gebhart/patrepeval huggingface dataset:
Cooperative Binding of the <i>Xenopus</i> RNA Polymerase I Transcription Factor xUBF to Repetitive Ribosomal Gene Enhancers (1992)

Upstream binding factor (UBF) is a DNA-binding transcription factor implicated in ribosomal gene promoter and enhancer function in vertebrates. UBF is unusual in that it has multiple DNA-binding domains with homology to high-mobility-group (HMG) nonhistone chromosomal proteins 1 and 2. However, a recognizable DNA consensus sequence for UBF binding is lacking. In this study, we have used gel retardation and DNase I footprinting to examine Xenopus UBF (xUBF) binding to Xenopus laevis ribosomal gene enhancers. We show that UBF has a minimum requirement for about 60 bp of DNA, the size of the short enhancer variant in X. laevis. Stronger UBF binding occurs on the longer enhancer variant (81 bp) and on multiple enhancers linked head to tail. In vivo, Xenopus ribosomal gene enhancers exist in blocks of 10 alternating 60- and 81-bp repeats within the intergenic spacer. In vitro, UBF binds cooperatively to probes with 10 enhancers, with five intermediate complexes observed in titration experiments. This suggests that, on average, one UBF dimer binds every two enhancers. A single UBF dimer can produce a DNase I footprint ranging in size from approximately 30 to about 115 bp on enhancer probes of different lengths. This observation is consistent with the hypothesis that multiple DNA-binding domains or subdomains within UBF bind independently, forming more-stable interactions on longer probes.
Precise AVHRR image navigation (1994)

A new AVHRR image navigation software package has been developed. Both direct and indirect image navigation capabilities are provided. An approach is used in which the orbital motion model for the satellite is an independent module. The attitude of the spacecraft is also modeled and the capability to estimate the attitude from ground control points is included. Descriptions of the various orbital and attitude models are presented along with the navigation algorithms. Image navigation examples, including attitude recovery from ground control points, are also shown. Overall, it is found that the software can provide navigation accuracies to within 1 km.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Directional structure-tensor-based coherence to detect seismic faults and channels (2017)

Seismic coherence is widely used in seismic interpretation and reservoir characterization to highlight (with low values) faults and stratigraphic features from a seismic image. A coherence image can be computed from the eigenvalues of conventional structure tenors, which are outer products of gradients of a seismic image. I have developed a simple but effective method to improve such a coherence image by using directional structure tensors, which are different from the conventional structure tensors in only two aspects. First, instead of using image gradients with vertical and horizontal derivatives, I use directional derivatives, computed in directions perpendicular and parallel to seismic structures (reflectors), to construct directional structure tensors. With these directional derivatives, lateral seismic discontinuities, especially those subtle stratigraphic features aligned within dipping structures, can be better captured in the structure tensors. Second, instead of applying Gaussian smoothing to each element of the constructed structure tensors, I apply approximately fault- and stratigraphy-oriented smoothing to enhance the lateral discontinuities corresponding to faults and stratigraphic features in the structure tensors. Real 3D examples show that the new coherence images computed from such structure tensors display much cleaner and more continuous faults and stratigraphic features compared with those computed from conventional structure tensors and covariance matrices.
Increased extracellular secretion in fragile mutants of Saccharomyces cerevisiae. (1989)

Evidences are presented for a generally increased extracellular secretion capability of the fragile mutants of S. cerevisiae. Proteins secreted in wild type yeasts to the periplasmic space can not be retained by the defective cell wall of the fragile cells and are released into the medium. Changes in the structure of non-mannan components of the cell wall might be the reason for the extracellular release of the periplasmic proteins.
Band residual difference algorithm for retrieval of SO/sub 2/ from the aura ozone monitoring instrument (OMI) (2006)

