gebhart/patrepeval huggingface dataset:
Molecular cloning, induction and taxonomic distribution of caffeoyl-CoA 3-O-methyltransferase, an enzyme involved in disease resistance. (1991)

Trans-Caffeoyl-CoA 3-O-methyltransferase is involved in the reinforcement of the plant cell wall under conditions that trigger the disease resistance response (Pakusch, A.-E., Kneusel, R.E., and Matern, U. (1989) Arch. Biochem. Biophys. 271, 488-494). Partial amino acid sequences of the enzyme from cultured parsley cells that had been treated with a crude elicitor were identified (Pakusch, A.-E., Matern, U., and Schiltz, E. (1991) Plant Physiol. 95, 137-143), and corresponding degenerated oligonucleotides of 29- and 30-nucleotide length were synthesized. Northern hybridizations with these probes revealed one specific RNA band, and the amount of this RNA appeared to be transiently induced upon elicitation of the cells. De novo enzyme synthesis was confirmed by Western blotting experiments using a specific antiserum. The time course of induction closely followed the pattern observed for phenylalanine ammonia-lyase and suggested the operational coordination of the methyltransferase with the general phenylpropanoid pathway in vivo. Full size cDNA of 1.258 kilobases was isolated in lambda gt11, sequenced and found to contain a remarkably long 5'-untranslated leader sequence followed by an open reading frame that codes for a 241-residue polypeptide representing the 27-kDa subunit of the native, dimeric parsley enzyme. Almost no homology was found to protein sequences filed in data banks. Southern hybridization with genomic DNA suggested that only one or two copies of the respective gene(s) are present in the parsley genome. Caffeoyl-CoA-specific methyltransferase activity was demonstrated in taxonomically widely diverse plants such as Dianthus caryophyllus (Caryophyllaceae), Carthamus tinctorius (Asteraceae) or Daucus carota, and Ammi majus (Apiaceae) where it is commonly induced by elicitor treatment. In Northern blots with RNA from Ammi or Daucus, parsley cDNA hybridized specifically to one band comparable in size to the parsley RNA, whereas Dianthus and Carthamus appear to code for slightly larger RNAs (roughly 1.45 and 1.3 kilobases, respectively). Slot-blot hybridizations revealed in all instances the rapid and transient increase of mRNA levels in response to elicitation. This emphasizes the integral role of the enzyme in disease resistance expression in plants far beyond parsley and also illustrates a new physiological context for the induction of 4-coumarate:CoA ligase.
Non-Linear Dimensionality Reduction (1992)

A method for creating a non--linear encoder--decoder for multidimensional data with compact representations is presented. The commonly used technique of autoassociation is extended to allow non--linear representations, and an objective function which penalizes activations of individual hidden units is shown to result in minimum dimensional encodings with respect to allowable error in reconstruction. 1 INTRODUCTION Reducing dimensionality of data with minimal information loss is important for feature extraction, compact coding and computational efficiency. The data can be tranformed into &quot;good&quot; representations for further processing, constraints among feature variables may be identified, and redundancy eliminated. Many algorithms are exponential in the dimensionalityof the input, thus even reduction by a single dimension may provide valuable computational savings. Autoassociating feedforward networks with one hidden layer have been shown to extract the principal components of the data ...
Resilient circuits (2009)

Voltage and frequency margins necessary to ensure correct processor operation under dynamic voltage, temperature, and aging variations result in performance and power overheads. Resilient circuit techniques, including embedded error-detection sequentials and tunable replica circuits, allow these margins to be reduced or eliminated, resulting in reliable, energy-efficient operation.
TEM STUDY OF MECHANISM OF STRAIN-AGE HARDENING OF INITIALLY DISORDERED (Co, Fe)_3V ALLOY (1992)

TEM study was made to explore the mechanism of the strain-age hardening of initially-disordered'(Co_(78)Fe_(22))_3V, which was found to be attributed to the formation of a special dislocation-stacking fault configuration in company with disorder-order transformation — dislocations extended to stacking faults on {111} planes and got connected with each other through partial dislocation reaction at intersections of {111} planes, leading to dense networks with cells bounded by stacking fault tetrahedrons. The results also indicated that ordered (Co_(78)Fe_(22))_3V has very low stacking fault energy on {111} planes and relative high and isotropic antiphase boundary energy, which implies that it is most likely to be Lomer-Cottrell locks, not Kear-Wilsdof locks, that are responsible for the high strength at high temperatures of this alloy.
A grating‐based single‐shot x‐ray phase contrast and diffraction method for <i>in vivo</i> imaging (2010)

