gebhart/patrepeval huggingface dataset:
Functional messenger RNAs are produced by SP6<i>in vitro</i>transcription of cloned cDNAs (1984)

We describe a method for the synthesis of microgram quantities of eucaryotic messenger RNAs. Injection into the cytoplasm of frog oocytes and addition to wheat germ extracts show that these synthetic RNAs function efficiently as messenger RNAs. We confirm that a 5' cap on the mRNA is essential for translation in injected oocytes and show that most of the 3' flanking region, including the poly A tail, can be deleted without the abolition of protein synthesis. The method of mRNA synthesis involves in vitro transcription of cDNAs which have been cloned into SP6 vectors (described in the accompanying paper). This method enables one to produce large amounts of mRNA and consequently protein from any cDNA clone.
A convergent approach to the dihydrotachysterol diene system. Application to the synthesis of dihydrotachysterol2 (DHT2), 25-hydroxydihydrotachysterol2 (25-OH-DHT2), 10(R),19-dihydro-(5E)-3-epivitamin D2 and 25-hydroxy-10(R),19-dihydro-(5E)-3-epivitamin D2 (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA convergent approach to the dihydrotachysterol diene system. Application to the synthesis of dihydrotachysterol2 (DHT2), 25-hydroxydihydrotachysterol2 (25-OH-DHT2), 10(R),19-dihydro-(5E)-3-epivitamin D2 and 25-hydroxy-10(R),19-dihydro-(5E)-3-epivitamin D2Miguel A. Maestro, Luis Castedo, and Antonio MourinoCite this: J. Org. Chem. 1992, 57, 19, 5208–5213Publication Date (Print):September 1, 1992Publication History Published online1 May 2002Published inissue 1 September 1992https://pubs.acs.org/doi/10.1021/jo00045a038https://doi.org/10.1021/jo00045a038research-articleACS PublicationsRequest reuse permissionsArticle Views391Altmetric-Citations23LEARN 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
Correlation of carbon‐13 substituent‐induced chemical shifts: <i>Meta</i>‐ and <i>para</i>‐substituted methyl benzoates (1989)

Abstract Carbon‐13 NMR spectra are reported for 69 substituted methyl benzoates in deuteriochloroform or in its mixture with dimethyl sulphoxide‐ d 6 . The substituent‐induced chemical shifts (SCS) of the CO carbon correlate poorly with dual substituent parameters (DSP) in all possible modifications, and for meta derivatives in particular this correlation is both overpara meterized and imprecise. A much better correlation was obtained with parameters (designated B m , B p and C p ) derived previously by principal component analysis (PCA) from a larger set. The SCS of the CH 3 carbon correlate very well with the original simple Hammett equation, and no DSP treatment is needed. The clustering of substituents is not consequential in such a large set.
<i>Ab initio</i>calculations for a hypothetical material: Silicon nanotubes (2000)

Electronic and structural properties of a hypothetical material, silicon nanotubes, are examined through first-principles calculations based on density functional theory. Even considering that Si nanotubes have never been observed, this paper attempts to establish the theoretical similarities between Si and C, like band structures and density of states, as well as the main differences, especially associated with cohesive energies. The band-structure calculations for silicon nanotubes show that, similar to carbon structures, depending on their chiralities, they may present metallic (armchair) or semiconductor (zigzag and mixed) behaviors.
Field Efficacy and Persistence of Entomogenous Nematodes in the Management of White Grubs (Coleoptera: Scarabaeidae) in Turf and Pasture (1991)

The entomogenous nematodes Steinernema carpocapsae (Weiser) and Heterorhabditis Heliothidis (Khan, Brooks &; Hirschmann) were used to control white grubs in turf and pasture. In the turf trial, nematode concentrations of 0.25, 0.5, or 1 million nematodes per m2 were evaluated. Only 12% of the grubs were killed by the nematodes at all three concentrations. In the pasture trial, nematode concentrations of 0.5 and 1.5 million per m2 were applied alone or in combination with diazinon (2.25 kg [AIl/ha). Comparisons (t tests) of the mean number of grubs recovered from each treatment area 2-4 wk after application showed significant reductions in the grub populations in both trials after certain nematode treatments. When applied at a rate of 1.5 million per m2, nematodes persisted for 8 wk after application in the pasture trial. In other tests of persistence, nematodes survived as long as 5 wk after application. Nematophagous fungi were recovered from treated areas and untreated plots; however, no significant increases in numbers of propagules occurred after application. Predaceous mite populations did significantly increase after application in one trial. Many of these mites are considered nematophagous.
Multicomponent Coupling Reactions for Organic Synthesis: Chemoselective Reactions with Amide–Aldehyde Mixtures (2003)

