gebhart/patrepeval huggingface dataset:
Structure-Function Relationships in Membrane Segment 5 of the Yeast Pma1 H+-ATPase (1998)

Membrane segment 5 (M5) is thought to play a direct role in cation transport by the sarcoplasmic reticulum Ca2+-ATPase and the Na+, K+-ATPase of animal cells. In this study, we have examined M5 of the yeast plasma membrane H+-ATPase by alanine-scanning mutagenesis. Mutant enzymes were expressed behind an inducible heat-shock promoter in yeast secretory vesicles as described previously (Nakamoto, R. K., Rao, R., and Slayman, C. W. (1991) J. Biol. Chem. 266, 7940-7949). Three substitutions (R695A, H701A, and L706A) led to misfolding of the H+-ATPase as evidenced by extreme sensitivity to trypsin; the altered proteins were arrested in biogenesis, and the mutations behaved genetically as dominant lethals. The remaining mutants reached the secretory vesicles in sufficient amounts to be characterized in detail. One of them (Y691A) had no detectable ATPase activity and appeared, based on trypsinolysis in the presence and absence of ligands, to be blocked in the E1-to-E2 step of the reaction cycle. Alanine substitution at an adjacent position (V692A) had substantial ATPase activity (54%), but was likewise affected in the E1-to-E2 step, as evidenced by shifts in its apparent affinity for ATP, H+, and orthovanadate. Among the mutants that were sufficiently active to be assayed for ATP-dependent H+ transport by acridine orange fluorescence quenching, none showed an appreciable defect in the coupling of transport to ATP hydrolysis. The only residue for which the data pointed to a possible role in cation liganding was Ser-699, where removal of the hydroxyl group (S699A and S699C) led to a modest acid shift in the pH dependence of the ATPase. This change was substantially smaller than the 13-30-fold decrease in K+ affinity seen in corresponding mutants of the Na+, K+-ATPase (Arguello, J. M., and Lingrel, J. B (1995) J. Biol. Chem. 270, 22764-22771). Taken together, the results do not give firm evidence for a transport site in M5 of the yeast H+-ATPase, but indicate a critical role for this membrane segment in protein folding and in the conformational changes that accompany the reaction cycle. It is therefore worth noting that the mutationally sensitive residues lie along one face of a putative alpha-helix.
Convenient Syntheses of 6-Methylpurine and Related Nucleosides (2000)

Efficient methods for the synthesis of 6-methylpurine (3), 9-(2-deoxy-beta-D-erythro-pentofuranosyl)-6-methylpurine (8), and 6-methyl-9-beta-D-ribofuranosylpurine (5) are described. Methodology involving the (Ph3P)4Pd catalyzed cross-coupling reaction of CH3ZnBr with several different 6-chloropurine derivatives is described in high yield. This methodology now provides a facile and high-yielding synthesis of 8, which is needed in significant amounts for studies in cancer gene therapy.
An NAC transcription factor orchestrates multiple features of cell wall development in Medicago truncatula (2010)

To identify genes controlling secondary cell wall biosynthesis in the model legume Medicago truncatula, we screened a Tnt1 retrotransposon insertion mutant population for plants with altered patterns of lignin autofluorescence. From more than 9000 R1 plants screened, four independent lines were identified with a total lack of lignin in the interfascicular region. The mutants also showed loss of lignin in phloem fibers, reduced lignin in vascular elements, failure in anther dehiscence and absence of phenolic autofluorescence in stomatal guard cell walls. Microarray and PCR analyses confirmed that the mutations were caused by the insertion of Tnt1 in a gene annotated as encoding a NAM (no apical meristem)-like protein (here designated Medicago truncatula NAC SECONDARY WALL THICKENING PROMOTING FACTOR 1, MtNST1). MtNST1 is the only family member in Medicago, but has three homologs (AtNST1-AtNST3) in Arabidopsis thaliana, which function in different combinations to control cell wall composition in stems and anthers. Loss of MtNST1 function resulted in reduced lignin content, associated with reduced expression of most lignin biosynthetic genes, and a smaller reduction in cell wall polysaccharide content, associated with reduced expression of putative cellulose and hemicellulose biosynthetic genes. Acid pre-treatment and cellulase digestion released significantly more sugars from cell walls of nst1 mutants compared with the wild type. We discuss the implications of these findings for the development of alfalfa (Medicago sativa) as a dedicated bioenergy crop.
Decoupling "when to update" from "how to update" (2017)

