gebhart/patrepeval huggingface dataset:
Transgene organization in rice engineered through direct DNA transfer supports a two-phase integration mechanism mediated by the establishment of integration hot spots (1998)

Organization of transgenes in rice transformed through direct DNA transfer strongly suggests a two-phase integration mechanism. In the "preintegration" phase, transforming plasmid molecules (either intact or partial) are spliced together. This gives rise to rearranged transgenic sequences, which upon integration do not contain any interspersed plant genomic sequences. Subsequently, integration of transgenic DNA into the host genome is initiated. Our experiments suggest that the original site of integration acts as a hot spot, facilitating subsequent integration of successive transgenic molecules at the same locus. The resulting transgenic locus may have plant DNA separating the transgenic sequences. Our data indicate that transformation through direct DNA transfer, specifically particle bombardment, generally results in a single transgenic locus as a result of this two-phase integration mechanism. Transgenic plants generated through such processes may, therefore, be more amenable to breeding programs as the single transgenic locus will be easier to characterize genetically. Results from direct DNA transfer experiments suggest that in the absence of protein factors involved in exogenous DNA transfer through Agrobacterium, the qualitative and/or quantitative efficiency of transformation events is not compromised. Our results cast doubt on the role of Agrobacterium vir genes in the integration process.
Leaching of Zinc Oxide in Acidic Solution (2003)

Leaching mechanism of zinc oxide is important not only to understand zinc smelting process but also to develop of new zinc recycling process. Recycling of zinc is mainly done by treatment of electric arc furnace dust (EAF dust). In Japan pyro metallurgical process is enhanced for EAF dust treatment, however only zinc oxide can be recovered by pyro metallurgical process. Hydro metallurgical process makes it possible to recover high purity zinc directly from EAF dust. One of the main components of zinc included in EAF dusts is zinc oxide. Thus the mechanism of zinc oxide leaching is important to develop the new hydro metallurgical zinc recycling process. Leaching test of zinc oxide in hydrochloric acid and sulfuric acid solution has been carried out kinetically. Zinc oxide disk was used for leaching test which the reaction area is clear. The experimental parameters of pH, temperature, leaching time and rotating speed of the disk specimen were varied. The results obtained are as follows;\\ oindent(1) The activation energy of leaching reaction by sulfuric acid was 17.5 kJmol−1 and 11.6 kJmol−1 by hydrochloric acid solutions.\\ oindent(2) The leaching rate increases in proportion to the square root of rotating speed of test specimen.These results indicate that the rate controlling factor of zinc oxide leaching reaction in acidic solution is mass transportation.
The photochemistry of the nitrate radical and the kinetics of the nitrogen pentoxide-ozone system (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe photochemistry of the nitrate radical and the kinetics of the nitrogen pentoxide-ozone systemRichard A. Graham and Harold S. JohnstonCite this: J. Phys. Chem. 1978, 82, 3, 254–268Publication Date (Print):February 1, 1978Publication History Published online1 May 2002Published inissue 1 February 1978https://pubs.acs.org/doi/10.1021/j100492a002https://doi.org/10.1021/j100492a002research-articleACS PublicationsRequest reuse permissionsArticle Views470Altmetric-Citations185LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Three‐dimensional mapping of brain neuropils in the cockroach, Diploptera punctata (2001)

Herein, we present a complete three-dimensional (3D) map of major neuropil structures in the central brain of the cockroach Diploptera punctata. The positions of the structures have been ascertained by confocal microscopy, which, until now-for reasons of tissue opacity and nonhomogeneity-has been thought impractical in imaging fluorescently labeled structures thicker than 150 microm. In this report, however, we have used digestive enzymes and microwave-aided fixation to stain, clear, and optically section, in its entirety, an intact central brain more than 500 microm thick. The central brain from an adult female cockroach was stained thoroughly with the membrane probe NBD-ceramide and the DNA probe propidium iodide. The central brain as well as such neuropil regions as mushroom bodies, central complex, antennal glomeruli, and lobus glomerulati were individually outlined, segmented, and reconstructed in three dimensions to a spatial resolution of approximately 1 microm in the X-Y plane and 3 microm in the Z plane. The volume and surface area of each neuropil compartment were determined, and Kenyon cells of the mushroom bodies were counted. We determined that each brain hemisphere contains about 230,000 Kenyon cells, 99 antennal lobe glomeruli, and 40 lobus glomerulatus glomeruli. Segmented compartments were assigned as separate channels and merged into a single data base to reconstruct a 3D central brain containing eight different channels. This is the first 3D map at submicron resolution of an entire animal's brain that measures more than 500 microm in thickness.
Differential metabolic effects of oral butyrate treatment in lean versus metabolic syndrome subjects (2018)

