gebhart/patrepeval huggingface dataset:
Two Isoforms of NADPH:Cytochrome P450 Reductase in<i>Arabidopsis thaliana</i> (1998)

We have investigated two NADPH-cytochrome (Cyt) P450 reductase isoforms encoded by separate genes (AR1 and AR2) in Arabidopsis thaliana. We isolated AR1 and AR2 cDNAs using a mung bean (Phaseolus aureus L.) NADPH-Cyt P450 reductase cDNA as a probe. The recombinant AR1 and AR2 proteins produced using a baculovirus expression system showed similar Km values for Cyt c and NADPH, respectively. In the reconstitution system with a recombinant cinnamate 4-hydroxylase (CYP73A5), the recombinant AR1 and AR2 proteins gave the same level of cinnamate 4-hydroxylase activity (about 70 nmol min-1 nmol-1 P450). The AR2 gene expression was transiently induced by 4- and 3-fold within 1 h of wounding and light treatments, respectively, and the induction time course preceded those of CYP73A5 and a phenylalanine ammonia-lyase (PAL1) gene. On the contrary, the AR1 expression level did not change during the treatments. Analysis of the AR1 and AR2 gene structure revealed that only the AR2 promoter contained three putative sequence motifs (boxes P, A, and L), which are involved in the coordinated expression of CYP73A5 and other phenylpropanoid pathway genes. These results suggest the possibility that AR2 transcription may be functionally linked to the induced levels of phenylpropanoid pathway enzymes.
Purification of telomerase from Euplotes aediculatus: requirement of a primer 3' overhang. (1996)

Telomerase is a ribonucleoprotein enzyme that uses its internal RNA moiety as a template for synthesis of telomeric repeats at chromosome ends. Here we report the purification of telomerase from Euplotes aediculatus by affinity chromatography with antisense 2'-O-methyl oligonucleotides, a method that was developed for small nuclear ribonucleoprotein particles (snRNPs). Elution of bound ribonucleoprotein from the antisense oligonucleotide under nondenaturing conditions was achieved by a novel approach, using a displacement oligonucleotide. Polypeptides of 120 kDa and 43 kDa (a doublet) copurify with the active telomerase and appear stoichiometric with telomerase RNA. A simple model for DNA end replication predicts that after semiconservative DNA replication, telomerase will extend the newly synthesized, blunt-ended leading strand. We show that purified Euplotes telomerase has no activity with blunt-ended primers. Instead, efficient extension requires 4 to 6 single-stranded nucleotides at the 3' end. Therefore, this model predicts the existence of other activities such as helicases or nucleases that generate a single-stranded 3' end from a blunt end, thus activating the end for telomerase extension.
Meltdown: reading kernel memory from user space (2018)

The security of computer systems fundamentally relies on memory isolation, e.g., kernel address ranges are marked as non-accessible and are protected from user access. In this paper, we present Meltdown. Meltdown exploits side effects of out-of-order execution on modern processors to read arbitrary kernel-memory locations including personal data and passwords. Out-of-order execution is an indispensable performance feature and present in a wide range of modern processors. The attack is independent of the operating system, and it does not rely on any software vulnerabilities. Meltdown breaks all security guarantees provided by address space isolation as well as paravirtualized environments and, thus, every security mechanism building upon this foundation. On affected systems, Meltdown enables an adversary to read memory of other processes or virtual machines in the cloud without any permissions or privileges, affecting millions of customers and virtually every user of a personal computer. We show that the KAISER defense mechanism for KASLR has the important (but inadvertent) side effect of impeding Meltdown. We stress that KAISER must be deployed immediately to prevent large-scale exploitation of this severe information leakage.
Leucocytes, cytokines and satellite cells: what role do they play in muscle damage and regeneration following eccentric exercise? (2012)