Deep learning requires data. A useful approach to obtain data is to be creative and mine data from various sources, that were created for different purposes. Unfortunately, this approach often leads to noisy labels. In this paper, we propose a meta algorithm for tackling the noisy labels problem. The key idea is to decouple ``when to update'' from ``how to update''. We demonstrate the effectiveness of our algorithm by mining data for gender classification by combining the Labeled Faces in the Wild (LFW) face recognition dataset with a textual genderizing service, which leads to a noisy dataset. While our approach is very simple to implement, it leads to state-of-the-art results. We analyze some convergence properties of the proposed algorithm.
Restricted internal rotations in some ortho-substituted diaryl sulfides and sulfones (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRestricted internal rotations in some ortho-substituted diaryl sulfides and sulfonesWilliam Y. Lam and J. C. MartinCite this: J. Org. Chem. 1981, 46, 22, 4458–4462Publication Date (Print):October 1, 1981Publication History Published online1 May 2002Published inissue 1 October 1981https://pubs.acs.org/doi/10.1021/jo00335a027https://doi.org/10.1021/jo00335a027research-articleACS PublicationsRequest reuse permissionsArticle Views74Altmetric-Citations11LEARN 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-Alertsclose Get e-Alerts
Effects of Endodontic Irrigation Solutions on Mineral Content of Root Canal Dentin Using ICP-AES Technique (2005)

The aim of this in vitro study was to evaluate mineral content of root canal dentin after treatment with several endodontic irrigation solutions. Sixty mandibular anterior teeth extracted for periodontal reasons used. The crowns of the teeth were removed at the cemento-enamel junction. Pulp tissues were removed and the teeth were randomly divided into six groups including 10 teeth each. Root canals were enlarged with gates-glidden burs (# 1, 2, and 3). The groups were treated as follows: group 1, 0.2% chlorhexidine gluconate for 15 min; group 2, 3% H2O2 for 15 min; group 3, 17% EDTA for 15 min; group 4, 5.25% NaOCl for 15 min; group 5, 2.5% NaOCl for 15 min; and group 6, distilled water (control). Dentin chips were obtained using gates-glidden burs (# 4, 5, and 6). The levels of five elements calcium, phosphorus, magnesium, potassium, and sulfur in each specimens were analyzed using ICP-AES (Inductively Coupled Plasma Atomic Emission Spectrometry) technique. Changes in the levels of the chemical elements were recorded. The results were then statistically analyzed by one-way ANOVA and Tukey tests. There was a significant decrease in the calcium and phosphorus levels after treatment with all irrigation solutions except for 5.25% NaOCl when compared with the control group (p < 0.05). The K, Mg, and S level changes were not statistically significant (p > 0.05). It has been concluded that endodontic irrigation solutions have an effect on mineral contents of root dentin.
Control of a three-phase PWM rectifier using estimated AC-side and DC-side voltages (1999)

A new control method of a pulsewidth modulation (PWM) rectifier without measuring AC- and DC-side voltages is proposed. As information about these voltages is necessary for the controller, all required voltage values are estimated from the measured line currents and the calculated values of the input reactor voltage during switching of the rectifier circuit. The input reactor voltage can be obtained by using a differentiator that produces the derivative of the line current or by detecting the voltage induced in a secondary winding wound on the input reactor. The secondary winding creates the electric isolation between the main circuit and the controller. The proposed method is verified by experiment. This paper describes the estimation method, gives the configuration of the controller, and discusses steady-state and transient performances of the rectifier.
Transparent, Incremental Checkpointing at Kernel Level: a Foundation for Fault Tolerance for Parallel Computers (2005)

We describe the software architecture, technical features, and performance of TICK (Transparent Incremental Checkpointer at Kernel level), a system-level checkpointer implemented as a kernel thread, specifi- cally designed to provide fault tolerance in Linux clusters. This implementation, based on the 2.6.11 Linux kernel, provides the essential functionality for transparent, highly responsive, and efficient fault tolerance based on full or incremental checkpointing at system level. TICK is completely user-transparent and does not require any changes to user code or system libraries; it is highly responsive: an interrupt, such as a timer interrupt, can trigger a checkpoint in as little as 2.5µs; and it supports incremental and full checkpoints with minimal overhead-less than 6% with full checkpointing to disk performed as frequently as once per minute.
Psychological benefits of Forest Bathing during the COVID-19 pandemic: a pilot study in a Mediterranean forest close to urban areas (2021)

