gebhart/patrepeval huggingface dataset:
The <i>Arabidopsis thaliana</i> DSB formation (<i>AtDFO</i>) gene is required for meiotic double‐strand break formation (2012)

DNA double-strand break (DSB) formation is the initial event for meiotic recombination catalyzed by the conserved Spo11 protein. In Arabidopsis, several proteins have been reported to be involved in DSB formation. Here, we report an Arabidopsis DSB forming (DFO) gene in Arabidopsis that is involved in DSB formation. The dfo mutant exhibits reduced fertility, producing polyads with an abnormal number of microspores, unlike the tetrads in the wild type. The dfo meiocytes were defective in homologous chromosome synapsis and segregation. Genetic analysis revealed that the homologous recombination of Atdfo-1 is severely affected in meiotic prophase I. DFO encodes a protein without any known conserved domain. There was no homologue identified outside the plant kingdom, indicating that AtDFO is a plant-specific protein. AtMRE11 has been reported to be responsible for processing SPO11-generated DSBs. The Atmre11 mutant displays chromosome fragmentation during meiosis. However, the Atdfo Atmre11 double mutant had no such chromosome fragmentation, indicating that AtDFO is required for DSB formation.
The role of instruction in learning to read: Preventing reading failure in at-risk children. (1998)

First and 2nd graders (N = 285) receiving Title 1 services received 1 of 3 kinds of classroom reading programs: direct instruction in letter–sound correspondences practiced in decodable text (direct code); less direct instruction in systematic sound–spelling patterns embedded in connected text (embe
Properties and Kinetic Analysis of UDP-glucose Dehydrogenase from Group A Streptococci (1997)

UDP-glucuronic acid is used by many pathogenic bacteria in the construction of an antiphagocytic capsule that is required for virulence. The enzyme UDP-glucose dehydrogenase catalyzes the NAD+-dependent 2-fold oxidation of UDP-glucose and provides a source of the acid. In the present study the recombinant dehydrogenase from group A streptococci has been purified and found to be active as a monomer. The enzyme contains no chromophoric cofactors, and its activity is unaffected by the presence of EDTA or carbonyl-trapping reagents. Initial velocity and product inhibition kinetic patterns are consistent with a bi-uni-uni-bi ping-pong mechanism in which UDP-glucose is bound first and UDP-glucuronate is released last. UDP-xylose was found to be a competitive inhibitor (Ki, 2.7 microM) of the enzyme. The enzyme is irreversibly inactivated by uridine 5'-diphosphate-chloroacetol due to the alkylation of an active site cysteine thiol. The apparent second order rate constant for the inhibition (ki/Ki) was found to be 2 x 10(3) mM-1 min-1. Incubation with the truncated compound, chloroacetol phosphate, resulted in no detectable inactivation when tested under comparable conditions. This supports the notion that uridine 5'-diphosphate-chloroacetol is bound in the place of UDP-glucose and is not simply acting as a nonspecific alkylating agent.
Measurement of ground reaction forces using unobtrusive, on-athlete instrumentation (2004)

The purpose of this research is to investigate the measurement and characterization of ground reaction force transmitted through the foot-shoe-ground interface during the course of athletic activity (e.g running) from unobtrusive, on-athlete instrumentation. Both contact (in-shoe load) and non-contact (centre of mass acceleration) forms of sensory means to evaluate ground reaction force, are under investigation. Instrumentation has been developed to simultaneously acquire in-shoe load and acceleration data and a signal processing method is proposed to determine ground reaction force data from the on-athlete instrumentation.
An In-depth Performance Characterization of CPU- and GPU-based DNN Training on Modern Architectures (2017)