Oral butyrate treatment beneficially affects glucose metabolism in lean but not metabolic syndrome subjects, presumably due to an altered SCFA handling in insulin-resistant subjects. Although preliminary, these first in men findings argue against oral butyrate supplementation as treatment for glucose regulation in human subjects with type 2 diabetes mellitus.
The effects of image misregistration on the accuracy of remotely sensed change detection (1998)

Image misregistration has become one of the significant bottlenecks for improving the accuracy of multisource data analysis, such as data fusion and change detection. In this paper, the effects of misregistration on the accuracy of remotely sensed change detection were systematically investigated and quantitatively evaluated. This simulation research focused on two interconnected components. In the first component, the statistical properties of the multispectral difference images were evaluated using semivariograms when multitemporal images were progressively misregistered against themselves and each other to investigate the band, temporal, and spatial frequency sensitivities of change detection to image misregistration. In the second component, the ellipsoidal change detection technique, based on the Mahalanobis distance of multispectral difference images, was proposed and used to progressively detect the land cover transitions at each misregistration stage for each pair of multitemporal images. The impact of misregistration on change detection was then evaluated in terms of the accuracy of change detection using the output from the ellipsoidal change detector. The experimental results using Landsat Thematic Mapper (TM) imagery are presented. It is interesting to notice that, among the seven TM bands, band 4 (near-infrared channel) is the most sensitive to misregistration when change detection is concerned. The results from false change analysis indicate a substantial degradation in the accuracy of remotely sensed change detection due to misregistration. It is shown that a registration accuracy of less than one-fifth of a pixel is required to achieve a change detection error of less than 10%.
Risk Stratification and Survival after Myocardial Infarction (1983)

We assessed the role of physiologic measurements of heart function in predicting mortality after myocardial infarction. Most of the 866 patients enrolled in our multicenter study underwent 24-hour Holter monitoring and determination of the resting radionuclide ventricular ejection fraction before discharge. Univariate analyses showed a progressive increase in cardiac mortality during one year as the ejection fraction fell below 0.40 and as the number of ventricular ectopic depolarizations exceeded one per hour. Only four risk factors among eight prespecified variables were independent predictors of mortality: an ejection fraction below 0.40, ventricular ectopy of 10 or more depolarizations per hour, advanced New York Heart Association functional class before infarction, and rales heard in the upper two thirds of the lung fields while the patient was in the coronary-care unit. Various combinations of these four factors identified five risk subgroups with two-year mortality rates ranging from 3 per cent (no factors) to 60 per cent (all four factors).
Human immunoglobulin C lambda 6 gene encodes the Kern+Oz-lambda chain and C lambda 4 and C lambda 5 are pseudogenes. (1987)

Six nonallelic immunoglobulin lambda constant region genes have been previously characterized on a 40-kilobase stretch of DNA. The nucleotide sequences of the three upstream genes of this cluster (C lambda 1, C lambda 2, C lambda 3) have been determined by other workers and shown to encode, respectively, the isotypic Mcg, Kern-Oz-, and Kern-Oz+ constant region of the lambda chains. In this paper, we report the sequence of the three downstream genes of this cluster and show that two of them (C lambda 4 and C lambda 5) are pseudogenes. However, C lambda 6 encodes a Kern+Oz- chain and corresponds to the fourth isotype described among the lambda proteins sequenced so far. A potentially active J lambda (joining) segment, with the canonical heptamer and nonamer sequences for rearrangement, is located 1.5 kilobases upstream of C lambda 6. The amino acid sequence encoded by the C lambda 6 gene is compared with the constant region sequences of various monoclonal Bence Jones lambda proteins. Allotypic and isotypic differences confirm the polymorphism and complexity of the human C lambda locus.
Mutations in the Sec61p Channel Affecting Signal Sequence Recognition and Membrane Protein Topology (2007)

The orientation of most single-spanning membrane proteins obeys the "positive-inside rule", i.e. the flanking region of the transmembrane segment that is more positively charged remains in the cytosol. These membrane proteins are integrated by the Sec61/SecY translocon, but how their orientation is achieved is unknown. We have screened for mutations in yeast Sec61p that alter the orientation of single-spanning membrane proteins. We identified a class of mutants that are less efficient in retaining the positively charged flanking region in the cytosol. Surprisingly, these mutations are located at many different sites in the Sec61/SecY molecule, and they do not only involve charged amino acid residues. All these mutants have a prl phenotype that so far have only been seen in bacteria; they allow proteins with defective signal sequences to be translocated, likely because the Sec61p channel opens more easily. A similar correlation between topology defects and prl phenotype was also seen with previously identified yeast Sec61 mutants. Our results suggest a model in which the regulated opening of the translocon is required for the faithful orientation of membrane proteins.
Synthesis and Optical Properties of Difluorobora‐s‐diazaindacene Dyes with Trifluoromethyl meso‐Substituents (2013)