The practice of Shinrin-Yoku or Forest Bathing is an outdoor therapeutic modality with mounting evidence suggesting positive effects on individuals' psychological wellbeing and overall health. However, its benefits have mainly been studied in Asian biomes and more research is needed to evaluate if its benefits are also generalizable to other regions such as European-Mediterranean forests. To preliminarily explore this issue, 16 healthy adults (87.5% women, mean age 47.5) were assessed before and after a 3-hour session of Forest Bathing with meditation exercises in a Mediterranean forest near Barcelona (Spain). Changes in state anxiety, negative affect, positive affect and state mindfulness were assessed. Results show significant increases in positive affect, vigour, friendship and mindfulness, and decreases in negative affect, anxiety, anger, fatigue, tension, and depressive mood. Effect sizes observed for all the outcomes were significant and large, ranging from d = 1.02 to d = 2.61. This study encourages more applied research of the forest therapy model and the practice of Shinrin-Yoku in Mediterranean forests to increase the general population's psychological wellbeing and to deal with the growing prevalence of the psychological side-effects generated by the COVID-19 in European countries such as Spain.
Robust and Communication-Efficient Federated Learning From Non-i.i.d. Data (2019)

Federated learning allows multiple parties to jointly train a deep learning model on their combined data, without any of the participants having to reveal their local data to a centralized server. This form of privacy-preserving collaborative learning, however, comes at the cost of a significant communication overhead during training. To address this problem, several compression methods have been proposed in the distributed training literature that can reduce the amount of required communication by up to three orders of magnitude. These existing methods, however, are only of limited utility in the federated learning setting, as they either only compress the upstream communication from the clients to the server (leaving the downstream communication uncompressed) or only perform well under idealized conditions, such as i.i.d. distribution of the client data, which typically cannot be found in federated learning. In this article, we propose sparse ternary compression (STC), a new compression framework that is specifically designed to meet the requirements of the federated learning environment. STC extends the existing compression technique of top- k gradient sparsification with a novel mechanism to enable downstream compression as well as ternarization and optimal Golomb encoding of the weight updates. Our experiments on four different learning tasks demonstrate that STC distinctively outperforms federated averaging in common federated learning scenarios. These results advocate for a paradigm shift in federated optimization toward high-frequency low-bitwidth communication, in particular in the bandwidth-constrained learning environments.
A measuring device for the determination of the electric permittivity of materials in the frequency range 0.1-300 MHz (1982)

A device for the measuring of the complex permittivity in the 0.1 MHz-300 MHz range is presented. It is a resonant system on which we can easily fit the measurement cells of the laboratory used in the 1 Hz-4 GHz range. This device allows us to measure the loss angle of materials down to 0.4*10-3. After the description of the mechanical and electronic parts of the device, the authors give the calibration method used to obtain the real and imaginary components of the electric permittivity. Finally, they report the results of dielectric measurements performed with this device for a liquid crystal and a synthetic zeolite. Automatic data processing by means of a computer increases the rapidity of measurement and decreases the number of manual operations.
An image synthesizing method based on human motion recognition from stereo images (2003)

This paper describes a method of synthesizing a human image in a virtual space by recognizing the human motion from stereo images. However it is difficult to detect the positions of all the human joints from actual images. This image synthesizing method uses an associative memory which has stored representative human motion patterns to compensate for the insufficient information detected from actual images.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Characterization of the Pseudomonas aeruginosa alginate lyase gene (algL): cloning, sequencing, and expression in Escherichia coli (1993)

Mucoid strains of Pseudomonas aeruginosa produce a viscous exopolysaccharide called alginate and also express alginate lyase activity which can degrade this polymer. By transposon mutagenesis and gene replacement techniques, the algL gene encoding a P. aeruginosa alginate lyase enzyme was found to reside between algG and algA within the alginate biosynthetic gene cluster at 35 min on the P. aeruginosa chromosome. DNA sequencing data for algL predicted a protein product of ca. 41 kDa, including a 27-amino-acid signal sequence, which would be consistent with its possible localization in the periplasmic space. Expression of the algL gene in Escherichia coli cells resulted in the expression of alginate lyase activity and the appearance of a new protein of ca. 39 kDa detected on sodium dodecyl sulfate-polyacrylamide gels. In mucoid P. aeruginosa strains, expression of algL was regulated by AlgB, which also controls expression of other genes within the alginate gene cluster. Since alginate lyase activity is associated with the ability to produce and secrete alginate polymers, alginate lyase may play a role in alginate production.
Thauera selenatis gen. nov., sp. nov., a Member of the Beta Subclass of Proteobacteria with a Novel Type of Anaerobic Respiration (1993)