The spatial harmonic method allowed us to obtain absorption, differential phase contrast, and diffraction images, all from a single raw image and is feasible in live animals. Because the sensitivity of the method scales with the density of the gratings, custom microfabricated gratings should be superior to off-the-shelf lead grids.
Er–carrier interaction and its effects on the Er3+ luminescence of erbium-doped Si/SiO2 superlattices (2000)

The Er–carrier interaction and its effects on the Er3+ photoluminescence properties of erbium-doped Si/SiO2 superlattices are investigated. The interaction between the erbium atoms and the electronic carriers was controlled by doping erbium into the SiO2 layers only and by depositing buffer layers of pure SiO2 between the erbium-doped SiO2 layers and the Si layers. We demonstrate that by controlling the erbium-carrier interaction, a three orders of the magnitude enhancement of the Er3+ luminescence intensity and a nearly complete suppression of the temperature-induced quenching of Er3+ luminescence can be achieved while still allowing the Er3+ ions to be excited by the carriers. We identify the asymmetry between the dominant carrier-mediated excitation and the de-excitation paths of Er3+ ions as the possible cause for the observed effects.
Electrical Properties of Phase Change and Channel Current Control in Ultrathin Phase-Change Channel Transistor Memory by Annealing (2006)

We studied phase-change channel transistor memory devices with an ultrathin Ge2Sb2Te5 chalcogenide film channel and tried to demonstrate two combined functions (memory: resistance change and selection: channel current control) by annealing in this paper. Drain–source resistance can be markedly decreased by 2–3 orders of magnitude after annealing due to the phase change from the amorphous to crystalline phases. A channel current control effect in which the drain current decreases with the gate voltage was clearly observed in 10- and 20-nm-thick Ge2Sb2Te5 devices. The absolute channel current modulation by the gate voltage in the crystalline state is much stronger than that in the amorphous state. Furthermore, the channel current control ability in devices with thin Ge2Sb2Te5 is stronger than that in devices with thick Ge2Sb2Te5. The channel current control effect might result from the potential change of the ultrathin Ge2Sb2Te5 channel by the gate voltage.
In situ Relationship between Sucrose Exposure and the Composition of Dental Plaque (1997)

The aim of this study was to analyze the composition of dental plaque according to sucrose exposure. Twelve adult volunteers took part in this crossover study done in four phases of 28 days each. For each phase of the study, an acrylic resin appliance containing four human dental enamel blocks was constructed for each volunteer. A 20% sucrose solution was dripped onto the enamel blocks from 0 to 8 times/day. The volunteers were randomly assigned to the treatments. During the experimental period all the subjects used fluoride-free dentifrice, refrained from brushing the enamel blocks and drank water fluoridated at 0.70 ppm F. After each phase the concentrations of fluoride (F), calcium (Ca), phosphorus (P) and total carbohydrate were determined in dental plaque. Statistical analyses showed that frequent sucrose exposure significantly (p < 0.05) reduced the F, Ca and P concentrations in dental plaque, but increased the alkali-soluble carbohydrate concentration. The results suggest that the cariogenicity of dental plaque formed in the presence of sucrose cannot be attributed only to its higher porosity, but the lower inorganic concentration may also be important.
Temporal Lobe Gliosarcoma After Gamma Knife Radiosurgery for Vestibular Schwannoma (2016)

De novo malignancy after radiosurgery for VS is rare. We present only the second case of a gliosarcoma arising within the low-dose radiation field of the radiosurgery treatment plan. Some of the challenges of establishing causality between radiation treatment and secondary tumor development are discussed. The reporting of malignancy after radiation therapy, and even microsurgery, warrants continued vigilance.
Structural control of d-f interaction in the CeFe1−xRuxAsO system system (2012)