Abstract A series of meso ‐CF 3 ‐4,4‐difluoro‐4‐bora‐3a,4a‐diaza‐ s ‐indacene (BODIPY) dyes with aryl and hetaryl substituents at the C‐3 and C‐5 positions, both symmetric and asymmetric, have been synthesized in 36–90 % yields by a new strategy involving as the key step the condensation of 2,2,2‐trifluoro‐1‐(5‐arylpyrrol‐2‐yl)‐1‐ethanols with diverse 2‐arylpyrroles. The starting 2,2,2‐trifluoro‐1‐(5‐arylpyrrol‐2‐yl)‐1‐ethanols are easily prepared by reduction of the available 2‐trifluoroacetyl‐5‐arylpyrroles. The synthesized dyes fluoresce in a longer wavelength region (626–698 nm) with high quantum yield (0.84–0.99).
Exonuclease VIII of Escherichia coli. II. Mechanism of action. (1983)

Exonuclease VIII from Escherichia coli was shown to preferentially degrade linear duplex DNA, although a limited amount of activity with single-stranded linear DNA substrates was detected. No nucleolytic activity was observed with double-stranded circular substrates containing single strand breaks or gaps. Exonuclease VIII was shown to degrade linear duplex DNA from the 5' termini of the molecules and proceed in the 5' to 3' direction via a processive reaction mechanism. Initiation could occur from either a 5'-hydroxyl or 5'-phosphate residue at equal rates. The products of degradation of linear duplex DNA were an equivalent amount of 5'-mononucleotides and single-stranded DNA. Possible roles for exonuclease VIII in genetic recombination are discussed.
Specificity of response in hamster cells induced to produce plasminogen activator by the tumor promoter, 12-O-tetradecanoylphorbol-13-acetate. (1978)

A phorbol ester promoting agent, 12-O-tetradecanoylphorbol-13-acetate, enhances plasminogen activator production in hamster cell lines that synthesize plasminogen activator immunologically identical with plasminogen activator of normal hamster lung cells. 12-O-Tetradecanoylphorbol-13-acetate exhibits a high degree of specificity in the type of plasminogen activator evoked, which is always of the lung form. No enhancement of plasminogen activator production was detected in hamster cell lines synthesizing plasminogen activator of different antigenic form, although in the presence of 12-O-tetradecanoylphorbol-13-acetate, cells of one such line initiated synthesis of plasminogen activator of the lung form.
Recent advances towards development and commercialization of plant cell culture processes for the synthesis of biomolecules (2011)

Plant cell culture systems were initially explored for use in commercial synthesis of several high-value secondary metabolites, allowing for sustainable production that was not limited by the low yields associated with natural harvest or the high cost associated with complex chemical synthesis. Although there have been some commercial successes, most notably paclitaxel production from Taxus sp., process limitations exist with regards to low product yields and inherent production variability. A variety of strategies are being developed to overcome these limitations including elicitation, in situ product removal and metabolic engineering with single genes and transcription factors. Recently, the plant cell culture production platform has been extended to pharmaceutically active heterologous proteins. Plant systems are beneficial because they are able to produce complex proteins that are properly glycosylated, folded and assembled without the risk of contamination by toxins that are associated with mammalian or microbial production systems. Additionally, plant cell culture isolates transgenic material from the environment, allows for more controllable conditions over field-grown crops and promotes secretion of proteins to the medium, reducing downstream purification costs. Despite these benefits, the increase in cost of heterologous protein synthesis in plant cell culture as opposed to field-grown crops is significant and therefore processes must be optimized with regard to maximizing secretion and enhancing protein stability in the cell culture media. This review discusses recent advancements in plant cell culture processing technology, focusing on progress towards overcoming the problems associated with commercialization of these production systems and highlighting recent commercial successes.
Avoiding TLB Shootdowns Through Self-Invalidating TLB Entries (2017)

Updates to a process's page table entry (PTE) renders any existing copies of that PTE in any of a system's TLBs stale. To prevent a process from making illegal memory accesses using stale TLB entries, the operating system (OS) performs a costly TLB shootdown operation. Rather than explicitly issuing shootdowns, we propose a coordinated TLB and page table management mechanism where an expirationtime is associated with each TLB entry. An expired TLB entry is treated as invalid. For each PTE, the OS then tracks the latest expiration time of any TLB entry potentially caching that PTE. No shootdown is issued if the OS modifies a PTE when its corresponding latest expiration time has already passed.In this paper, we explain the hardware and OS support required to support Self-invalidating TLB entries (SITE). As an emerging use case that needs fast TLB shootdowns, we consider memory systems consisting of different types of memory (e.g., faster DRAM and slower non-volatile memory) where aggressive migrations are desirable to keep frequently accessed pages in faster memory, but pages cannot migratetoo often because each migration requires a PTE update and corresponding TLB shootdown. We demonstrate that such heterogeneous memory systems augmented with SITE can allow an average performance improvement of 45.5% over a similar system with traditional TLB shootdowns by avoiding more than 65% of the shootdowns.
Electron-Rich PNP- and PNN-Type Ruthenium(II) Hydrido Borohydride Pincer Complexes. Synthesis, Structure, and Catalytic Dehydrogenation of Alcohols and Hydrogenation of Esters (2011)