The Ozone Monitoring Instrument (OMI) on EOS/Aura offers unprecedented spatial and spectral resolution, coupled with global coverage, for space-based UV measurements of sulfur dioxide (SO/sub 2/). This paper describes an OMI SO/sub 2/ algorithm (the band residual difference) that uses calibrated residuals at SO/sub 2/ absorption band centers produced by the NASA operational ozone algorithm (OMTO3). By using optimum wavelengths for retrieval of SO/sub 2/, the retrieval sensitivity is improved over NASA predecessor Total Ozone Mapping Spectrometer (TOMS) by factors of 10 to 20, depending on location. The ground footprint of OMI is eight times smaller than TOMS. These factors produce two orders of magnitude improvement in the minimum detectable mass of SO/sub 2/. Thus, the diffuse boundaries of volcanic clouds can be imaged better and the clouds can be tracked longer. More significantly, the improved sensitivity now permits daily global measurement of passive volcanic degassing of SO/sub 2/ and of heavy anthropogenic SO/sub 2/ pollution to provide new information on the relative importance of these sources for climate studies.
Lipid remodeling in <i>Rhodopseudomonas palustris <scp>TIE</scp>‐1</i> upon loss of hopanoids and hopanoid methylation (2015)

The sedimentary record of molecular fossils (biomarkers) can potentially provide important insights into the composition of ancient organisms; however, it only captures a small portion of their original lipid content. To interpret what remains, it is important to consider the potential for functional overlap between different lipids in living cells, and how the presence of one type might impact the abundance of another. Hopanoids are a diverse class of steroid analogs made by bacteria and found in soils, sediments, and sedimentary rocks. Here, we examine the trade-off between hopanoid production and that of other membrane lipids. We compare lipidomes of the metabolically versatile α-proteobacterium Rhodopseudomonas palustris TIE-1 and two hopanoid mutants, detecting native hopanoids simultaneously with other types of polar lipids by electrospray ionization mass spectrometry. In all strains, the phospholipids contain high levels of unsaturated fatty acids (often >80%). The degree to which unsaturated fatty acids are modified to cyclopropyl fatty acids varies by phospholipid class. Deletion of the capacity for hopanoid production is accompanied by substantive changes to the lipidome, including a several-fold rise of cardiolipins. Deletion of the ability to make methylated hopanoids has a more subtle effect; however, under photoautotrophic growth conditions, tetrahymanols are upregulated twofold. Together, these results illustrate that the 'lipid fingerprint' produced by a micro-organism can vary depending on the growth condition or loss of single genes, reminding us that the absence of a biomarker does not necessarily imply the absence of a particular source organism.
Detection Of Phishing Websites And Secure Transactions (2011)

Phishing is an electronic online identity theft in which the attackers use a combination of social engineering and web site spoofing techniques to trick a user into revealing confidential information. It steals the user’s personal identity data and financial credentials. Most of the phishing attacks emerge as spoofed E-Mails appearing as legitimate ones which makes the users to trust and divulge into them by clicking the link provided in the E-Mail. To detect a Phishing website, human experts compare the claimed identity of a website with features in the website. For example, human experts often compare the domain name in the URL against the claimed identity. Most legitimate websites have domain names that match their identities, while Phishing websites usually have less relevance between their domain names and their claimed (fake) identities. In addition to blacklists, white lists, heuristics, and classifications used in the state-of-the-art systems, we propose to consider websites’ identity claims. To enable secure transactions ,Password hashing has been done with MD5 hashing algorithms that strengthens web password authentication. It is also shown that getting original password from hashed form is not an easy task due to addition of salt value. If the user is valid, get a session key via mobile, through which further access can be done
1,2,3-Trimethoxypropane, a glycerol-based solvent with low toxicity: new utilization for the reduction of nitrile, nitro, ester, and acid functional groups with TMDS and a metal catalyst (2013)

1,2,3-Trimethoxypropane (1,2,3-TMP) was prepared from glycerol in one step in good yield and selectivity by phase transfer catalysis. According to OECD guidelines, a toxicity study was realized for this compound. It revealed that 1,2,3-TMP has a low acute toxicity, no skin sensitization, no mutagenicity and no ecotoxicity in an aquatic environment. This compound was also used as a solvent for the reduction of organic functions using either aluminium hydride or 1,1,3,3-tetramethyldisiloxane (TMDS) as a benign hydride source. In particular, a new process for the reduction of nitriles to amines in 2-MeTHF and in 1,2,3-TMP was developed, using TMDS in combination with copper triflate (Cu(OTf)2).
Range-Doppler Imaging with Motion through Resolution Cells (1969)