Traditionally, Deep Learning (DL) frameworks like Caffe, TensorFlow, and Cognitive Toolkit exploited GPUs to accelerate the training process. This has been primarily achieved by aggressive improvements in parallel hardware as well as through sophisticated software frameworks like cuDNN and cuBLAS. However, recent enhancements to CPU-based hardware and software has the potential to significantly enhance the performance of CPU-based DL training. In this paper, we provide a complete performance landscape of CPU- and GPU-based DNN training. We characterize performance of DNN training for AlexNet and ResNet-50 for a wide-range of CPU and GPU architectures including the latest Intel Xeon Phi (Knights Landing) processors and NVIDIA Pascal GPUs. We also present multi-node DNN training performance results for AlexNet and ResNet-50 using Intel Machine Learning Scaling (MLSL) Library and Intel-Caffe. In addition, we provide a CPU vs. GPU comparison for multi-node training using OSU-Caffe and Intel-Caffe. To the best of our knowledge, this is the first study that dives deeper into the performance of DNN training in a holistic manner yet provides an in-depth look at layer-wise performance for different DNNs. We provide multiple key insights: 1) Convolutions account for the majority of time (up to 83% time) consumed in DNN training, 2) GPU-based training continues to deliver excellent performance (up to 18% better than KNL) across generations of GPU hardware and software, and 3) Recent CPU-based optimizations like MKL-DNN and OpenMP-based thread parallelism leads to excellent speed-ups over under-optimized designs (up to 3.2X improvement for AlexNet training).
Synthesis of Five-, Six-, and Seven-Membered Heterocycles by Intramolecular Ring Opening Reactions of 3-Oxetanol Derivatives (1998)

Intramolecular ring opening reactions of 2-phenyl-3-oxetanols have been studied. The starting materials were prepared by the photocycloaddition of benzaldehyde and various silyl enol ethers. The intramolecular nucleophile was either incorporated into the silyl enol ether prior to the Paternò−Büchi reaction (oxetanes 3, 16) or was later installed by functional group interconversion (oxetanes 5, 12). With anionic heteroatom nucleophiles (O, N, S) which were attached to the carbon atom C-3 of the trimethylsilyl-protected oxetanol via an alkyl chain, a substitution at the less substituted position C-4 was observed and the corresponding heterocycles (6, 8, 13, 19) were obtained in moderate to good yields (52−91%). Upon acid catalysis a ring opening of the Boc-protected 3-oxetanol 23 to cyclic carbonates occurred. The reaction did not proceed stereospecifically and resulted in a mixture of diastereomeric products 24 and 25.
Molecular Structure of B. stearothermophilus Cyclodextrin Glucanotransferase and Analysis of Substrate Binding Site. (1991)

The 3-dimensional X-ray crystallographic structure of cyclodextrin glucanotransferase (CGT-ase) from B. stearothermophilus showed that the CGTase molecule fold into four globular domains, A, B, C and D. The N-terminal domains, A and B, are similar to those of Taka-amylase. The C and D domains, which are unique to this enzyme, both consist of antiparallel β-barrel structure. With a substrate binding analysis in the crystal, two binding sites have been found on the enzyme molecule, one in a cleft of the A-domain and the other in the D-domain. The first one is considered to be related to the enzyme activity in a same manner with a-amylase and the second to the raw starch binding activity of the CGTase.
Structural Analysis and Detection of Biological Inositol Pyrophosphates Reveal That the Family of VIP/Diphosphoinositol Pentakisphosphate Kinases Are 1/3-Kinases (2008)

We have characterized the positional specificity of the mammalian and yeast VIP/diphosphoinositol pentakisphosphate kinase (PPIP5K) family of inositol phosphate kinases. We deployed a microscale metal dye detection protocol coupled to a high performance liquid chromatography system that was calibrated with synthetic and biologically synthesized standards of inositol pyrophosphates. In addition, we have directly analyzed the structures of biological inositol pyrophosphates using two-dimensional 1H-1H and 1H-31P nuclear magnetic resonance spectroscopy. Using these tools, we have determined that the mammalian and yeast VIP/PPIP5K family phosphorylates the 1/3-position of the inositol ring in vitro and in vivo. For example, the VIP/PPIP5K enzymes convert inositol hexakisphosphate to 1/3-diphosphoinositol pentakisphosphate. The latter compound has not previously been identified in any organism. We have also unequivocally determined that 1/3,5-(PP)2-IP4 is the isomeric structure of the bis-diphosphoinositol tetrakisphosphate that is synthesized by yeasts and mammals, through a collaboration between the inositol hexakisphosphate kinase and VIP/PPIP5K enzymes. These data uncover phylogenetic variability within the crown taxa in the structures of inositol pyrophosphates. For example, in the Dictyostelids, the major bis-diphosphoinositol tetrakisphosphate is 5,6-(PP)2-IP4 ( Laussmann, T., Eujen, R., Weisshuhn, C. M., Thiel, U., Falck, J. R., and Vogel, G. (1996) Biochem. J. 315, 715-725 ). Our study brings us closer to the goal of understanding the structure/function relationships that control specificity in the synthesis and biological actions of inositol pyrophosphates.
A Quick Survey of MultiVersion Concurrency Algorithms (2007)

