gebhart/patrepeval huggingface dataset:
Use of Length Heterogeneity PCR and Fatty Acid Methyl Ester Profiles To Characterize Microbial Communities in Soil (2000)

In length heterogeneity PCR (LH-PCR) a fluorescently labeled primer is used to determine the relative amounts of amplified sequences originating from different microorganisms. Labeled fragments are separated by gel electrophoresis and detected by laser-induced fluorescence with an automated gene sequencer. We used LH-PCR to evaluate the composition of the soil microbial community. Four soils, which differed in terms of soil type and/or crop management practice, were studied. Previous data for microbial biomass, nitrogen and carbon contents, and nitrogen mineralization rates suggested that the microbial characteristics of these soils were different. One site received two different treatments: no-till and conventional till perennial ryegrass. The other sites were no-till continuous grass plots at separate locations with different soil types. Community composition was characterized by assessing the natural length heterogeneity in eubacterial sequences amplified from the 5' domain of the 16S rRNA gene and by determining fatty acid methyl ester (FAME) profiles. We found that LH-PCR results were reproducible. Both methods distinguished the three sites. The most abundant bacterial community members, based on cloned LH-PCR products, were members of the beta subclass of the class Proteobacteria, the Cytophaga-Flexibacter-Bacteriodes group, and the high-G+C-content gram-positive bacterial group. Strong correlations were found between LH-PCR results and FAME results. We found that the LH-PCR method is an efficient, reliable, and highly reproducible method that should be a useful tool in future assessments of microbial community composition.
Metabolic relationships between pyridoxine (vitamin B6) and serine biosynthesis in Escherichia coli K-12 (1990)

We propose a pathway leading from erythrose-4-phosphate and glutamate to nitrogen 1 and carbons 5,5', and 6 of the pyridoxine ring. This pathway, which parallels the phosphorylated pathway of serine biosynthesis, is predicted on the homology between PdxB and SerA, the structural similarity between serine and 4-hydroxythreonine, and the possible involvement of SerC in pyridoxine biosynthesis. Several predictions of this hypothetical scheme were tested. Consistent with the proposed pathway, supplement inhibition patterns strongly suggest that SerA enzyme acts in a an alternate pathway of pyridoxine biosynthesis in pdxB mutants. Direct enzyme assays detected erythrose-4-phosphate dehydrogenase activity in crude extracts, which again supports the proposed pathway. Chromosomal insertions in serC caused a requirement for pyridoxine, serine, and aromatic compounds, which directly verified that SerC functions in the pyridoxine biosynthetic pathway. Complementation analysis showed that pdxF and pdxC mutations reported previously are most likely alleles of serC. Growth of serC chromosomal insertion mutants on glycoalaldehyde was found to occur without acquisition of second-site mutations and confirmed that pdxB and serC, but not pdxA, function in the same branch of the pyridoxine pathway. In addition, serC::mini-Mu d insertions revealed that the complex serC-aroA operon lacks internal promoters, that the amino terminus of SerC is not strictly essential for activity, and that antisense transcription occurs in the serC-aroA operon. Growth responses of pdxA, pdxB, and serC mutants to beta-hydroxypyruvate, D-alanine, and glycolate could also be reconciled with the proposed pathway. Finally, the proposed scheme is consistent with previous isotope labeling data and accounts for several other observations about pyridoxine biosynthesis. Together, these physiological and biochemical analyses support the proposed pathway and an evolutionary scenario in which this branch of the pyridoxine pathway evolved from the serine pathway by gene recruitment.
Design and Dynamic Characterization of an Orientation Insensitive Microwave Water-Cut Sensor (2017)