The acid-catalyzed condensation chemistry of simple amides and aldehydes provides a highly prolific source of diverse reactants for irreversible follow-up reactions. Amide-aldehyde mixtures have been successfully employed in multicomponent syntheses of N-acyl alpha-amino acids (via palladium-catalyzed amidocarbonylation) and various cyclohexene, cyclohexadiene, and benzene derivatives (via the amide-aldehyde-dienophile (AAD) reaction).
HEARING IN THE GIANT SEA TURTLE, <i>Chelonia mydas</i> (1969)

Measurement were made of the cochlear potentials in three specimens of the giant sea turtle, Chelonia mydas, in response to both aerial and mechanical stimulation of the ear. The results show maximum sensitivity in the region of 300 to 400 Hz, with a rather rapid decline in sensitivity for lower and especially for higher tones. The upper limit for the observation of cochlear potentials without injury is 2000 Hz, and a practical limit of usefulness of this ear is probably about 1000 Hz.
Denoising and Completion of 3D Data via Multidimensional Dictionary Learning (2015)

In this paper a new dictionary learning algorithm for multidimensional data is proposed. Unlike most conventional dictionary learning methods which are derived for dealing with vectors or matrices, our algorithm, named KTSVD, learns a multidimensional dictionary directly via a novel algebraic approach for tensor factorization as proposed in [3, 12, 13]. Using this approach one can define a tensor-SVD and we propose to extend K-SVD algorithm used for 1-D data to a K-TSVD algorithm for handling 2-D and 3-D data. Our algorithm, based on the idea of sparse coding (using group-sparsity over multidimensional coefficient vectors), alternates between estimating a compact representation and dictionary learning. We analyze our KTSVD algorithm and demonstrate its result on video completion and multispectral image denoising.
Effectiveness of matrix and pipeline FPGA-based arithmetic components of safety-related systems (2015)

The paper is devoted to design of the digital components for safety-related instrumentation and control systems using the modern CAD tools. Traditionally, the digital components are built with matrix parallelism that reduces fault tolerance of circuits and safety of systems in their checkability. Circuits with bitwise pipeline data processing have advantage in checkability, but are considered as less efficient. Matrix and pipeline methods for multiplying the numbers are compared with respect to the ratio of throughput to complexity. To estimate the relative effectiveness of these methods the resource approach is applied. The obtained estimations are verified experimentally using the multipliers realized on FPGA. Qualitatively, the expected and experimental estimations are consistent, and the reasons of their quantitative deviations are analyzed <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> .
4-Bromo-2-octenoic acid specifically inactivates 3-ketoacyl-CoA thiolase and thereby fatty acid oxidation in rat liver mitochondria (1988)

In an attempt to develop a compound which would specifically inhibit 3-ketoacyl-CoA thiolase (EC 2.3.1.16) in whole mitochondria, 4-bromo-2-octenoic acid was synthesized and studied. After rat liver mitochondria were preincubated with 4-bromo-2-octenoic acid for 3 min, respiration supported by either palmitoylcarnitine or pyruvate was completely abolished, whereas no inhibition was observed with rat heart mitochondria. Addition of carnitine stimulated respiration supported by pyruvate without relieving inhibition of palmitoylcarnitine-dependent respiration. Hence, this compound seems to be a specific inhibitor of beta-oxidation. When the enzymes of beta-oxidation were assayed in a soluble extract prepared from mitochondria preincubated with 4-bromo-2-octenoic acid, only 3-ketoacyl-CoA thiolase was found to be inactivated. 4-Bromo-2-octenoic acid is metabolized by mitochondrial beta-oxidation enzymes to 3-keto-4-bromooctanoyl-CoA which effectively and irreversibly inhibits 3-ketoacyl-CoA thiolase but not acetoacetyl-CoA thiolase (EC 2.3.1.9). Even though 3-keto-4-bromooctanoyl-CoA inhibits the latter enzyme reversibly, 4-bromo-2-octenoic acid does not inhibit ketogenesis in rat liver mitochondria with acetylcarnitine as a substrate. It is concluded that 4-bromo-2-octenoic acid specifically inhibits mitochondrial fatty acid oxidation by inactivating 3-ketoacyl-CoA thiolase in rat liver mitochondria.
Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry (2015)