The isovalent substitution effect of Ru in CeFe1−xRuxAsO (0 ≤ x ≤ 1) has been systematically studied by powder X-ray diffraction, electrical resistivity, magnetization, and specific heat measurements. The antiferromagnetic (AFM) ordering of both d and 4f electrons are suppressed upon Ru doping, followed by Pauli paramagnetism (d electrons) and local moment paramagnetism (4f electrons) with strong ferromagnetic fluctuation, respectively. Neither superconductivity above 2K nor pronounced Kondo screening are observed in the substitution phase diagram. Combined with published results of the cerium-based quaternary compounds CeMXO(M =Fe, Ru; X =P, As), our data suggest that the end member CeRuAsO is on the verge of becoming an FM Kondo lattice. Meanwhile, the ground state of 4f electrons in the quaternary CeMXO system should be determined by both the interlayer d-f Kondo coupling (JKondo) and the intralayer Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction (JRKKY ), which are both very sensitive to the change in crystal structure.
Linkage of familial breast cancer to chromosome 17q21 may not be restricted to early-onset disease. (1992)

Lod scores for linkage between familial breast and ovarian cancer and markers on chromosome 17q21 are more frequently positive among families with disease diagnosed at younger ages than they are among older-onset families, suggesting that linkage is restricted to early-onset disease. However, for late-onset cases, the relative probability of sporadic rather than inherited disease is higher than previously suggested. If this correction is made, then later-onset families are much less informative; linkage heterogeneity based on age at onset is no longer significant; and for the sample of families as a whole, linkage is significant at a recombination fraction since demonstrated to be close to the correct local. There is probably more than one gene for inherited breast cancer, but heterogeneity may not be due to age at disease onset.
Cellulose Acetate Blends - Effect of Plasticizers on Properties and Biodegradability (2014)

Cellulose acetate (CDA) cannot be processed as raw material because it starts to decompose before melting. Triacetin and diacetin were tested to improve CDA processing versus conventional phthalate as environmentally sustainable plasticizers, because of their low toxicity and fast biodegradability. The addition of triacetin and diacetin allowed melt processing of CDA and the results of tensile tests outlined their effect as plasticizers. The values of mechanical properties were compatible with the requirements for applications in rigid packaging. From the results of biodegradation tests it can be concluded that for pure cellulose acetate, complete biodegradation was obtained within 200 days of testing after reinoculation. Incomplete biodegradation was observed for test items with 20% triacetin or with 30% phthalate. After 46 days of incubation, the test samples with 30% plasticizer based on triacetin or triacetin-diacetin were completely biodegraded. These formulations can be selected for the production of compostable blends and/or biocomposites.
Catalyst-Free and Selective C–N Bond Functionalization: Stereospecific Three-Component Coupling of Amines, Dichloromethane, and >P(O)H Species Affording α-Aminophosphorus Compounds (2014)

Catalyst-free and selective C-N bond functionalization has been achieved through three-component coupling of amines, dihalomethane, and >P(O)H species. This reaction takes place stereospecifically with retention of configuration at phosphorus, which can produce various new optically active phosphorus analogues of α-amino acids.
Properties of Components Obtained by Treatment of Semliki Forest Virus with Tween 80 and Tri(n-butyl)phosphate (1973)

SUMMARY Purified Semliki Forest virus was analysed by analytical sedimentation, rate zonal sedimentation, isopycnic sedimentation, polyacrylamide gel electrophoresis and electron microscopy. It was found that the spherical virus particles had a sedimentation coefficient of 241 S (249 S determined by rate zonal sedimentation), and a buoyant density in sucrose of 1.190 g/ml; one protein and one glycoprotein were present in the virus; after fixation and negative staining with phosphotungstic acid the diameter of the particles was measured to be 50 to 56 nm. Treatment of Semliki Forest virus with 0.1% Tween 80 and 1% tri(n-butyl)phosphate (TNBP) for 1 h at 4 °C destroyed infectivity and resulted in the appearance of the following haemagglutinating and immunizing virus components. (1) A spherical 211 S (217 S) component, 69 to 75 nm in diameter, consisting of an envelope and a core; one protein and one glycoprotein were present; the [3H]-uridine:[14C)-protein ratio was 2.8-fold higher than that of double-labelled untreated virus. (2) A spherical component, 70 to 73 nm in diameter, consisting of the virus envelope lacking intact cores; s 20,w = 140 S (153 S); one glycoprotein was detected; the [3H]-uridine: [14C]-protein ratio was about 1/3 of untreated virus. (3) A 135 S component. (4) Structures assumed to represent envelope fragments; much of them had a sedimentation coefficient of 49 S. It was concluded from experiments with [3H]-uridine-[14C]-amino acids double-labelled and [14C]-stearic acid-labelled virus that Tween 80-TNBP dissociates lipids and some protein components from the virus.
Long-range interaction and correlation between <i>MYC</i> enhancer and oncogenic long noncoding RNA <i>CARLo-5</i> (2014)

