem and it turns out that it corresponds to the problem of reducing the Probability Hypothesis Density (PHD) function to a Dirac mixture density. Finally, we discuss a generalization of the kernel distance called LCD distance, which does not require to choose a specific kernel width. The presented methods are evaluated in a Multiple-Hypotheses Tracker (MHT) setting with up to ten targets.