Electron-rich PNP- and PNN-type ruthenium(II) hydrido borohydride pincer complexes, [RuH(BH4)(tBu-PNP)] (tBu-PNP = (2,6-bis(di-tert-butylphosphinomethyl)pyridine) (5) and [RuH(BH4)(tBu-PNN)] (tBu-PNN = 2-di-tert-butylphosphinomethyl-6-diethylaminomethylpyridine) (6), were prepared from their corresponding N2-bridged dinuclear Ru(II) complexes [(tBu-PNP)RuCl2]2(μ-N2) (3) and [(tBu-PNN)RuCl2]2(μ-N2) (4), respectively. The X-ray structure of 5 reveals a BH4– anion η2 coordinated to ruthenium through two bridging hydrides. A variable-temperature 1H NMR study of 6 exhibits interesting fluxional behavior of the BH4– ligand. Similarly, the Ru(II) hydrido borohydride complex 9, in which the BH4– moiety is coordinated in a η1 bonding mode, was obtained by reaction of [RuCl2(PPh3)(iPr-PNP)] (iPr-PNP = 2,6-bis(diisopropylphosphinomethyl)pyridine) (8) with two equivalents of NaBH4 at room temperature. The hydrido borohydride pincer complexes 5, 6, and 9 catalyze the acceptorless dehydrogenative coupling of primary alcohols to esters and the dehydrogenation of secondary alcohols to the corresponding ketones, accompanied by evolution of hydrogen gas. The reactivity follows the order 6 > 9 > 5. With the hydrido borohydride complex 6 as catalyst, high yields (up to 98%) and high turnover numbers (TON ∼1000) were obtained in the dehydrogenation of primary alcohols under mild and neutral conditions. In addition, 6 effectively catalyzes the hydrogenation of nonactivated aromatic and aliphatic esters to the corresponding alcohols with TON ∼200 under a relatively mild pressure of dihydrogen and neutral and homogeneous conditions. Thus, an efficient homogeneous catalytic system for the dehydrogenation–hydrogenation reactions of alcohols is developed, which is relevant to the current interest in hydrogen storage.
Coordination chemistry of microbial iron transport. 42. Structural and spectroscopic characterization of diastereomeric chromium(III) and cobalt(III) complexes of desferrithiocin (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCoordination chemistry of microbial iron transport. 42. Structural and spectroscopic characterization of diastereomeric chromium(III) and cobalt(III) complexes of desferrithiocinF. Ekkehardt Hahn, Thomas J. McMurry, Alain Hugi, and Kenneth N. RaymondCite this: J. Am. Chem. Soc. 1990, 112, 5, 1854–1860Publication Date (Print):February 1, 1990Publication History Published online1 May 2002Published inissue 1 February 1990https://pubs.acs.org/doi/10.1021/ja00161a032https://doi.org/10.1021/ja00161a032research-articleACS PublicationsRequest reuse permissionsArticle Views292Altmetric-Citations39LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Conformational Study of cis-1,4-Di-tert-butylcyclohexane by Dynamic NMR Spectroscopy and Computational Methods. Observation of Chair and Twist-Boat Conformations (2005)

[reaction: see text] Low-temperature 13C NMR spectra of cis-1,4-di-tert-butylcyclohexane (1) showed signals for the twist-boat (1a) and chair (1b) conformations. 13C NMR signals were assigned to specific carbons based on the different populations, different symmetries (time-averaged C(2v) for 1a and time-averaged C(s) for 1b), and calculated chemical shifts (GIAO, HF/6-311+G*). In addition to slow ring inversion and interconversion of the chair and twist-boat conformations, slow rotation of the tert-butyl groups was found. Most of the expected 13C peaks were observed. Free-energy barriers of 6.83 and 6.35 kcal/mol were found for interconversion of 1a (major) and 1b (minor) at -148.1 degrees C. Conformational space was searched with Allinger's MM3 and MM4 programs, and free energies were obtained for several low-energy conformations 1a-c. Calculations were repeated with ab initio methods up to the HF/6-311+G* level. Molecular symmetries, relative free energies, relative enthalpies and entropies, frequencies, and NMR chemical shifts were obtained. A boat conformation (1d; C(2v) symmetry) was generated and optimized as a transition state by ab initio, MM3, and MM4 calculations.