gebhart/patrepeval huggingface dataset:
Retrieval of Quantitative and Qualitative Information about Plant Pigment Systems from High Resolution Spectroscopy (2006)

Life on Earth depends on photosynthesis. Photosynthetic systems evolved early in Earth history and have been stable for 2.5 billion years, providing <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">prima</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">facie</i> evidence for these significance of evolutionary functions. Pigments perform multiple plant functions from increasing the range of energy captured for photosynthesis to a range of protective functions. Given the importance of pigments to leaf functioning, greater effort is needed to determine whether individual pigments can be identified and quantified by high fidelity spectroscopy. New methods to identify overlapping pigment absorptions would provide a major advance for understanding plant functions, quantifying net carbon exchange, and identifying plant stresses.
Monte Carlo Simulation of the Microstructure of Linear Olefin Block Copolymers (2012)

Abstract Summary: Linear olefin block copolymers (OBCs) are novel polyolefins with unique properties developed using the chain shuttling polymerization technology. Typically, OBCs are made in a single reactor with two catalysts having different 1‐olefin reactivity ratios and a chain shuttling agent (CSA), producing linear polymer chains with complex, multi‐block structures, although a dual reactor approach is also possible In this study, OBC chain microstructures were examined using Monte Carlo simulation. Effects of polymerization parameters (chain shuttling probability, propagation probability, and catalyst ratio) on the distribution of number of blocks per chain were investigated and reported for the first time. These results provide useful insights on how to control and describe the microstructures of these important polymers and can be used to establish quantitative relationships between the microstructure and properties of OBCs.
Regional Cerebral Blood Flow Changes as a Function of Delta and Spindle Activity during Slow Wave Sleep in Humans (1997)

In the present study, we investigated changes in regional cerebral blood flow (rCBF) in humans during the progression from relaxed wakefulness through slow wave sleep (SWS). These changes were examined as a function of spindle (12-15 Hz) and delta (1.5-4.0 Hz) electroencephalographic (EEG) activity of SWS. rCBF was studied with positron emission tomography (PET) using the H215O bolus method. A maximum of six 60 sec scans were performed per subject during periods of wakefulness and stages 1-4 of SWS, as determined by on-line EEG monitoring. Spectral analysis was performed off-line on the EEG epochs corresponding to the scans for computation of activity in specific frequency bands. The relationship between EEG frequency band activity and normalized rCBF was determined by means of a voxel-by-voxel analysis of covariance. delta activity covaried negatively with rCBF most markedly in the thalamus and also in the brainstem reticular formation, cerebellum, anterior cingulate, and orbitofrontal cortex. After the effect of delta was removed, a significant negative covariation between spindle activity and the residual rCBF was evident in the medial thalamus. These negative covariations may reflect the disfacilitation and active inhibition of thalamocortical relay neurons in association with delta and spindles, as well as the neural substrates underlying the progressive attenuation of sensory awareness, motor responsiveness, and arousal that occur during SWS. delta activity covaried positively with rCBF in the visual and auditory cortex, possibly reflecting processes of dream-like mentation purported to occur during SWS.
Expression of the<i>Streptomyces coelicolor</i>A3(2)<i>ptpA</i>gene encoding a phosphotyrosine protein phosphatase leads to overproduction of secondary metabolites in<i>S. lividans</i> (1996)

A DNA fragment that caused pigment production in Streptomyces lividans was isolated from a gene library of PstI-digested chromosomal fragments of S. coelicolor A3(2). Subcloning and nucleotide sequencing proved the identity of the cloned gene to ptpA encoding a low-molecular-mass phosphotyrosine protein phosphatase. The S. lividans transformant containing ptpA on pIJ41 with a copy number of 3 4 per genome produced large amounts of undecylprodigiosin and A-factor, in addition to the pigmented antibiotic actinorhodin, whereas the transformant containing ptpA on an SCP2* derivative with a copy number of 1-2 did not. The PtpA protein produced as a fusion to the maltose binding protein in Escherichia coli showed phosphatase activity toward o-phosphotyrosine, but not toward o-phosphoserine or a-threonine. Introduction of a mutant ptpA gene encoding an inactive protein with serine instead of the 9th cysteine caused no pigmentation. Disruption of the chromosomal ptpA gene of S. coelicolor A3(2), however, appeared to cause no detectable effect on the production of the pigmented antibiotics or A-factor and the ptpA disruptants developed aerial mycelium and spores normally.
Preliminary Pond Evaluation of a Natural-Based Algicide for Managing Musty Off-Flavor in Channel Catfish Aquaculture (2007)