Exercise-induced muscle damage is an important topic in exercise physiology. However several aspects of our understanding of how muscles respond to highly stressful exercise remain unclear In the first section of this review we address the evidence that exercise can cause muscle damage and inflammation in otherwise healthy human skeletal muscles. We approach this concept by comparing changes in muscle function (i.e., the force-generating capacity) with the degree of leucocyte accumulation in muscle following exercise. In the second section, we explore the cytokine response to 'muscle-damaging exercise', primarily eccentric exercise. We review the evidence for the notion that the degree of muscle damage is related to the magnitude of the cytokine response. In the third and final section, we look at the satellite cell response to a single bout of eccentric exercise, as well as the role of the cyclooxygenase enzymes (COX1 and 2). In summary, we propose that muscle damage as evaluated by changes in muscle function is related to leucocyte accumulation in the exercised muscles. 'Extreme' exercise protocols, encompassing unaccustomed maximal eccentric exercise across a large range of motion, generally inflict severe muscle damage, inflammation and prolonged recovery (> 1 week). By contrast, exercise resembling regular athletic training (resistance exercise and downhill running) typically causes mild muscle damage (myofibrillar disruptions) and full recovery normally occurs within a few days. Large variation in individual responses to a given exercise should, however be expected. The link between cytokine and satellite cell responses and exercise-induced muscle damage is not so clear The systemic cytokine response may be linked more closely to the metabolic demands of exercise rather than muscle damage. With the exception of IL-6, the sources of systemic cytokines following exercise remain unclear The satellite cell response to severe muscle damage is related to regeneration, whereas the biological significance of satellite cell proliferation after mild damage or non-damaging exercise remains uncertain. The COX enzymes regulate satellite cell activity, as demonstrated in animal models; however the roles of the COX enzymes in human skeletal muscle need further investigation. We suggest using the term 'muscle damage' with care. Comparisons between studies and individuals must consider changes in and recovery of muscle force-generating capacity.
Remote sensing of suspended sediments and shallow coastal waters (2003)

Ocean color sensors were designed mainly for remote sensing of chlorophyll concentrations over the clear open oceanic areas (Case 1 water) using channels between 0.4-0.86 /spl mu/m. The Moderate Resolution Imaging Spectroradiometer (MODIS) launched on the National Aeronautics and Space Administration Terra and Aqua spacecrafts is equipped with narrow channels located within a wider wavelength range between 0.4-2.5 /spl mu/m for a variety of remote sensing applications. The wide spectral range can provide improved capabilities for remote sensing of the more complex and turbid coastal waters (Case 2 water) and for improved atmospheric corrections for ocean scenes. We describe an empirical algorithm that uses this wide spectral range to identify areas with suspended sediments in turbid waters and shallow waters with bottom reflections. The algorithm takes advantage of the strong water absorption at wavelengths longer than 1 /spl mu/m that does not allow illumination of sediments in the water or a shallow ocean floor. MODIS data acquired over the east coast of China, west coast of Africa, Arabian Sea, Mississippi Delta, and west coast of Florida are used.
Enhancement of the nonreciprocal magneto-optic effect of TM modes using iron garnet double layers with opposite Faraday rotation (1995)

Garnet films of composition Lu3−xBixFe5−yGayO12 are grown by liquid-phase epitaxy on [111]-oriented substrates of gadolinium gallium garnet. Faraday rotation and saturation magnetization are measured as a function of substitution levels, which range up to x=1.4 and y=1.8, respectively. Nonreciprocal propagation of the TM0 is studied at a wavelength of 1.3 μm. It is shown that the difference between forward and backward propagation constants can be optimized using double layers with opposite sign of the Faraday rotation. Agreement between experiments and calculations is excellent.
PRODUCTION OF 2-PHENYLETHANOL IN THE BIOTRANSFORMATION OF CINNAMYL ALCOHOL BY THE PLANT PATHOGENIC FUNGUS <I>Colletotrichum acutatum</I> (2010)

Biocatalytic processes may offer a cheaper alternative to natural production of flavours. The biotransformation of cinnamyl alcohol is investigated using the plant pathogenic fungus Colletotrichum acutatum as a biocatalyst. Results show that substrate is converted to 3-phenyl-1-propanol, 1-phenyl-1,3- propanediol, 2-phenylethanol, 1-phenyl-1,2-ethanediol, 3-phenyl propyl acetate, and hydrocinnamic acid. The structures of the metabolic products are elucidated on the basis of their spectral data. 2-phenylethanol has a sweet, floral odor and a wide variety of applications, especially, for the perfume and food industries. A time-course experiment demonstrates that 2-phenylethanol appeared after 120 hours, reaching almost 8% of relative abundance. Additionally, the influence that the culture broth has on the conversion capacity is investigated. It has been discovered that cinnamyl alcohol is converted faster when the substrate is incorporated in a Sabouraud medium; under this condition, 2-phenylethanol is the most common product after 288 hours reaching about 90% of the relative abundance. Biotransformation of cinnamyl alcohol using C. acutatum in a Sabouraud medium can offer a simple and efficient way to obtain 2-phenylethanol with high yield.
Anticancer Drugs: Antimetabolite Metabolism and Natural Anticancer Agents (1994)