This document looks at some of the problems with traditional methods of concurrency control via locking, and explains how Multi-Version Concurrency algorithms help to resolve some of these problems. It describes the approaches to Multi-Version concurrency and examines a couple of implementations in greater detail.
October 14 Highlights (2003)

Rasmussen's encephalitis: Autoantibodies and cytotoxic T cellsTakahashi et al. found autoantibodies against the NMDA-type GluR epsilon2 in patients with chronic epilepsia partialis continua, including patients with proven or clinically suspected Rasmussen's encephalitis, with an acute encephalitis or encephalopathy, and with nonprogressive epilepsia partialis continua.Antibodies were predominantly against cytoplasmic (C-terminal) epitopes but antibody profiles did not show consistent changes during the course of disease.The data suggest that cytotoxic T-cell-mediated neuronal damage occurs in these conditions.
Current Understanding of the Role of Complement in IgA Nephropathy (2015)

Complement activation has a role in the pathogenesis of IgA nephropathy, an autoimmune disease mediated by pathogenic immune complexes consisting of galactose-deficient IgA1 bound by antiglycan antibodies. Of three complement-activation pathways, the alternative and lectin pathways are involved in IgA nephropathy. IgA1 can activate both pathways in vitro, and pathway components are present in the mesangial immunodeposits, including properdin and factor H in the alternative pathway and mannan-binding lectin, mannan-binding lectin-associated serine proteases 1 and 2, and C4d in the lectin pathway. Genome-wide association studies identified deletion of complement factor H-related genes 1 and 3 as protective against the disease. Because the corresponding gene products compete with factor H in the regulation of the alternative pathway, it has been hypothesized that the absence of these genes could lead to more potent inhibition of complement by factor H. Complement activation can take place directly on IgA1-containing immune complexes in circulation and/or after their deposition in the mesangium. Notably, complement factors and their fragments may serve as biomarkers of IgA nephropathy in serum, urine, or renal tissue. A better understanding of the role of complement in IgA nephropathy may provide potential targets and rationale for development of complement-targeting therapy of the disease.
Copper in Green Hair: A Quantitative Investigation by Electron Probe X-Ray Microanalysis (1980)

Eleven cases of green hair were collected and hair tips were analyzed in the electron microscope by energy-dispersive x-ray microanalysis. In all cases, remarkable copper concentrations could be demonstrated (0.2-1.8% w/w). In normal hair the concentration of copper was below the detection limit (0.02% w/w). Analyses of hair cross sections showed a concentration gradient from the periphery toward the center, the periphery having higher values. This observation is in agreement with suspected contamination of the hair with copper from extraneous sources: analysis of the tapwater in patients' homes showed elevated copper concentrations. In addition, the water showed aggressive properties (pH outside the recommended range, high nitrate concentrations, heavily chlorinated). Investigations by transmission electron microscopy showed damage in the endocuticula. Experimental studies of normal unaffected hair fibers showed that treatment with a copper salt alone could result in binding of copper to the hair but that the extent of copper binding could be greatly increased by damaging the cuticula with chlorinated water. It is suggested that aggressive water attacks copper tubings leading to increased copper concentrations in tapwater and causes cuticular damage, which facilitates entry of copper into the hair.
Chemical Modifications of Furan-Based Calixarenes by Diels-Alder Reactions (1999)

The Diels–Alder reactions of the cyclic hexamer of furan and acetone C 6 with benzyne and DMAD (dimethylacetylenedicarboxylate) are described. In this way, C 6 can be exploited as a framework on which to place sets of carboxyl functions to obtain a novel family of furan-based calixarenes, such as 1, with potential applications in supramolecular chemistry.
Physical Properties of Sodium, Potassium, and Ammonium Lactate Solutions (1941)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhysical Properties of Sodium, Potassium, and Ammonium Lactate SolutionsAlbert A. Dietz, Ed. F. Degering, and H. H. SchopmeyerCite this: Ind. Eng. Chem. 1941, 33, 11, 1444–1447Publication Date (Print):November 1, 1941Publication History Published online1 May 2002Published inissue 1 November 1941https://pubs.acs.org/doi/10.1021/ie50383a027https://doi.org/10.1021/ie50383a027research-articleACS PublicationsRequest reuse permissionsArticle Views428Altmetric-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 options Get e-Alerts
Involvement of Group VI Ca2+-independent Phospholipase A2 in Protein Kinase C-dependent Arachidonic Acid Liberation in Zymosan-stimulated Macrophage-like P388D1 Cells (1999)