The mechanism by which the 8q24 MYC enhancer region, including cancer-associated variant rs6983267, increases cancer risk is unknown due to the lack of protein-coding genes at 8q24.21. Here we report the identification of long noncoding RNAs named cancer-associated region long noncoding RNAs (CARLos) in the 8q24 region. The expression of one of the long noncoding RNAs, CARLo-5, is significantly correlated with the rs6983267 allele associated with increased cancer susceptibility. We also found the MYC enhancer region physically interacts with the active regulatory region of the CARLo-5 promoter, suggesting long-range interaction of MYC enhancer with the CARLo-5 promoter regulates CARLo-5 expression. Finally, we demonstrate that CARLo-5 has a function in cell-cycle regulation and tumor development. Overall, our data provide a key of the mystery of the 8q24 gene desert.
Identification of the cDNA for Human Red Blood Cell–Specific Hexokinase Isozyme (1997)

A unique cDNA for hexokinase (HK) was identified from poly(A)+ RNA of human reticulocytes by anchored polymerase chain reaction. This appeared to represent the cDNA for the red blood cell (RBC)-specific HK isozyme (HKR) described in our previous study (Murakami et al: Blood 75:770, 1990). Its nucleotide sequence was identical to HKI cDNA except for the 5' extreme end. It lacked the first 62 nucleotides of the HKI coding region: instead, it contained a unique sequence of 60 nucleotides at the beginning of the coding sequence as well as another unique sequence upstream of the putative translation initiation site. It lacked the porin-binding domain which facilitates binding to the mitochondria, thus explaining the exclusive cytoplasmic localization of HKR. It was the major cDNA derived from reticulocytes, consistent with the observation that HKR activity is predominant in reticulocytes. Northern blot analysis showed that it was expressed in the reticulocytes and in the K562 erythroleukemic cell line, but not in a lymphocytic cell line. In the extract of K562 cells, HKR activity co-eluted with the HKR of human RBCs on a MonoQ column (Pharmacia, Piscataway, NJ) chromatography, using a salt gradient elution. The separate genetic control of the RBC-specific HK isozyme explains the clinical reports of two types of HK deficiency, one in which the HK activity was reduced exclusively in the RBC (HKR defect) and another with general decrease of HK activity in several tissues (HKI defect).
Characterization of Deoxyribonucleic Acid (DNA) Obtained from Teeth Subjected to Various Environmental Conditions (1991)

This study was designed to determine the effects of various environmental factors on the deoxyribonucleic acid (DNA) obtained from dental pulp. Extracted teeth were subjected to the following conditions: varying pH (3,7,10); temperature (4 degrees C, 25 degrees C, 37 degrees C, incineration); humidity (20%, 66%, 98%); various types of soil (sand, potting soil, garden soil); seawater; burying the teeth outdoors, and aging (one week to six months). In addition, teeth that had been extracted and held at room temperature for 16 and 19 years were also examined. Following isolation of DNA, the samples were analyzed on yield gels to determine the concentration and integrity of the recovered DNA. Restriction digestion with Pst I was followed by electrophoresis of the generated fragments, Southern transfer to nylon membranes, and hybridization to both human and bacterial probes. It was determined that, aside from soil, the environmental conditions examined did not affect the ability to obtain high-molecular-weight human DNA from dental pulp. Restriction fragment length polymorphic (RFLP) analysis of selected samples was performed. Dental pulp patterns were compared with bloodstain exemplars, revealing matching patterns, although an increase in band-shifting was observed with extended exposure to elevated temperatures.
The Effect of Capture on Collision-Resolution Algorithms (1985)