Part 1 Control of cancer by amino acid analogs, G.S. Ahluwalia et al: azaserine. Part 2 Metabolism of pyrimidine analogues and their nucleosides, G.C. Daher et al: fluoropyrimidines azacytidine. Part 3 Metabolism and action of purine nucleoside analogs, W. Plunkett and P.P. Saunders: tiazofurin neplanocin A. Part 4 The basis for antifolate cytotoxicity, selectivity and metabolic transformation - effects on utilization of endogenous and exogenous folate cofactors, L.H. Matherly et al: mammalian folylpolyglutamate synthetase. Part 5 The metabolic basis for combination chemotherapy, L.E. Damon and E.C. Cadman: synergistic modulation. Part 6 The metabolism of antihormonal anticancer agents, S.P. Robinson and V.C. Jordan: treatment strategies for hormone-dependent cancers antiestrogens. Part 7 Metabolism of natural and synthetic steroids used in cancer treatment, R.Y. Kirdani et al: metabolism of natural and synthetic androgens used in cancer therapy. Part 8 Metabolism of plant-derived anticancer agents, G. Cragg and M. Suffness: bruceantin taxol. Part 9 Metabolism of protein anticancer agents, V. Bocci: cytotoxins tuftsin. Part 10 Metabolism of new anticancer agents, Z.H. Siddik and R.A. Newman: caracemide trimelamol flavone acetic acid hycamptamine sulofenur. Part 11 Metabolism of cancer drugs as a basis for drug resistance, S. Kuzmich and K.D. Tew: glutathione S-transferases - structure and function future perspectives. (Part Contents).
Least squares arrival time estimators for single and piled up scintillation pulses (1993)

A new time arrival estimator is developed for the detection of gamma rays using scintillation detectors. The estimator structure reduces to a weighted least squares (WLS) estimate of the arrival time and is found to be the optimal estimator for scintillation pulses. This WLS estimator is applied to scintillation type pulses with fast rise times and exponential decays. The timing resolution is calculated and compared to the resolution of leading edge and constant fraction triggers for a Burle 8850 photomultiplier tube, and to the Cramer-Rao lower bound on estimator performance. The WLS estimator outperforms these conventional arrival time estimators and has the added ability of simultaneously estimating the arrival times of multiple overlapping pulses. This allows for piled up pulses to be effectively separated permitting their individual energies to be estimated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High-resolution image reconstruction from multiple low-resolution images (1999)

In this paper, we demonstrate a digital signal processing (DSP) algorithm for improving spatial resolution of images captured by CMOS cameras. The basic approach is to reconstruct a high resolution (HR) image from a shift-related low resolution (LR) image sequence. The aliasing relationship of Fourier transforms between discrete and continuous images in the frequency domain is used for mapping LR images to a HR image. The method of projection onto convex sets (POCS) is applied to trace the best estimate of pixel matching from the LR images to the reconstructed HR image. Computer simulations and preliminary experimental results have shown that the algorithm works effectively on the application of post-image-captured processing for CMOS cameras. It can also be applied to HR digital image reconstruction, where shift information of the LR image sequence is known.
Microbial Fuel Cells (2007)