Modern reservoir management in oil and gas industry relies on accurate water fraction measurement which is produced as a by-product with oil. This paper presents a novel and contactless water fraction (also known as water-cut) measurement technique which is independent of geometric distribution of oil and water inside the pipe. The sensor is based on a modified T-resonator implemented directly on the pipe's outer surface and whose resonance frequency decreases by increasing the water content in oil. The E-fields have been made to rotate and distribute well inside the pipe, despite having narrow and curved ground plane. It makes the sensor's reading dependent only on the water fraction and not on the mixture distribution inside the pipe. That is why, the presented design does not require any flow conditioner to homogenize the oil/water mixture unlike many commercial water-cut (WC) sensors. The presented sensor has been realized by using extremely low-cost methods of screen printing and reusable 3-D printed mask. Complete characterization of the proposed WC sensor, both in horizontal and vertical orientations, has been carried out in an industrial flow loop. Excellent repeatability of the sensor's response has been observed in “dispersed bubble” as well as in “stratified wavy” flow regimes. The performance test of the sensor confirms that the water fraction measurement is independent of the flow pattern, flow rate or orientation. The measured performance results of the sensor show full range accuracy of ±2%-3% while tested under random orientations and wide range of flow rates.
Pulse Oximeter Plethysmographic Waveform Changes in Awake, Spontaneously Breathing, Hypovolemic Volunteers (2010)

These results support the use of pulse oximeter waveform analysis as a potential diagnostic tool to detect clinically significant hypovolemia before the onset of cardiovascular decompensation in spontaneously breathing patients.
On the reaction of methoxide ion with bromoiodothiophenes (1980)

Abstract The reaction of 3‐bromo‐2‐iodothiophene with sodium methoxide in methanol, pyridine or hexamethylphosphoric triamide and the same reaction of 4‐bromo‐2‐iodo‐ and 4‐bromo‐3‐iodo‐thiophene in pyridine led to a halogen‐dance, giving the same mixture of 3‐bromothiophene, bromo‐iodothiophenes, diiodo‐bromothiophenes and triiodo‐bromothiophenes. The reaction of all three isomeric bromo‐iodothiophenes with sodium methoxide in methanol in the presence of cupric oxide gave 4‐bromo‐2‐methoxythiophene.
Inhibition of DNA synthesis by chemical carcinogens in cultures of initiated and normal proliferating rat hepatocytes. (1985)

Rat hepatocytes in primary culture can be stimulated to replicate under the influence of rat serum and sparse plating conditions. Higher replication rates are induced by serum from two-thirds partially hepatectomized rats (Michalopoulos, G., Cianciulli, H. D., Novotny, A. R., Kligerman, A. D., Strom, S. C., and Jirtle, R. L. Cancer Res., 42: 4673-4682, 1982). The effects of carcinogens and noncarcinogens on the ability of hepatocytes to synthesize DNA were examined by measuring the incorporation of [3H]thymidine by liquid scintillation counting and autoradiography. Hepatocyte DNA synthesis was not decreased by ethanol or dimethyl sulfoxide at concentrations less than 0.5%. No effect was observed when 0.1 mM ketamine, Nembutal, hypoxanthine, sucrose, ascorbic acid, or benzo(e)pyrene was added to cultures of replicating hepatocytes. Estrogen, testosterone, tryptophan, and vitamin E inhibited DNA synthesis by approximately 50% at 0.1 mM, a concentration at which toxicity was noticeable. Several carcinogens requiring metabolic activation as well as the direct-acting carcinogen N-methyl-N'-nitro-N-nitrosoguanidine interfered with DNA synthesis. Aflatoxin B1 inhibited DNA synthesis by 50% (ID50) at concentrations between 1 X 10(-8) and 1 X 10(-7) M. The ID50 for 2-acetylaminofluorene was between 1 X 10(-7) and 1 X 10(-6) M. Benzo(a)pyrene and 3'-methyl-4-dimethylaminoazobenzene inhibited DNA synthesis 50% between 1 X 10(-5) and 1 X 10(-4) M. Diethylnitrosamine and dimethylnitrosamine (ID50 between 1 X 10(-4) and 5 X 10(-4) M) and 1- and 2-naphthylamine (ID50 between 1 X 10(-5) and 5 X 10(-4) M) caused inhibition of DNA synthesis at concentrations which overlapped with concentrations that caused measurable toxicity. The ability of hepatocytes to activate 2-acetylaminofluorene to reactive intermediates capable of binding to DNA and inhibiting new DNA synthesis decreased as a function of time in culture. gamma-Glutamyl-transferase-positive hepatocytes from diethylnitrosamine-treated rats were observed to be relatively insensitive to carcinogen inhibition of DNA synthesis.
An improved method for the synthesis of mercurated dUTP. Enzymic synthesis of Hg-labelled DNA of high molecular weight suitable for use in an image based DNA sequencing strategy (1996)