A recently isolated, selenate-respiring microorganism (strain AXT [T = type strain]) was classified by using a polyphasic approach in which both genotypic and phenotypic characteristics were determined. Strain AXT is a motile, gram-negative, rod-shaped organism with a single polar flagellum. On the basis of phenotypic characteristics, this organism can be classified as a Pseudomonas sp. However, a comparison of the 16S rRNA sequence of strain AXT with the sequences of other organisms indicated that strain AXT is most similar to members of the beta subclass (level of similarity, 86.8%) rather than to members of the gamma subclass (level of similarity, 80.2%) of the Proteobacteria. The presence of the specific polyamine 2-hydroxyputrescine and the presence of a ubiquinone with eight isoprenoid units in the side chain (ubiquinone Q-8) excluded strain AXT from the authentic genus Pseudomonas and allowed placement in the beta subclass of the Proteobacteria. Within the beta subclass, strain AXT is related to Iodobacter fluvatile. The phylogenetic distance (level of similarity, less than 90%), as well as a lack of common phenotypic characteristics between these organisms, prevents classification of strain AXT as a member of the genus Iodobacter. In addition, strain AXT possesses a unique mechanism for anaerobic respiration, which allows it to utilize selenate as an electron acceptor without interference by nitrate. Therefore, we propose that strain AXT should be the first member of a new genus and species, Thauera selenatis.
Monomeric and dimeric thiodithiazyl cations, S3N2+ and S6N42+. Preparation and crystal structures of (S3N2)(AsF6), (S6N4)(S2O2F)2 and (S6N4)(SO3F)2 (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMonomeric and dimeric thiodithiazyl cations, S3N2+ and S6N42+. Preparation and crystal structures of (S3N2)(AsF6), (S6N4)(S2O2F)2 and (S6N4)(SO3F)2Ronald J. Gillespie, James P. Kent, and Jeffery F. SawyerCite this: Inorg. Chem. 1981, 20, 11, 3784–3799Publication Date (Print):November 1, 1981Publication History Published online1 May 2002Published inissue 1 November 1981https://pubs.acs.org/doi/10.1021/ic50225a041https://doi.org/10.1021/ic50225a041research-articleACS PublicationsRequest reuse permissionsArticle Views180Altmetric-Citations64LEARN 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
Antibodies to the quinolones and fluoroquinolones for the development of generic and specific immunoassays for detection of these residues in animal products (2003)

Several quinolone and fluoroquinolone haptens have been used to raise polyclonal antibodies exhibiting both specific and generic properties for these classes of antimicrobial compounds. The antisera have been assessed in rapid enzyme immunoassays (ELISAs) designed to exploit the specificities obtained. A direct generic ELISA for both the quinolones and fluoroquinolones has been developed that uses the cross-reactivity of an antibody raised against norfloxacin (1-ethyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinoline carboxylic acid) linked to ovalbumin via a secondary amine group on the piperazinyl moiety to detect nine different drugs in these classes. Specific ELISAs to ciprofloxacin (1-cyclopropyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinoline carboxylic acid), enrofloxacin (1-cyclopropyl-7-(4-ethyl-1-piperazinyl)-6-fluoro-1,4-dihydro-4-oxo-3-quinoline carboxylic acid), flumequin (9-fluoro-6,7-dihydro-5-methyl-1-oxo-1H,5H-benzo(ij)quinolizine-2-carboxylic acid) and nalidixic acid (1-ethyl-1,4-dihydro-7-methyl-4-oxo-1,8-naphthyridine-3-carboxylic acid) have also been developed with a high degree of specificity to the individual compounds. The assays measure drug residues in bovine milk and ovine kidney with an interassay relative standard deviation (s(r)) of 10.5% or less and intra-assay s(r) of 11.2% or less. Sensitivity is less than 4 microg x kg(-1) for both the generic and specific assays for all but one of the compounds tested. (Pipemidic acid (8-ethyl-5,8-dihydro-5-oxo-2-(1-piperazinyl)pyrido(2,3-d)pyrimidine-6-carboxylic acid) is detectable at 6 microg x kg(-1) in kidney.)
Polymerization of Non-conjugated Diynes by Complex Metal Catalysts<sup>1,2</sup> (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymerization of Non-conjugated Diynes by Complex Metal Catalysts1,2J. K. Stille and D. A. FreyCite this: J. Am. Chem. Soc. 1961, 83, 7, 1697–1701Publication Date (Print):April 1, 1961Publication History Published online1 May 2002Published inissue 1 April 1961https://pubs.acs.org/doi/10.1021/ja01468a034https://doi.org/10.1021/ja01468a034research-articleACS PublicationsRequest reuse permissionsArticle Views411Altmetric-Citations74LEARN 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-Alertsclose Get e-Alerts