Preface. 1. Introduction. 1.1. Energy needs. 1.2. Energy and the challenge of global climate change. 1.3. Bioelectricity generation using a microbial fuel cell --the process of electrogenesis. 1.4. MFCs and energy sustainability of the water infrastructure. 1.5. MFC technologies for wastewater treatment. 1.6. Renewable energy generation using MFCs. 1.7. Other applications of MFC technologies. 2. Exoelectrogens. 2.1. Introduction. 2.2. Mechanisms of electron transfer. 2.3. MFC studies using known exoelectrogenic strains. 2.4. Community analysis. 2.5. MFCs as tools for studying exoelectrogens. 3. Voltage generation. 3.1. Voltage and current. 3.2. Maximum voltages based on thermodynamic relationships. 3.3. Anode potentials and enzyme potentials. 3.4. Role of enzymes versus communities in setting anode potentials. 3.5. Voltage generation by fermentative bacteria? 4. Power generation. 4.1. Calculating power. 4.2. Coulombic and energy efficiency. 4.3. Polarization and power density curves. 4.4. Measuring internal resistance. 4.5. Chemical and electrochemical analysis of reactors. 5. Materials. 5.1. Finding low-cost, highly efficient materials. 5.2. Anode materials. 5.3. Membranes and separators (and chemical transport through them). 5.4. Cathode materials. 5.5. Long term stability of different materials. 6. Architecture. 6.1. General requirements. 6.2. Air-cathode MFCs. 6.3. Aqueous cathodes using dissolved oxygen. 6.4. Two chamber reactors with soluble catholytes or poised potentials. 6.5. Tubular packed bed reactors. 6.6. Stacked MFCs. 6.7. Metal catholytes. 6.8. Biohydrogen MFCs. 6.9. Towards a scaleable MFC architecture. 7. Kinetics and Mass transfer. 7.1. Kinetic or mass transfer models? 7.2. Boundaries on rate constants and bacterial characteristics. 7.3. Maximum power from a monolayer of bacteria. 7.4. Maximum rate of mass transfer to a biofilm. 7.5. Mass transfer per reactor volume. 8. MECs for hydrogen production. 8.1. Principle of operation. 8.2. MEC systems. 8.3. Hydrogen yields. 8.4. Hydrogen recovery. 8.5. Energy recovery. 8.6. Hydrogen losses. 8.7. Differences between the MEC and MFC systems. 9. MFCs for Wastewater Treatment. 9.1. Process trains for WWTPs. 9.2. Replacement of the biological treatment reactor with an MFC. 9.3. Energy balances for WWTPs. 9.4. Implications for reduced sludge generation. 9.5. Nutrient removal. 9.6. Electrogenesis versus methanogensis. 10. Other MFC Technologies. 10.1. Different applications for MFC-based technologies. 10.2. Sediment MFCs. 10.3. Enhanced sediment MFCs. 10.4. Bioremediation using MFC technologies. 11. Fun! 11.1 MFCs for new scientists and inventors. 11.2 Choosing your inoculum and media. 11.3 MFC materials: electrodes and membranes. 11.4 MFC architectures that are easy to build. 11.5 MFC reactors 11.6 Operation and assessment of MFCs. 12. Outlook. 12.1 MFCs yesterday and today. 12.2 Challenges for bringing MFCs to commercialization. 12.3 Accomplishments and outlook. Notation. References. Index.
Molecular characterization and chromosomal localization of a third alpha-class hypoxia inducible factor subunit, HIF3alpha. (1998)

Hypoxia inducible factors (HIFs) are heterodimeric transcription factors that regulate a number of adaptive responses to low oxygen tension. They are composed of alpha- and beta-subunits that belong to the basic helix-loop-helix-PAS (bHLH-PAS) superfamily. In our efforts to identify new bHLH-PAS proteins, we cloned a cDNA encoding a novel alpha-class hypoxia inducible factor, HIF3alpha. The HIF3alpha open reading frame encodes a 662-amino acid protein with a predicted molecular weight of 73 kDa and is expressed in adult thymus, lung, brain, heart, and kidney. The N-terminal bHLH-PAS domain of this protein shares amino acid sequence identity with that of HIF1alpha and HIF2alpha (57% and 53% identity, respectively). The C-terminus of HIF3alpha contains a 36-amino acid sequence that shares 61% identity with the hypoxia responsive domain-1 (HRD1) of HIF1alpha. In transient transfections, this domain confers hypoxia responsiveness when linked to a heterologous transactivation domain. In vitro studies reveal that HIF3alpha dimerizes with a prototype beta-class subunit, ARNT, and that the resultant heterodimer recognizes the hypoxia responsive element (HRE) core sequence, TACGTG. Transient transfection experiments demonstrate that the HIF3alpha-ARNT interaction can occur in vivo, and that the activity of HIF3alpha is upregulated in response to cobalt chloride or low oxygen tension.
Linkage of proximal myotonic myopathy to chromosome 3q (1999)

We performed genetic linkage analysis in nine German proximal myotonic myopathy (PROMM) families using DNA-markers D3S1541 and D3S1589 from the region of the recently discovered gene locus of myotonic dystrophy type 2 (DM2) on chromosome 3q. Two-point analysis supplied an lod score of 5.9. We conclude that a gene causing PROMM is located on chromosome 3q. PROMM and DM2 may be allelic disorders or may be caused by closely linked genes.
Experimental observation of spatial correlation of scintillations from an extended incoherent source (2013)

The optical irradiance scintillation for an extended source and a dual-aperture system with variable aperture separation is analyzed with respect to the effect of turbulence. The scintillation index and the correlation between the dual-aperture signals emanating from an extended source are used to study the turbulence spectral model and the deviation from the common Kolmogorov atmospheric weak-turbulence model. Signal decorrelation as a function of aperture separation is presented. The relative errors introduced by using dual-aperture systems are also discussed.
Metallation and Metal-halogen Exchange Reactions of Imidazoles (1985)