The development of high-resolution scanning-probe microscopes has reawakened interest in the possibility of sequencing large nucleic acid molecules by direct imaging. Such an approach would be facilitated by the availability of effective methods for increasing contrast by labelling specific nucleotides, and the utility of introducing mercury atoms into complete DNA molecules through the enzymic polymerisation of mercurated pyrimidine deoxynucleoside triphosphates has been re-investigated. A simplified and improved method for the synthesis of a heat- and thiol-stable, mercurated derivative of deoxyuridine triphosphate in high yield and the incorporation of this precursor into full-length copies of a single-stranded phage M13 template are described. The DNA product has been fully characterised and the quantitative and specific replacement of thymidylic acid residues by the mercurated analogue demonstrated.
WBest: A bandwidth estimation tool for IEEE 802.11 wireless networks (2008)

Bandwidth estimation techniques seek to provide an accurate estimation of available bandwidth such that network applications can adjust their behavior accordingly. However, most current techniques were designed for wired networks and produce relatively inaccurate results and long convergence times on wireless networks where capacity can vary dramatically. This paper presents a new Wireless Bandwidth estimation tool, WBest, designed for fast, non-intrusive, accurate estimation of available bandwidth in IEEE 802.11 networks. WBest is a two-stage algorithm: 1) a packet pair technique estimates the effective capacity over a flow path where the last hop is a wireless LAN (WLAN); and 2) a packet train technique estimates achievable throughput to infer the available bandwidth. WBest parameters are optimized given the tradeoffs of accuracy, intrusiveness and convergence time. The advantage of WBest stems from avoiding a search algorithm to detect the available bandwidth by statistically detecting the available fraction of the effective capacity to mitigate estimation delay and the impact of random wireless channel errors. WBest is implemented and evaluated on an 802.11 wireless testbed. Comparisons with other available bandwidth estimation tools shows WBest to have higher accuracy, lower intrusiveness and faster convergence times. Thus, WBest demonstrates the potential for improving the performance of applications that need bandwidth estimation, such as multimedia streaming, on wireless networks.
Developing cell-free biology for industrial applications (2006)

Although cell-free protein synthesis has been practiced for decades as a research tool, only recently have advances suggested its feasibility for commercial protein production. This focused review, based on the 2005 Amgen Award lecture, summarizes the relevant progress from the Swartz laboratory. When our program began, projected costs were much too high, proteins with disulfide bonds could not be folded effectively, and no economical scale-up technologies were available. By focusing on basic biochemical reactions and by controlling cell-free metabolism, these limitations have been methodically addressed. Amino acid supply has been stabilized and central metabolism activated to dramatically reduce substrate costs. Control of the sulfhydral redox potential has been gained and a robust disulfide isomerase added to facilitate oxidative protein folding. Finally, simple scale-up technologies have been developed. These advances not only suggest production feasibility for pharmaceutical proteins, they also provide enabling technology for producing patient-specific vaccines, for evolving new enzymes to enable biological hydrogen production from sunlight, and for developing new and highly effective water filters. Although many challenges remain, this newly expanded ability to activate and control protein production holds much promise for both research and commercial applications.
EUK-134, a synthetic superoxide dismutase and catalase mimetic, prevents oxidative stress and attenuates kainate-induced neuropathology (1999)

The present study tested the effects of EUK-134, a synthetic superoxide dismutase/catalase mimetic, on several indices of oxidative stress and neuropathology produced in the rat limbic system as a result of seizure activity elicited by systemic kainic acid (KA) administration. Pretreatment of rats with EUK-134 did not modify the latency for or duration of KA-induced seizure activity. It did produce a highly significant reduction in increased protein nitration, activator protein-1- and NF-kappaB-binding activity, and spectrin proteolysis as well as in neuronal damage resulting from seizure activity in limbic structures. These results support the hypothesis that kainate-induced excitotoxicity is caused, at least in part, by the action of reactive oxygen species. Furthermore, they suggest that synthetic superoxide dismutase/catalase mimetics such as EUK-134 might be used to prevent excitotoxic neuronal injury.
Lung clearance of intratracheally instilled 99mTc‐tobramycin using pulmonary surfactant as vehicle (1999)