In many communication systems, the stronger of two or more overlapping packets might capture the receiver and thus be received without error. The effect of capture on collision-resolution algorithms in a slotted ALOHA type broadcasting network is investigated here. Extensions to the algorithms are suggested for both the situations in which the receiver can or cannot distinguish between success slots and capture slots. In particular, we present a class of retransmission schemes for packets that have been transmitted during capture slots but have not been received correctly. The performance analysis is confined to a simplified model in which the nodes of the network are divided into two groups and only packets sent by the nodes of one of them might be captured. For this simplified model and for each extended algorithm, explicit recursive equations are given, from which the average conditional collision-resolution interval length, as well as the maximal throughput, can be determined. As expected, we show that in the presence of capture, the performance of the network is improved and the maximal attainable throughput is increased. Extensions of the simplified model such as dividing the nodes into <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</tex> groups instead of two, or considering the situation that capture depends on relative distances and transmission powers, are also discussed. For the latter situation we give simulation results.
Amplicon‐based high‐throughput pooled sequencing identifies mutations in <i>CYP7B1</i> and <i>SPG7</i> in sporadic spastic paraplegia patients (2011)

Hereditary spastic paraplegia (HSP) is a neurodegenerative disorder defined clinically by progressive lower limb spasticity and weakness. HSP is a genetically highly heterogeneous condition with at least 46 gene loci identified so far, involving X-linked, autosomal recessive (AR) and autosomal dominant inheritance. For correct diagnosis, molecular testing is essential because clinical parameters by themselves are not reliable to differentiate HSP forms. The purpose of this study was to establish amplicon-based high-throughput genotyping for AR-HSP. A sample of 187 index cases with apparently sporadic or recessive spastic paraplegia were analyzed by applying an array-based amplification strategy. Amplicon libraries of the CYP7B1-(SPG5) and SPG7-gene were generated followed by a pooled next-generation sequencing (NGS) approach. We identified three SPG5 and seven SPG7 patients. All had one homozygous or two heterozygous mutations. In total, 20 distinct mutations (CYP7B1,n = 4and SPG7,n = 16) including two novel CYP7B1 mutations (p.G51R and p.E211KfsX3) and eight novel SPG7 mutations (p.Leu8delinsLeuLeu, p.W29X, p.R139X, p.R247X, p.G344D, p.Leu346_Leu347ins11, p.R398X and p.R398Q) were detected by this comprehensive genetic testing. Our study illustrates how amplicon-based NGS can be used as an efficient tool to study genotypes and mutations in large patient cohorts and complex phenotypes.
Multiscale Finite Volume Formulation for the Saturation Equations (2009)

Abstract Recent advances in multiscale methods have shown great promise in modeling multiphase flow in highly detailed heterogeneous domains. Existing multiscale methods, however, solve for the flow field (pressure and total-velocity) only. Once the fine-scale flow field is reconstructed, the saturation equations are solved on the fine scale. With the efficiency in dealing with the flow equations greatly improved by multiscale formulations, solving the saturation equations on the fine scale becomes the relatively more expensive part. In this paper, we describe an adaptive multiscale finite-volume (MSFV) formulation for the nonlinear transport (saturation) equations. A general algebraic multiscale formulation consistent with the operator based framework proposed by Zhou and Tchelepi (SPEJ 13:267-173) is presented. Thus, the flow and transport equations are solved in a unified multiscale framework. Two types of multiscale operators, namely restriction and prolongation, are used to construct the multiscale saturation solution. The restriction operator is defined according to the local sum of the fine-scale transport equations in a coarse gridblock. Three adaptive prolongation operators are defined according to the local saturation history at a particular coarse block. The three operators have different computational complexity, and they are used adaptively in the course of a simulation run. When properly used, they yield excellent computational efficiency while preserving accuracy. This adaptive multiscale formulation has been tested using several challenging problems with strong heterogeneity, large buoyancy effects, and changes in the well operating conditions (e.g., switching injectors and producers during simulation). The results demonstrate that adaptive multiscale transport calculations are in excellent agreement with fine-scale reference solutions, but with a much lower computational cost.