Doppler processing in pulsed radar is analyzed for time intervals which involve motion through range resolution cells, the emphasis being on the range-Doppler imaging of a rigid rotating body. The objective of the theory is to derive a method for compensating for motion through range and cross-range resolution cells. The compensation ion procedure described is compatible with optical data processing. With such a two-dimensional processor, the method permits simultaneous eous compensation for all points in the target field. The s consists of taking the Fourier transform in the range dimension, followed by a gentle distortion of this range-transform plane, and that followed by a two-dimensional Fourier transform. Two implementations with experimental results are briefly mentioned. One implementation is all optical and utilizes a holographic hyperbolic lens and/or holographic conical lens. The other implementation, involves applying the appropriate te distortion electronically as th " range sweeps" from the pulse train are received and put on film.
Characterization of ATP‐induced cell death in the GL261 mouse glioma (2010)

Gliomas have one of the worst prognosis among cancers. Their resistance to cell death induced by endogenous neurotoxic agents, such as extracellular ATP, seems to play an important role in their pathobiology since alterations in the degradation rate of extracellular ATP drastically affects glioma growth in rats. In the present work we characterized the mechanisms of cell death induced by extracellular ATP in a murine glioma cell line, GL261. ATP and BzATP, a P2X7 agonist, induced cell death at concentrations that are described to activate the P2X7 receptor in mouse. oATP, an antagonist of P2X7, blocked the ATP-induced cell death. Agonists of purinergic receptors expressed in GL261 such as adenosine, ADP, UTP did not cause any cell death, even at mM concentrations. A sub-population of cells more sensitive to ATP expressed more P2X7 when compared to a less sensitive subpopulation. Accordingly, RNA interference of the P2X7 receptor drastically reduced ATP-induced cell death, suggesting that this receptor is necessary for this effect. The mechanism of ATP-induced cell death is predominantly necrotic, since cells presented shrinkage accompanied by membrane permeabilization, but not apoptotic, since no phosphatidylserine externalization or caspase activity was observed. These data show the importance of P2X7 in ATP-induced cell death and shed light on the importance of ATP-induced cell death in glioma development.
Comparison of behavior of <i>N</i>‐substituted acrylamides and celluloses on double‐stranded DNA separations by capillary electrophoresis at 25° and 60°C (1996)

The behavior of N-substituted poly(acrylamides) and of cellulose in the separation of double-stranded DNA by capillary zone electrophoresis (CZE) is evaluated. Contrary to previously held belief, which attributed best separations in poly(acrylamides) to small DNA fragments (typically in the 50-1000 bp size range) and in celluloses to large DNA fragments, we show that also celluloses can achieve fine sieving of short DNA sizes provided they are used at much higher concentrations than previously reported. For example, in the case of hydroxyethylcellulose (HEC), typically used at 0.2-0.8% concentrations, levels of 3% produce excellent patterns, at 25 degrees C, in the 50-600 bp size range. If separations are conducted at 60 degrees C, sieving is lost in most liquid polymers. However, if the concentration of HEC is raised to 6% and that of hydroxypropylmethylcellulose (HPMC) above 1%, sieving is fully restored. Also, N-substituted acrylamido derivatives, notably N-acryloylaminoethoxyethanol (AAEE) and N-acryloylaminopropanol (AAP) offer excellent performance at both 25 degrees and 60 degrees C, whereas plain poly(acrylamide) irreversibly collapses at high temperatures, possibly due to intrinsic instability of the amido bond under such harsh conditions. Among all the polymers investigated, an 8% solution of poly(AAP) offers the best performance and highest theoretical plates in the 25 degree-60 degree C interval. Separations at high temperatures are necessary when dealing with detection of point mutations in temperature-programmed CZE and are preferred in DNA sequencing. Two additional advantages are evident when running DNA separations at 60 degrees C: a marked reduction of analysis times and a linearization of the transit times of the larger (434-587 bp) DNA fragments, in all polymers tested.
Feedback Reduction for Spatial Multiplexing with Linear Precoding (2007)