1. The use of pulmonary exogenous surfactant as a vehicle for intratracheally administered antibiotics to improve local antimicrobial therapy has been proposed. The present study investigated lung clearance rates in the rat of intratracheally instilled technetium labelled tobramycin with and without the addition of surfactant to the antibiotic solution. 2. The influence of surfactant on 99mTc-tobramycin lung clearance rates was studied dynamically with a gamma-camera in anaesthetized spontaneously breathing animals and in mechanically ventilated animals. 3. The results show that instillation of 99mTc-tobramycin with use of surfactant as vehicle significantly increases 99mTc-tobramycin lung clearance compared to instillation of 99mTc-tobramycin solution alone (P=0.006 between the two spontaneously breathing groups of animals and P=0.02 between the two ventilated groups of animals, ANOVA for repeated time measurements). The half life (t1/2) of composite clearance curves in spontaneous breathing animals was 147 min for animals receiving 99mTc-tobramycin versus 61 min for animals receiving 99mTc-tobramycin with surfactant. In mechanically ventilated animals this was 163 min versus 51 min, respectively. 4. It is concluded that exogenous surfactant, used as vehicle for intratracheally instilled 99mTc-tobramycin, increases lung clearance rate of 99mTc-tobramycin in rats.
Highly Efficient Deep‐Blue Electrophosphorescent Pt(II) Compounds with Non‐Distorted Flat Geometry: Tetradentate versus Macrocyclic Chelate Ligands (2016)

A new class of deep blue electrophosphorescent Pt(II) emitters have been designed and synthesized. This new class of deep blue Pt(II) emitters employ tetradentate and macrocyclic chelate chromophores to constrain the Pt(II) molecules in a non‐distorted flat geometry in both the ground state and the excited state. The new deep blue emitters do not produce excimer emission, with emission quantum efficiency as high as 95% in 10% doped PMMA (poly(methyl methacrylate) films, and excellent UV stability, compared to the corresponding bidentate Pt(II) emitters. The macrocyclic tetradentate chelate Pt(II) compounds are the first examples of fully sterically constrained deep blue Pt(II) emitters that do not display structural distortion and have a higher thermal stability and a higher emission quantum efficiency than the corresponding non‐macrocyclic tetradentate Pt(II) analogues. A computational study supports that the macrocylic Pt(II) compounds are structurally more stable than the tetradentate Pt(II) molecules. Bright and efficient deep blue electrophosphorescent devices using a macrocyclic Pt(II) emitter have been successfully fabricated with a maximum brightness of 10 680 cd m −2 , maximum external quantum efficiency of 15.4% (at 490 cd m −2 ), and Commission Internationale de L'Eclairage (1931) coordinates ( x + y ) of less than or near 0.30, respectively.
13C NMR spectroscopy of indole derivatives (1987)

Abstract The chemical shifts of 298 naturally occurring and synthetic compounds containing the indole chromophoric group are listed. Substituent effects on 13 C chemical shifts (SCS) induced by substitution on the heteroaromatic five‐membered ring are discussed. The data provide a reference set for future 13 C NMR investigations and highlight the need for unambiguous experimental evidence to resolve controversial assignments for differently substituted representative indole derivatives. Many original assignments have been changed, and values not considered to be unambiguously assinged are delineated. The 1 J (CH) values for the parent indole were measured.
LUCIFERASES FROM DIFFERENT SPECIES OF FIREFLIES ARE ANTIGENICALLY SIMILAR (1985)

Abstract— Antibodies raised against luciferase purified from adult Photinus pyralis are shown to bind to luciferases from several species of the families Lampyridae and Elateridae. Based on their migration in denaturing gels, the enzymes from Pyrophorus plagiophthalamus are smaller and Photuris species larval enzyme is larger than the P. pvralis enzvme. All of the enzvmes examined are antieenicallv similar.
Structure of the activation domain of the GM-CSF/IL-3/IL-5 receptor common β-chain bound to an antagonist (2000)