We investigated the possible involvement of group VI Ca2+-independent phospholipase A2 (iPLA2) in arachidonic acid (AA) liberation in zymosan-stimulated macrophage-like P388D1 cells. Zymosan-induced AA liberation was markedly inhibited by methyl arachidonoyl fluorophosphonate, a dual inhibitor of group IV cytosolic phospholipase A2 (cPLA2) and iPLA2. We found that a relatively specific iPLA2 inhibitor, bromoenol lactone, significantly decreased the zymosan-induced AA liberation in parallel with the decrease in iPLA2 activity, without an effect on diacylglycerol formation. Consistent with this, attenuation of iPLA2 activity by a group VI iPLA2 antisense oligonucleotide resulted in a decrease in zymosan-induced prostaglandin D2 generation. These findings suggest that zymosan-induced AA liberation may be, at least in part, mediated by iPLA2. A protein kinase C (PKC) inhibitor diminished zymosan-induced AA liberation, while a PKC activator, phorbol 12-myristate 13-acetate (PMA), enhanced the liberation. Bromoenol lactone suppressed the PMA-enhanced AA liberation without any effect on PMA-induced PKC activation. Down-regulation of PKCalpha on prolonged exposure to PMA also decreased zymosan-induced AA liberation. Under these conditions, the remaining AA liberation was insensitive to bromoenol lactone. Furthermore, the PKC depletion suppressed increases in iPLA2 proteins and the activity in the membrane fraction of zymosan-stimulated cells. In contrast, the zymosan-induced increases in iPLA2 proteins and the activity in the fraction were facilitated by simultaneous addition of PMA. Although intracellular Ca2+ depletion prevented zymosan-induced AA liberation, the translocation of PKCalpha to membranes was also inhibited. Taken together, we propose that zymosan may stimulate iPLA2-mediated AA liberation, probably through a PKC-dependent mechanism.
Rosiglitazone is more effective than metformin in improving fasting indexes of glucose metabolism in severely obese, non‐diabetic patients (2007)

Our study shows that in severely obese, non-diabetic, hyperinsulinaemic patients undergoing a nutritional programme, rosiglitazone is more effective than metformin in producing favourable changes in fasting-based indexes of glucose metabolism, with a reduction of both insulin resistance and hyperinsulinaemia. In spite of previous studies reporting rosiglitazone-induced body weight gain, in our study the joint treatment with diet and rosiglitazone was accompanied by weight loss and fat mass reduction.
Regulation of phosphatidate phosphatase activity from the yeast Saccharomyces cerevisiae by sphingoid bases (1993)

The regulation of Saccharomyces cerevisiae membrane-associated phosphatidate phosphatase (3-sn-phosphatidate phosphohydrolase, EC 3.1.3.4) activity by sphingoid bases was examined using Triton X-100/lipid-mixed micelles. Sphingosine, phytosphingosine, and sphinganine inhibited purified preparations of the 104- and 45-kDa forms of phosphatidate phosphatase in a dose-dependent manner. The structural requirements for the sphingoid base inhibition of phosphatidate phosphatase activity were a free amino group and a long chain hydrocarbon. A detailed kinetic analysis was performed to determine the mechanism of phosphatidate phosphatase inhibition by sphingoid bases. The phosphatidate phosphatase dependence on phosphatidate was cooperative (Hill numbers of approximately 2) in the absence and presence of sphingoid bases. Sphingosine, phytosphingosine, and sphinganine were parabolic competitive inhibitors of phosphatidate phosphatase activity. This indicated that more than one inhibitor molecule contributed to the exclusion of phosphatidate from the enzyme. The aKi values (inhibitor constants) for sphingosine, phytosphingosine, and sphinganine were 1.5, 0.4, and 0.2 mol %, respectively, and the Km value for phosphatidate was 2.2 mol %. The cellular concentrations of free phytosphingosine and sphinganine were 0.16 and 0.53 mol %, respectively, relative to the total phospholipids in S. cerevisiae. The cellular concentrations of phytosphingosine and sphinganine were in the range of the aKi values for these sphingoid bases. These results raised the suggestion that phosphatidate phosphatase activity may be regulated in vivo by sphingoid bases.
The dynamic interplay of host and viral enzymes in type III CRISPR-mediated cyclic nucleotide signalling (2020)