This paper presents two novel methods to optimally compress the feedback for spatial multiplexing with linear precoding. The methods exploit the time correlation of the channel and the knowledge of the previously fed back precoder matrices to estimate the conditional probabilities of the different possible feedback indices. These probabilities are then used to losslessly compress the actual feedback using variable-length codes. Two compression schemes are presented, one for a non-dedicated feedback channel and one for a dedicated feedback channel.
STUDIES ON THYMINE‐DERIVED UV PHOTOPRODUCTS IN DNA—I. FORMATION AND BIOLOGICAL ROLE OF PYRIMIDINE ADDUCTS IN DNA (1977)

Abstract— Pyrimidine (Pyr) adducts constitute a significant fraction of the photoproducts formed in DNA exposed to far UV light. The primary and secondary DNA structure affects the rate of Pyr adduct formation; for example, it increases with decreasing (Ade + Thy)/(Gua + Cyt) of the DNA and with increasing dehydration, and it is greater in double‐stranded than in single‐stranded DNA. Pyrimidine adducts do not appear to be involved in inter‐strand cross‐links, and 313 nm‐induced photolysis of Pyr adducts does not cause strand breakage. The action spectrum for Pyr adduct formation is qualitatively similar to that for Pyr < > Pyr formation; the calculated quantum yields for its formation is essentially wavelength independent over the range 254 nm to 280 nm, but decreased somewhat at shorter wavelengths (240 nm). The biological role of Pyr adducts is still not clear. The data suggest that either Pyr adducts and their photolysis products are not lethal, or that both are lethal but can be repaired under certain conditions.
EBR-II Project: Run 102, June 25, 1979-August 20, 1979 (1979)

Run 102 started on July 4 and ended on August 20, 1979, following 2513 MWd of reactor operation.
Functional Mapping of Mu Transposition Machinery : MuA Protein Modification and Engineering for Hyperactivity (2013)

Transposable DNA elements constitute a class of discrete genome segments, which use fundamentally similar reactions for their movement within and between genomes without the need for sequence homology to the target site. Transposons are ubiquitous and abundant residents scattered throughout the genomes of virtually all living organisms. The ability of transposons to integrate into various DNA sequences is utilized as tools in molecular biology. \n\nThe similarity of the transposition reaction mechanisms is reflected by their enzymes, the transposases. Many DNA transposases share a conserved RNase H-like fold that contains a catalytic DDE motif. The bacteriophage Mu encodes MuA transposase, which is a well characterized member of the DDE transposases. Mu transposition proceeds within a nucleoprotein complex known as a transpososome, the minimal core of which contains four MuA molecules and two synapsed transposon ends. It forms the basis of Mu transposon tools that are widely used in genetics/genomics applications. The study reveals important structure-function relationships of MuA in the context of the transpososome. In addition, this study critically evaluates different random DNA mutagenesis methods and describes a universal assay to quantitatively analyse DNA transposition events. Initially, we characterized mutagenic properties of several most commonly used random mutagenesis methods and used them for MuA mutant library generation. Then, we established the quantitative transposition assay for mutant screening purposes. \n\nWe analysed MuA structure-function relationships by scanning pentapeptide insertion library to dissect insertion tolerant against insertion intolerant regions in MuA structure. The comprehensive structure-function analysis was complemented with data from the sequence alignment of protein homologues. We identified potential sites for protein modifications. In addition, the different random MuA mutant libraries were screened for increased transposition frequency. We show that MuA mutant variants with enhanced activity could be generated. By the mapping of hyperactivity-inducing substitutions to the Mu transpososome structure, we could characterize the factors behind the activity enhancement. Furthermore, several MuA mutants were discovered to be valuable for Mu in vitro transposition applications. \n\nThe results of this study provide a comprehensive structure-function map of MuA transposase. Moreover, the methods described in this study and the activity enhancing substitutions discovered in RNase H-like fold can be used for mechanistic analyses of other DDE transposases or used for the analyses of their close relatives such as HIV integrase and the RAG recombinase of the V(D)J recombination.
1,2,3-Benzotriazinone 1-oxides (1989)