Accurate knowledge of retention time (RT) in liquid chromatography-based mass spectrometry data facilitates peptide identification, quantification, and multiplexing in targeted and discovery-based workflows. Retention time prediction is particularly important for peptide analysis in emerging data-independent acquisition (DIA) experiments such as SWATH-MS. The indexed RT approach, iRT, uses synthetic spiked-in peptide standards (SiRT) to set RT to a unit-less scale, allowing for normalization of peptide RT between different samples and chromatographic set-ups. The obligatory use of SiRTs can be costly and complicates comparisons and data integration if standards are not included in every sample. Reliance on SiRTs also prevents the inclusion of archived mass spectrometry data for generation of the peptide assay libraries central to targeted DIA-MS data analysis. We have identified a set of peptide sequences that are conserved across most eukaryotic species, termed Common internal Retention Time standards (CiRT). In a series of tests to support the appropriateness of the CiRT-based method, we show: (1) the CiRT peptides normalized RT in human, yeast, and mouse cell lysate derived peptide assay libraries and enabled merging of archived libraries for expanded DIA-MS quantitative applications; (2) CiRTs predicted RT in SWATH-MS data within a 2-min margin of error for the majority of peptides; and (3) normalization of RT using the CiRT peptides enabled the accurate SWATH-MS-based quantification of 340 synthetic isotopically labeled peptides that were spiked into either human or yeast cell lysate. To automate and facilitate the use of these CiRT peptide lists or other custom user-defined internal RT reference peptides in DIA workflows, an algorithm was designed to automatically select a high-quality subset of datapoints for robust linear alignment of RT for use. Implementations of this algorithm are available for the OpenSWATH and Skyline platforms. Thus, CiRT peptides can be used alone or as a complement to SiRTs for RT normalization across peptide spectral libraries and in quantitative DIA-MS studies.
Herbivory-induced changes in the small-RNA transcriptome and phytohormone signaling in <i>Nicotiana attenuata</i> (2008)

Phytohormones mediate the perception of insect-specific signals and the elicitation of defenses during insect attack. Large-scale changes in a plant's transcriptome ensue, but how these changes are regulated remains unknown. Silencing of RNA-directed RNA polymerase 1 (RdR1) makes Nicotiana attenuata highly susceptible to insect herbivores, suggesting that defense elicitation is under the direct control of small-RNAs (smRNAs). Using 454-sequencing, we characterized N. attenuata's smRNA transcriptome before and after insect-specific elicitation in wild-type (WT) and RdR1-silenced (irRdR1) plants. We predicted the targets of N. attenuata smRNAs in the genes related to phytohormone signaling (jasmonic acid, JA-Ile, and ethylene) known to mediate resistance responses, and we measured the elicited dynamics of phytohormone biosynthetic transcripts and phytohormone levels in time-course experiments with field- and glasshouse-grown plants. RdR1 silencing severely altered the induced transcript accumulation of 8 of the 10 genes, reduced JA, and enhanced ethylene levels after elicitation. Adding JA completely restored the insect resistance of irRdR1 plants. irRdR1 plants had photosynthetic rates, growth, and reproductive output indistinguishable from that of WT plants, suggesting unaltered primary metabolism. We conclude that the susceptibility of irRdR1 plants to herbivores is due to altered phytohormone signaling and that smRNAs play a central role in coordinating the large-scale transcriptional changes that occur after herbivore attack. Given the diversity of smRNAs that are elicited after insect attack and the recent demonstration of the ability of ingested smRNAs to silence transcript accumulation in lepidopteran larvae midguts, the smRNA responses of plants may also function as direct defenses.
Genome Editing of Plants (2017)