Abstract Environmentally derived “off-flavors” such as “earthy” and “musty” in cultured channel catfish Ictalurus punctatus are attributed to the presence of certain species of cyanobacteria (blue-green algae) in ponds. The musty off-flavor is caused by absorption of the metabolite 2-methylisoborneol (MIB) into channel catfish flesh. Most channel catfish producers manage off-flavor episodes by the application of algicides; however, these algicides have high environmental persistence and broad-spectrum toxicity. Recent research has discovered several natural and natural-based quinones that are effective and selective in reducing the abundance of the MIB-producing cyanobacterium Planktothrix perornata. In this study, efficacy testing of one of these quinones, anthraquinone-59, in a channel catfish pond found that it is effective in reducing the abundance of P. perornata and subsequently lowering the MIB levels in channel catfish.
Rapid X-ray diffraction analysis of HIV-1 protease–inhibitor complexes: inhibitor exchange in single crystals of the bound enzyme (1998)

The ability to replace an inhibitor bound to the HIV-1 protease in single crystals with other potent inhibitors offers the possibility of investigating a series of protease inhibitors rapidly and conveniently with the use of X-ray crystallography. This approach affords a fast turnaround of structural information for iterative rational drug designs and obviates the need for studying the complex structures by co-crystallization. The replacement approach has been successfully used with single crystals of the HIV-1 protease complexed with a weak inhibitor. The structures of the complexes obtained by the replacement method are similar to those determined by co-crystallization.
Winter Foot and Equipment Traffic Impacts on a ‘L93’ Creeping Bentgrass Putting Green (2008)

Creeping bentgrass ( Agrostis stolonifera var. palustris Huds.) is desirable as a putting green turfgrass in the transition zone as a result of year-round green color, ball roll, and playability. However, management challenges exist for bentgrass greens, including winter temperature fluctuations. Frosts often cause cancellations or delays of tee time resulting in lost revenue. In response to this winter golf course management issue, a research project was initiated at Clemson University from 1 Dec. 2005 and 2006 to 1 Aug. 2006 and 2007 on a ‘L93’ creeping bentgrass putting green to determine the impacts of foot traffic or mower traffic and time of traffic application on bentgrass winter performance. Treatments consisted of no traffic (control), foot traffic, and walk-behind mower traffic (rolling) at 0700 and 0900 hr when canopy temperatures were at or below 0 °C. Foot traffic included ≈75 steps within each plot using size 10 SP-4 Saddle Nike golf shoes (soft-spiked sole) administered by a researcher weighing ≈75 kg. A Toro Greensmaster 800 walk-behind greens mower weighing 92 kg with a 45.7-cm roller was used for rolling traffic. Data collected included canopy and soil temperatures (7.6 cm depth), visual turfgrass quality (TQ), clipping yield (g·m −2 ), shoot chlorophyll concentration (mg·g −1 ), root total nonstructural carbohydrates (TNC) (mg·g −1 ), soil bulk density (g·cm −3 ), and water infiltration rates (cm·h −1 ). Time and type of traffic significantly influenced bentgrass winter performance. On all TQ rating dates, 0700 hr rolling traffic decreased TQ by ≈1.1 units compared with foot traffic at 0700 hr . In December, regardless of traffic application time, rolling traffic reduced bentgrass shoot growth ≈17%. However, in February, chlorophyll, soil bulk density, and water infiltration differences were not detected. By the end of March, all treatments had acceptable TQ. Root TNC was unaffected in May, whereas shoot chlorophyll concentrations were unaffected in May and August. This study indicates bentgrass damage resulting from winter traffic is limited to winter and early spring months and full recovery should be expected by summer.
<i>Dasheng</i>and<i>RIRE2</i>. A Nonautonomous Long Terminal Repeat Element and Its Putative Autonomous Partner in the Rice Genome (2002)

Dasheng is one of the highest copy number long terminal repeat elements and one of the most recent elements to amplify in the rice (Oryza sativa) genome. However, the absence of any significant coding capacity for retroviral proteins, including gag and pol, suggests that Dasheng is a nonautonomous element. Here, we have exploited the availability of 360 Mb of rice genomic sequence to identify a candidate autonomous element. RIRE2 is a previously described gypsy-like long terminal repeat retrotransposon with significant sequence similarity to Dasheng in the regions where putative cis factors for retrotransposition are thought to be located. Dasheng and RIRE2 elements have similar chromosomal distribution patterns and similar target site sequences, suggesting that they use the same transposition machinery. In addition, the presence of several RIRE2-Dasheng element chimeras in the genome is consistent with the copackaging of element mRNAs in the same virus-like particle. Finally, both families have recently amplified members, suggesting that they could have been co-expressed, a necessary prerequisite for RIRE2 to serve as the source of transposition machinery for Dasheng. Consistent with this hypothesis, transcripts from both elements were found in the same expressed sequence tag library.
Yeast plasmid 2-micron circle promotes recombination within bacterial transposon Tn5. (1983)