3-Substituted 1,2,3-benzotriazin-4(3H)-one 1-oxides are formed on peracid oxidation of 3-alkyl- and 3-methoxy-1,2,3-benzotriazin-4(3H)-ones. The 3-(α-alkoxyalkyl) 1-oxide derivatives could be dealkylated to the tautomeric 3-unsubstituted compound. The acidities of the isomeric N-oxides of the 1,2,3-benzotriazinone system are compared. Phenyl iodosodiacetate converts o-nitrobenzaldehyde benzyl- and phenyl-hydrazones into the 2-substituted 4-oxido-1,2,3-benzotriazine 1-oxide betaines (1).
Niemann Pick Disease type A in Israeli Arabs: 677delT, a common novel single mutation. Mutations in brief no. 161. Online. (1998)

A novel single base pair deletion in the acid sphingomyelinase (ASM) gene (677delT in the cDNA) was identified in 12 Israeli Arab families with Niemann-Pick disease (NPD) type A. This deletion creates a premature stop codon which explains the complete deficiency of ASM activity in these patients and the severe clinical manifestation. A single mutation in 12 families living in a relatively small geographical region suggests a founder effect and explains the high frequency of this disease in this population. This is in contrast to multiple mutations found in two other lysosomal storage disorders prevalent in this population, namely, Hurler disease (MPSI) and metachromatic leukodystrophy. Mutations analysis is therefore an important tool in characterizing the grounds for the high frequency of inherited diseases as well as a basis for prevention programs for prevalent diseases through carrier identification and the ascertainment of high risk families.
IRRADIATION EFFECTS ON ZR-2.5NB IN POWER REACTORS (2016)

Zirconium alloys are widely used as structural materials in nuclear applications because of their attractive properties such as a low absorption cross-section for thermal neutrons, excellent corrosion resistance in water, and good mechanical properties at reactor operating temperatures. Zr-2.5Nb is one of the most commonly used zirconium alloys and has been used for pressure tube materials in CANDU (Canada Deuterium Uranium) and RBMK (Reaktor Bolshoy Moshchnosti Kanalnyy, “High Power Channel-type Reactor”) reactors for over 40 years. In a recent report from the Electric Power Research Institute, Zr-2.5Nb was identified as one of the candidate materials for use in normal structural applications in light-water reactors owing to its increased resistance to irradiation-induced degradation as compared with currently used materials. Historically, the largest program of in-reactor tests on zirconium alloys was performed by Atomic Energy of Canada Limited. Over many years of in-reactor testing and CANDU operating experience with Zr-2.5Nb, extensive research has been conducted on the irradiation effects on its microstructures, mechanical properties, deformation behaviours, fracture toughness, delayed hydride cracking, and corrosion. Most of the results on Zr-2.5Nb obtained from CANDU experience could be used to predict the material performance under light water reactors. This paper reviews the irradiation effects on Zr-2.5Nb in power reactors (including heavy-water and light-water reactors) and summarizes the current state of knowledge.
Differences in virulence between two noncytopathic bovine viral diarrhea viruses in calves (1992)

A noncytopathic bovine viral diarrhea virus (BVDV), BVDV-890, isolated from a yearling heifer that died with extensive internal hemorrhages, was compared for virulence in calves with noncytopathic BVDV-TGAN, isolated from an apparently healthy persistently infected calf. After challenge exposure with BVDV-890, nonimmune calves (n = 7) developed fever > 40 C, diarrhea, leukopenia, lymphopenia, neutropenia, and thrombocytopenia. Most calves (n = 6) died or were euthanatized by 19 days after challenge exposure. Challenge exposure with BVDV-890 did not induce disease in 2 calves that had congenital persistent infection with BVDV or in 3 calves that had neutralizing antibody titer > 4 against BVDV-890. After challenge exposure with BVDV-TGAN, nonimmune calves (n = 7) developed fever > 40 C and, rarely, diarrhea or lymphopenia. All of those calves survived challenge exposure. The average maximal titer of BVDV-890 isolated from serum was 1,000 times that of BVDV-TGAN. In calves infected with BVDV-890, the average maximal percentages of lymphocytes and platelets associated with virus were greater than those found in calves infected with BVDV-TGAN. Additional findings of epidemiologic significance were prolonged shedding of virus and delayed production of viral-neutralizing antibody in 1 calf challenge-exposed with BVDV-890. Also, after production of neutralizing antibody, mutant virus that was refractory to neutralization was isolated from calves challenge-exposed with BVDV-TGAN.