Genome editing in organisms via random mutagenesis is a naturally occurring phenomenon. As a technology, genome editing has evolved from the use of chemical and physical mutagenic agents capable of altering DNA sequences to biological tools such as designed sequence-specific nucleases (SSN) to produce knock-out (KO) or knock-in (KI) edits and Oligonucleotide Directed Mutagenesis (ODM) where specific nucleotide changes are made in a directed manner resulting in custom single nucleotide polymorphisms (SNPs). Cibus' SU Canola™, which the US Department of Agriculture (USDA) views as non-genetically modified (non-GM), is Cibus' first commercial product arising from plant genome editing and had its test launch in 2014. Regulatory aspects of the various genome editing tools will be discussed.
EDİRNE İLİ MERKEZ İLÇE YEŞİL ALAN SİSTEMİNİN PEYZAJ MİMARLIĞI İLKELERİ YÖNÜNDEN İRDELENMESİ (2016)

Kent yaşamı denilen çağdaş yaşam biçiminin sunduğu yapay çevre, özellikle insan doğasına aykırı, biyolıojik anlamda yetersiz bir çevre kimliği yansıtmaktadır. Böyle bir ortamda insanların sağlıklı ve mutlu yaşamaları, kentin sosyo-ekonomik yapısının gelişmişliği buna bağlı olarak yeşil alan sisteminin gereksinimlere cevap verecek düzeyde olmasına bağlıdır. Açık ve yeşil alanların işlevsel olabilmeleri için, kişi başına düşen alan miktarı, donatı elemanları, her bir yeşil alanın kendi sınırları içinde hizmet yönünden niteliği ve görsel etkinliği önemlidir, bir başka deyişle alanın peyzaj mimarlığı ilkeleri doğrultusunda planlanmış olması gerekmektedir. Bu çalışma kapsamında, Edirne ili merkez ilçesinin mevcut yeşil alan sistemi peyzaj mimarlığı ilkeleri açısından irdelenmeye çalışılmış ve bu ilkeler doğrultusunda alınması gereken önlemler sunulmuştur. Araştırmalar sonucunda Edirne kentinde kişi başına düşen yeşil alan miktarlarının Türkiye standartlarının üzerinde olmasına rağmen aktif yeşil alanların işlevsel ve estetik yönlerden zayıf kaldığı belirlenmiştir. Aktif yeşil alanlardaki donatı elemanlarının yetersizliği, planlamalarda tasarım ilkelerine dikkat edilmemesi alanların kalitesini düşürmektedir.
STUDIES OF PENICILLIN IN PEDIATRICS (1949)

A study is made of the relative degrees of in vitro sensitivity to penicillin of various pathogenic bacteria. Different strains vary considerably in their sensitivity to penicillin. The concentrations of penicillin obtained in the serum following varying dosages per unit body weight in infants and children when given in the following forms are reported: crystalline sodium penicillin G in saline given intramuscularly; the same compound of penicillin in gelatin capsules and in cocoa-butter and beeswax suppositories given rectally; crystalline sodium penicillin G in sesame oil given intramuscularly, and crystalline potassium penicillin G in a new type Romansky formula given intramuscularly. The last preparation, when given in doses of 4,000 u./lb., maintained serum penicillin concentrations 24 hours after administration in 94% of cases, which was above the minimum concentration required to inhibit most strains of α and β Str. hemolyticus and of M. pneumoniae, and the serum concentrations obtained with this preparation 12 hours after administration were equal to or above the minimum concentration required to inhibit most strains of Staph. aureus hemolyticus and of meningococcus.
Oligonucleotide derivatives bearing reactive and stabilizing groups attached to C5 of deoxyuridine (1993)

Oligonucleotides bearing an aliphatic amino group at the C5-position of deoxyuridine (ULNH2TCCCA, TULNH2CCCA, ULNH2CCACTT, where L = -CH2-, -CH2OCH2CH2- or -CH2NHCOCH2CH2-) have been synthesized. The photoactive (p-azidotetrafluorobenzamido, 2-nitro-5-azidobenzamido, or p-azidobenzamido), alkylating [4-[N-(2-chloroethyl)-N-methylamino]benzyl], or intercalating [N-(2-hydroxyethyl)phenazinium] groups were attached to the amino linker of oligonucleotides. The Tm values were determined for the duplexes formed by the above oligonucleotide derivatives. The alkylating group does not change the melting temperature of the corresponding duplex. The duplex stability is increased a little in the case of photoactive groups. The influence of the phenazinium residue on the duplex stability strongly depends on its location in the oligonucleotide. The spacer length between the C5 atom of deoxyuridine and the photoactive or phenazinium group was shown to influence the complementary duplex stability.
An ecological risk assessment for spinosad use on cotton (2001)