The site-specific recombination system (FLP) encoded by the yeast plasmid 2-micron circle can also act in yeast on the inverted repeats of the bacterial transposon Tn5. The efficiency of this recombination is dependent on the location of Tn5 within the 2-micron circle genome but can be as high as that observed for 2-micron circle itself. Comparison of the DNA sequences between the Tn5 repeat and the 2-micron circle recombination region reveals certain strikingly similar structural features that might be important in the recombination reaction.
Darstellung und Umwandlung funktioneller Gruppen: Abschnitt 2.1 – 2.4 (1991)

Das Kapitel enthält die folgenden Abschnitte: 2.1 Alkene und Alkine 2.1.1 Alkene A-l Cyclohexen A-2 Hepten A-3 (Z)-6-(Tetrahydro-2-pyranyloxy)hex-3-en-1-ol A-4a-b (Z)-Hex-3-en-1,6-dioldiacetat 2.1.2 Alkine A-5 3,3-Dimethylbutin-1 A-6a-b Cyclooctin A-7a-b Diphenylacetylen A-8 4,4-Dimethyl-6-heptin-2-on A-9 1-Hexin 2.2 Halogenalkane B-1 1,2-Dibrom-3,3-dimethylbutan B-2 1-Bromheptan B-3 2,2′-Bis(brommethyl)biphenyl B-4 1-Brom-3-methyl-2-buten (Phenylbromid) B-5 n-Pentylchlorid B-6 1-Chlornonan B-7 Phenacylbromid B-8 Dibrommeldrumsäure (5,5-Dibrom-2,2-dimethyl-4,6-dioxo-1,3-dioxan) B-9 2-Bromhexanal B-10 4-(Brommethyl)benzoesäure B-11 Benzyliodid 2.3 Alkohole C-1 5-Nonanol C-2 4-(p-Tolyl)-4-hydroxy butansäure C-3 1-(p-Tolyl)butan-1,4-diol C-4 2,2′-Bis(hydroxymethyl)biphenyl C-5 2-Cyclohexenol C-6( (−)-cis-Myrtanol C-7 β-Phenylethanol C-8 trans-1,2-Cyclohexandiol 2.4 Ether und Oxirane D-1 Resorcindimethylether D-2 (+)-(R,R)-2,3-Dimethoxy-N,N,N′,N′-tetramethylweinsäurediamid D-3 Isophoronoxid D-4 cis-2,3-Epoxycyclohexanol D-5 1-Phenyl-1-β-styryloxiran
Cross-Talk-Free Dual-Color Fluorescence Cross-Correlation Spectroscopy for the Study of Enzyme Activity (2010)

We have developed an instrument for spectral cross-talk-free dual-color fluorescence cross-correlation spectroscopy (FCCS), which provides a readout modality for the study of enzyme activity in application areas such as high-throughput screening. Two spectrally distinct (approximately 250 nm) fluorophores, Cy3 and IRD800, were excited simultaneously using two different excitation sources: one poised at 532 nm and the other at 780 nm. The fluorescence information was processed on two different color channels monitored with single-photon avalanche diodes (SPADs) that could transduce events at the single-molecule level. The system provided no color cross-talk (cross-excitation and/or cross-emission) and/or fluorescence resonance energy transfer (FRET), significantly improving data quality. To provide evidence of cross-talk-free operation, the system was evaluated using bright microspheres (lambda(abs) = 532 nm, lambda(em) = 560 nm) and quantum dots (lambda(abs) = 532 nm, lambda(em) = 810 nm). Experimental results indicated that no color leakage from the microspheres or quantum dots into inappropriate color channels was observed. To demonstrate the utility of the system, the enzymatic activity of APE1, which is responsible for nicking the phosphodiester backbone in DNA on the 5' side of an apurinic/apyrimidinic site, was monitored by FCCS using a double-stranded DNA substrate dual labeled with Cy3 and IRD800. Activity of APE1 was also monitored in the presence of an inhibitor (7-nitroindole-2-carboxylic acid) of the enzyme using this cross-talk-free FCCS platform. In all cases, no spectral leakage from single-molecule events into inappropriate color channels was observed.
Energetic ion and neutral energy analyzer for extreme-ultraviolet light sources (2012)