Imidazotes synthesised & organometaZZic d e r i v a t i v e s , particuZarZyorganolithium d e r i v a t i u e s prepared by metaZZation and metal-halogen ezchmige reactions, are reviewed.
Forces and frequency shifts in atomic-resolution dynamic-force microscopy (1997)

True atomic resolution in vacuum with a force microscope is now obtained routinely by using the frequency shift of an oscillating cantilever as the imaging signal. Here, a calculation is presented that relates the frequency shift to the forces between tip and sample for both large and small oscillation amplitudes. Also, the frequency versus distance data for van der Waals dominated tip-sample interactions is related to the geometry of the tip apex. Published frequency versus distance data are used to show that the apex of tips providing atomic resolution is faceted and not rounded. Further, an extended jump-to-contact criterion for large amplitudes is established.
A Multimarker Prognostic Assay for Primary Cutaneous Melanoma (2009)

These results describe a multimarker assay with independent prognostic effect on the prediction of survival associated with melanoma in two distinct cohorts.
Rigid cyanine dye nucleic acid labels (2008)

Cyanine dyes attached to DNA via a rigid linker show useful fluorescence and FRET properties without altering the stability of duplex DNA.
The <i>Arabidopsis</i> transcription factor HY5 integrates light and hormone signaling pathways (2004)

The role of the Arabidopsis transcription factor LONG HYPOCOTYL 5 (HY5) in promoting photomorphogenic development has been extensively characterized. Although the current model for HY5 action largely explains its role in this process, it does not adequately address the root phenotype observed in hy5 mutants. In our search for common mechanisms underlying all hy5 traits, we found that they are partly the result of an altered balance of signaling through the plant hormones auxin and cytokinin. hy5 mutants are resistant to cytokinin application, and double mutant analyses indicate that a decrease in auxin signaling moderates hy5 phenotypes. Microarray analyses and semiquantitative RT-PCR indicate that two negative regulators of auxin signaling, AUXIN RESISTANT 2 (AXR2)/INDOLE ACETIC ACID 7 (IAA7) and SOLITARY ROOT (SLR)/IAA14, are underexpressed in hy5 mutants. The promoters of these genes contain a putative HY5 binding site, and in line with this observation, HY5 can bind to the promoter of AXR2 in vitro. Increased AXR2 expression in a hy5 background partially rescues the elongated hypocotyl phenotype. In summary, it appears that auxin signaling is elevated in hy5 mutants because HY5 promotes the expression of negative regulators of auxin signaling, thereby linking hormone and light signaling pathways.
Role of RNA Polymerase, ρ Factor, and Ribosomes in Transcription Termination (1983)

INTRODUCTION Efficient transcription of the Escherichia coli genome depends on the ability of the cell to regulate the type and amount of mRNA produced from each of its 3000 to 4000 genes. This not only requires the information to specify precise starting points for transcription, but stopping points as well. The operon, as the functional polycistronic unit of gene expression, may in fact be defined by the occurrence of an efficient termination site at its distal end. This simple housekeeping function prevents transcriptional readthrough by RNA polymerase into adjoining regions of the genome. In addition, however, a termination site can be utilized within a regulatory region to alter gene expression by controlling the ability of RNA polymerase to transcribe beyond that site. Thus, sites that specify termination may have several purposes in the cell. (1) As efficient punctuation signals, they permit the differential regulation of adjacent gene clusters. (2) As modulating elements (e.g., in attenuation), they permit differential control of expression within operons. (3) As conditional abortive elements (e.g., in mutational polarity), they prevent wasteful depletion of cellular metabolites. (4) As barriers to elongation, they minimize sequestering of important enzymes (e.g., RNA polymerase or other RNA-binding macromolecules) that might be engaging in unnecessary transcription or binding to excess unusable products. It has been generally expected that all termination sites, regardless of their function in regulation, would contain certain common structural features required for the termination response of RNA polymerase at that site. The primary structures (sequences) of a large number...
The IBM System/360 Model 91: Storage System (1967)

This paper discusses the design concepts employed in the development of the IBM System/360 Model 91 storage system. Particular attention is paid to the exploitation of System/360 capabilities in the areas of large storage capacity, concurrent operation, and flexibility, as they apply to the highly overlapped Model 91 system.