Spinosad is a reduced-risk insecticide with a novel mode of action that provides an alternative to older classes of insecticides such as organophosphates, carbamates and pyrethroids. A comprehensive ecological risk assessment for spinosad use in US cotton crops is presented within a framework of tiered levels of refinement following the guidelines of the US EPA for ecological risk assessments. Toxicity information for a variety of species is documented and utilized, environmental concentrations estimated, and risk characterizations in the form of risk quotients are quantified. Results indicate that spinosad use in cotton does not exceed the most conservative Tier I levels of concern (LOC) values for groundwater, mammals and birds or acute risk to aquatic organisms. Use of very conservative Tier I screening methods resulted in exceeding LOC values for chronic exposure for some aquatic organisms, thus prompting further refinement. When the exposure prediction was refined using less conservative, Tier II mechanistic environmental fate transport models to predict offsite transport and environmental concentrations, chronic risk was not predicted for these species. Spinosad is acutely toxic to bees under laboratory conditions, but toxicity of residue studies and field studies indicate that under actual use conditions the impact on bees is minimal.
<i>In Vitro</i>Destruction of Streptococcus pneumoniae Biofilms with Bacterial and Phage Peptidoglycan Hydrolases (2011)

Host- and phage-coded cell wall hydrolases have been used to fight Streptococcus pneumoniae growing as planktonic cells in vitro as well as in animal models. Until now, however, the usefulness of these enzymes in biofilm-grown pneumococci has gone untested. The antipneumococcal activity of different cell wall hydrolases produced by S. pneumoniae and a number of its phages was examined in an in vitro biofilm model. The major pneumococcal autolysin LytA, an N-acetylmuramoyl-l-alanine amidase, showed the greatest efficiency in disintegrating S. pneumoniae biofilms. The phage-encoded lysozymes Cpl-1 and Cpl-7 were also very efficient. Biofilms formed by the close pneumococcal relatives Streptococcus pseudopneumoniae and Streptococcus oralis were also destroyed by the phage endolysins but not by the S. pneumoniae autolysin LytA. A cooperative effect of LytA and Cpl-1 in the disintegration of S. pneumoniae biofilms was recorded.
Acceleration of Adipose Conversion of 3T3-L1 Cells by Dextran Sulfate (1994)

When dextran sulfate was added at concentrations of 0.001% or 0.01% (w/v) to cultures of 3T3-L1 fibroblasts, their spontaneous adipose conversion was accelerated. The expression of a marker enzyme (glycerophosphate dehydrogenase) peaked on day 16 but later declined due to the cytotoxicity of dextran sulfate. Heparin had similar effects on adipose conversion.
Structure of Stems in Relation to Differentiation and Abortion of Blossom Buds (1941)

1. Soybean, Salvia, Cosmos, and Xanthium, all short-day plants, initiate blossom primordia after different durations of exposure to short days. Soybean and Salvia require 9, Cosmos 12, and Xanthium 5 days of short-day treatment for the appearance of blossom primordia at the appropriate temperature and cultural conditions. Stock, a long-day plant (at a medium or cool temperature), requires approximately 18 days for the appearance of primordia. 2. In order that the blossom primordia may continue to develop, it is necessary to expose the plants studied (except Xanthium) to a favorable environment for a greater length of time than just the induction period. Xanthium requires an induction period of only 2-3 short days at a warm temperature for the initiation and development of blossom buds. One short day is sufficient for the initiation of staminate blossoms. 3. Alterations in the anatomical structure of the stem occurred early in the development of plants placed in an environment favorable to the formation of blossom primordia. The first indication of a change in structure was a decrease in the number of meristematic cells of the cambial zone. Associated with this was the simultaneous decrease in the formation of xylem and phloem cells and a thickening of the cell walls of the vascular tissue. The cambium generally remained somewhat active, giving rise to new xylem but little phloem. The most recently formed phloem was composed almost entirely of phloem parenchyma cells. The stems of flowering and fruiting plants had little or no meristematic tissue, and the walls of the cells had become greatly thickened. 4. Plants of soybean, Salvia, Cosmos, and stock exposed to an environment favorable to flowering for a limited time only, and then returned to conditions inducive to vegetative growth, soon showed renewed cambial activity and differentiation of vascular elements with the failure of the blossom primordia to continue development. Plants of Xanthium given 2-3 short days became reproductive regardless of subsequent treatment.