The Center for Plasma-Material Interactions has developed a detector capable of diagnosing the energetic ion and neutral spectrums emanating from extreme ultraviolet light sources. This tool has been used in the past for high-power output sources, but it is readily evident that actinic inspections tools require the use of debris mitigation analyzers. Using this tool, manufacturers can optimize the use of debris mitigation techniques, as well as analyze the effects brightness increases have on tool lifetime.
<b>Expression of brain nitric oxide synthase mRNA in various tissues and cultured cells of </b><b>rat </b> (1992)

Nitric oxide (NO) is produced from L-arginine by the catalytic action of NO synthase (NOS). To elucidate the expression of brain NOS mRNA by tissues other than brain, we extracted poly(A)+RNA from various rat tissues and cultured cells and performed Northern blot analysis using a subcloned polymerase chain reaction product as a probe. Northern blot analysis revealed a single band corresponding to the size of brain NOS mRNA (about 10.5 kb), which was expressed abundantly in cerebellum, moderately in cerebrum, stomach and adrenal gland, and minimally in atrium, aorta, kidney and ovary, but not in ventricle, lung, liver, intestine, spleen, pancreas or urinary bladder. Rat pituitary tumor cell line (GH3) also expressed brain NOS mRNA. These data suggest that brain NOS gene is constitutively and widely expressed throughout rat tissues.
Faculty Opinions recommendation of Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome. (2007)

Noonan syndrome is a developmental disorder characterized by short stature, facial dysmorphia, congenital heart defects and skeletal anomalies. Increased RAS-mitogen-activated protein kinase (MAPK) signaling due to PTPN11 and KRAS mutations causes 50% of cases of Noonan syndrome. Here, we report that 22 of 129 individuals with Noonan syndrome without PTPN11 or KRAS mutation have missense mutations in SOS1, which encodes a RAS-specific guanine nucleotide exchange factor. SOS1 mutations cluster at codons encoding residues implicated in the maintenance of SOS1 in its autoinhibited form. In addition, ectopic expression of two Noonan syndrome-associated mutants induces enhanced RAS and ERK activation. The phenotype associated with SOS1 defects lies within the Noonan syndrome spectrum but is distinctive, with a high prevalence of ectodermal abnormalities but generally normal development and linear growth. Our findings implicate gain-of-function mutations in a RAS guanine nucleotide exchange factor in disease for the first time and define a new mechanism by which upregulation of the RAS pathway can profoundly change human development. PMID: 17143282 Funding information This work was supported by: NHLBI NIH HHS, United States Grant ID: HL71207 Telethon, Italy Grant ID: GGP04172 NHLBI NIH HHS, United States Grant ID: HL074728 NCI NIH HHS, United States Grant ID: CA28146 NICHD NIH HHS, United States Grant ID: HD01294 NCI NIH HHS, United States Grant ID: CA55360 More Less keyboard_arrow_down
Analysis of Overlapping Bands by an Analytic Geometric Approach: The Potential of Band-Stripping and the Complementary Matching Method in Extraction of Band Components from Overlapping Bands (2003)

As a novel method for extracting individual band components from heavily overlapping bands, we propose a band stripping/complementary matching method that is based on first-derivative-second-derivative (D1-D2) plots of an experimental spectrum, coupled with a new concept called a complementary band. By using the concept of complement of a set, the ith band can be indirectly expressed by using a complementary band created by subtracting all the bands, exclusive of the ith estimated band, from an experimental spectrum. The degree of coincidence of both shapes between an estimated band and its complementary band provides a very suitable measure for the quality of fit for each individual band. The analysis method consists of two stages. The first stage is concerned with the geometric approach, which estimates a set of values for the parameters of a component band in the overlapping bands, and repeats band decomposition of the remaining bands in the same manner after removing the estimated band from the overlapping bands. The second stage is to minimize the difference between the profiles of the estimated band and its complementary band by a least-squares optimization and then determine the optimum values of the band parameters with the best-fit band shape. The algorithm and procedures of this method are illustrated by use of a synthetic spectrum consisting of a number of component bands, a background component, and random noise. The quality of fit is so satisfactory in terms of the coincidence between the individual estimated band and the corresponding complementary one that visual observation permits us to determine the optimum estimates of the band parameters and avoid potential problems of curve fitting.
Katalytische Umsetzungen von Olefinen an Platinmetall‐Verbindungen Das Consortium‐Verfahren zur Herstellung von Acetaldehyd (1959)