Heterodimeric cytokine receptors generally consist of a major cytokine-binding subunit and a signaling subunit. The latter can transduce signals by more than 1 cytokine, as exemplified by the granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin-2 (IL-2), and IL-6 receptor systems. However, often the signaling subunits in isolation are unable to bind cytokines, a fact that has made it more difficult to obtain structural definition of their ligand-binding sites. This report details the crystal structure of the ligand-binding domain of the GM-CSF/IL-3/IL-5 receptor beta-chain (beta(c)) signaling subunit in complex with the Fab fragment of the antagonistic monoclonal antibody, BION-1. This is the first single antagonist of all 3 known eosinophil-producing cytokines, and it is therefore capable of regulating eosinophil-related diseases such as asthma. The structure reveals a fibronectin type III domain, and the antagonist-binding site involves major contributions from the loop between the B and C strands and overlaps the cytokine-binding site. Furthermore, tyrosine(421) (Tyr(421)), a key residue involved in receptor activation, lies in the neighboring loop between the F and G strands, although it is not immediately adjacent to the cytokine-binding residues in the B-C loop. Interestingly, functional experiments using receptors mutated across these loops demonstrate that they are cooperatively involved in full receptor activation. The experiments, however, reveal subtle differences between the B-C loop and Tyr(421), which is suggestive of distinct functional roles. The elucidation of the structure of the ligand-binding domain of beta(c) also suggests how different cytokines recognize a single receptor subunit, which may have implications for homologous receptor systems. (Blood. 2000;95:2491-2498)
High k<inf>t</inf><sup>2</sup>&#x00D7;Q, multi-frequency lithium niobate resonators (2013)

This paper presents design and vacuum measurements of lithium niobate (LN) contour-mode resonators (CMR). By carefully positioning the interdigital transducer (IDT), we achieved CMRs with k <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</inf> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ×Q of 7%∗2150=148 (IDT @ node) or resonators with very high k <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</inf> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> of 12.3% and spur-attenuated response (IDT @ anti-node). In addition, we demonstrated resonators with frequencies ranging from 400MHz to 800MHz on a single chip.
Effects of Different Concentrations of Atropine on Controlling Myopia in Myopic Children (1999)

Although 1% atropine effectively slows myopia progression, it is associated with adverse effects, including photophobia, blurred near vision, and poor compliance. We investigated whether lower doses of atropine would control myopia progression. One hundred and eighty-six children, from 6 to 13 years of age, were treated each night with different concentrations of atropine eye drops or a control treatment for up to 2 years. The mean myopic progression in each of the groups was 0.04 +/-0.63 diopter per year (D/Y) in the 0.5% atropine group, 0.45+/-0.55 D/Y in the 0.25% atropine group, and 0.47+/-0.91 D/Y in the 0.1% atropine group. All atropine groups showed significantly less myopic progression than the control group (1.06+/-0.61 D/Y) (p<0.01). Our study also showed that 61% of students in the 0.5% atropine group, 49% in the 0.25% atropine group and 42% in the 0.1% atropine group had no myopic progression. However, 4% of children in the 0.5% atropine group, 17% in the 0.25% atropine group, and 33% in the 0.1% atropine group still had fast myopic progression (>-1.0 D/Y). In contrast, only 8% of the control group showed no myopic progression and 44% had fast myopic progression. These results suggest that all three concentrations of atropine had significant effects on controlling myopia; however, treatment with 0.5% atropine was the most effective.
<title>High-performance 32-channel HDWDM multiplexer with 1-nm channel spacing and 0.7-nm bandwidth</title> (1992)

A high performance HDWDM multiplexer capable of combining 32 channels spaced 1 nm apart onto a monomode fiber is reported. A microlens array is utilized to give a channel bandwidth of 0.7 nm. The wavelength range is 1.5285 micrometers to 1.5595 micrometers , within the erbium fiber amplification range. The mean insertion loss over 32 channels is 6.7 dB, and the polarization sensitivity is less than 0.7 dB. A design for a more compact and lower loss device is also presented.