Abstract Cyclic nucleotide second messengers are increasingly implicated in prokaryotic anti-viral defence systems. Type III CRISPR systems synthesise cyclic oligoadenylate (cOA) upon detecting foreign RNA, activating ancillary nucleases that can be toxic to cells, necessitating mechanisms to remove cOA in systems that operate via immunity rather than abortive infection. Previously, we demonstrated that the Sulfolobus solfataricus type III-D CRISPR complex generates cyclic tetra-adenylate (cA 4 ), activating the ribonuclease Csx1, and showed that subsequent RNA cleavage and dissociation acts as an “off-switch” for the cyclase activity (Rouillon et al. , 2018). Subsequently, we identified the cellular ring nuclease Crn1, which slowly degrades cA 4 to reset the system, and demonstrated that viruses can subvert type III CRISPR immunity by means of a potent anti-CRISPR ring nuclease variant. Here, we present a comprehensive analysis of the dynamic interplay between these enzymes, governing cyclic nucleotide levels and infection outcomes in virus-host conflict.
Cerium-based conversion coatings on aluminium alloys: a process review (2013)

AbstractRare earths are among the most promising options for replacing chromate conversion coatings on aluminium. In nearly three decades of research, several hundred papers have been published in the area, the bulk of which has never been reviewed. This paper reviews the literature on rare earth coating processes, with particular emphasis on those based on cerium. It is concluded that several process areas are poorly understood, some of which are critical to further progress in the field. These include the development of industrially suitable pretreatments, technologies for coating non-aerospace alloys and seals to enhance corrosion performance and paint adhesion.
Highly stretchable dielectric elastomer composites containing high volume fractions of silver nanoparticles (2015)

A composite of Ag/SiO<sub>2</sub>core–shell nanoparticles 20 vol% in polydimethylsiloxane with<italic>ε</italic>′ = 5.9,<italic>E</italic><sub>b</sub>= 13.4 V μm<sup>−1</sup>,<italic>Y</italic><sub>100%</sub>= 350 kPa, and a strain at break of 800% is presented.
Synthesis of (±)-8-Aza-11-deoxy-10-oxaprostaglandin E1 (1982)

Synthesis of new oxazolidine prostanoids, racemic
Anastomosis of Small Veins with Suture or Nakayama's Apparatus (1976)

In controlled experiments, the posterior facial veins in the rabbits neck (diameter 1.5-2.0 mm) were repaired, either by manual suture with 10-0 nylon or by the use of Nakayama's ring pin stapler. The so-called Nakayama "animal" rings, made from metal alloy, as well as the "human" rings, made from tantalum, were employed. A Nakayama anastomosis was performed in only one-third of the time required to complete a suture anastomosis. Evaluation of anastomotic patency was carried out after 7 days, and the vessels were examined histologically in serial sections. Veins anastomosed by the Nakayama technique had a statistically significant lower rate of early thrombosis than the sutured veins, while no difference was found in the occurrence of late thrombosis. The histological analysis showed a perfect endothelium-to-endothelium coaptation in the Nakayama anastomoses, and endothelium covered the anastomotic site in one week. In suture anastomoses the histological picture was more complex, with disintegration of the layers of the vessel wall and hyaline degeneration betweeen sutures. The "animal" rings almost constantly caused local phlebitis, but these changes were not reflected in the patency rates at one week.
THE CHEMISTRY OF 1,3,4-OXADIAZOLE DERIVATIVES (1964)

CONTENTS I. Introduction 508 II. Preparation of mono-substituted 1,3,4-oxadiazoles 508 III. Preparation of symmetrical 2,5-substituted 1,3,4-oxadiazoles 508 IV. Preparation of asymmetrical 2,5-substituted 1,3,4-oxadiazoles 509 V. Preparation of poly-1,3,4-oxadiazoles 511 VI. Properties and uses of 1,3,4-oxadiazole derivatives 512