Abstract Es wird über einen neuen Weg der katalytischen Oxydation von Olefinen mit Platinmetall‐Verbindungen berichtet. Mit Sauerstoff und Oxydationsüberträgern gelingt eine kontinuierliche, selektive Umsetzung zu Carbonyl‐Verbindungen, die offensichtlich über Edelmetall‐Olefin‐Komplexe abläuft. Die Oxydation ist auch bei anderen ungesättigten Verbindungen möglich und eröffnet neue präparative Möglichkeiten. Die Methode ist Grundlage aussichtsreicher technischer Verfahren für die Herstellung von Carbonyl‐Verbindungen aus niederen Olefinen, insbesondere von Acetaldehyd aus Äthylen.
<title>Ion beam figuring of nickel mandrels for x-ray replication optics</title> (2001)

The x-ray telescopes foreseen for future x-ray missions will need an high number of mirrors. Using for their production the replication method, an high number of mandrels will be necessary. A cost-effective approach that offers accurate control of the mandrels shape is the ion beam figuring. Using this procedure the aluminum-kanigen mandrels are initially optically figured by diamond turning or by other means, superpolished to the specified microroughness and then ion beam figured to the required shape. An ion beam facility has been built to test the concept. A small test mandrel has been measured obtaining the map of its surface. From this map and from the beam removal function of the ion head a time matrix has been computed to remove the shape errors. Using this time matrix as input to the program that control the movement of the ion head, the mandrel has been corrected from the errors. In this paper is given a description of the ion beam facility and the results obtained figuring the surface of the test mandrel.
Kinetics of Air Absorption by Water in Sparged Agitated Pressure Vessels (2003)

In this work, the transfer rate of air to water in a sparged agitated pressure vessel was studied. The mass-transfer coefficient of air was proved to depend on the mixing energy per liquid volume (Pg/V), the air flow rate per liquid volume (Qa/V) as well as the vessel's pressure and temperature. The derived equation, which correlates these parameters with the mass-transfer coefficient, can be used for the design of a pressure vessel included in a dissolved air flotation process.
ChemInform Abstract: SYNTHETIC REACTIONS BY COMPLEX CATALYSTS PART 33, SYNTHESIS OF VINYLCYCLOPROPANE DERIVATIVES BY COPPER ISONITRILE COMPLEXES, COPPER VINYLCARBENOID INTERMEDIATES (1974)

Abstract Bei der Behandlung mit Cu‐Isonitrilkomplexen (II) erhält man aus den beiden Dichlorpropenen (I) bzw. (V), ggf. über eine Umlagerung des zunächst gebildeten Komplexes (IV), die Komplexe (III) , die mit den aktivierten Olefinen (VI) zu den Cyclopropa= I nen (VII) reagieren.
Rod phototransduction in transgenic mice expressing a mutant opsin gene (1996)

Rod-mediated electroretinograms (ERG's) were recorded from transgenic mice expressing a mouse opsin gene with three point mutations (V20G, P23H, and P27L; termed VPP mice) and from normal littermates. The leading edge of the alpha wave was analyzed in relation to a computational model of rod phototransduction [J. Physiol. 499, 719 (1992)], in which values for the maximum response (RmP3), transduction gain (S), and transduction delay (td) are derived from alpha-wave data. VPP mice exhibited an age-related decrease in RmP3. This decrease was consistent with reductions in the number of rod photoreceptors and in the length of rod outer segments observed in previous histological studies of the VPP retina. Values of S determined for the VPP mice were within the normal range, consistent with a normal amplification of the visual signal in VPP rods. At high stimulus intensities, both normal and VPP mice exhibited a decrease in S, which may reflect depletion of a phototransduction substrate at these stimulus levels. We examined the recovery of the alpha wave after a bright conditioning flash by measuring the rod alpha-wave response to a probe flash presented at varying times after the conditioning stimulus. In both normal and VPP mice a fourfold (0.6-log-unit) increase in conditioning stimulus intensity increased both T50%, the period required for half-maximal recovery, and tau, the exponential time constant describing recovery. However, the increases in T50% and tau were significantly greater in VPP mice, indicating an abnormally slow recovery of the flash response in VPP rods.
Multivalent Dendrons for High‐Affinity Adhesion of Proteins to DNA (2006)

Strength in numbers: Multivalent dendrons that have an N-maleimido group at the focal point can be used to construct monodisperse one-to-one protein–dendron conjugates. The second generation polyamine dendron with spermine surface groups clearly imparts its high-affinity DNA binding to a protein of choice.