gebhart/patrepeval huggingface dataset:
Relaxation of Transcription-induced Negative Supercoiling Is an Essential Function of Escherichia coli DNA Topoisomerase I (1999)

It has been suggested that the essential function of DNA topoisomerase I in Escherichia coli is to prevent chromosomal DNA from reaching an unacceptably high level of global negative supercoiling. However, other in vivo studies have shown that DNA topoisomerase I is very effective in removing local negative supercoiling generated during transcription elongation. To determine whether topoisomerase I is essential for controlling global or local DNA supercoiling, we have prepared a set of topA null mutant strains in combination with different plasmid DNAs. Although we found a correlation between the severity of the growth defect with both transcription-induced and global supercoiling, near to complete growth inhibition correlated only with transcription-induced supercoiling. This result strongly suggests that the major function of DNA topoisomerase I is to relax local negative supercoiling generated during transcription elongation.
Non-invasive inspection of baggage using coherent X-ray scattering (1995)

The requirement for equipment to detect with a high degree of specificity (low false positive rate) explosive materials in passenger baggage is an obvious one. X-ray equipments commercially available at present include dual energy transmission imagers and computer aided tomography (CAT) scanners. These essentially yield effective atomic number and density information in 2D and 3D respectively. Both technologies provide highly capable and practical equipment for screening bags and are improving all the time in terms of the precision with which the effective atomic number and density may be determined. They do, however, remain inherently chemically nonspecific. In this paper, we report work carried out to evaluate X-ray coherent scattering. The aim is to achieve the excellent chemical specificity of NQR, allied with the penetration of X-ray and nuclear methods.
Provably efficient scheduling for languages with fine-grained parallelism (1999)

Many high-level parallel programming languages allow for fine-grained parallelism. As in the popular work-time framework for parallel algorithm design, programs written in such languages can express the full parallelism in the program without specifying the mapping of program tasks to processors. A common concern in executing such programs is to schedule tasks to processors dynamically so as to minimize not only the execution time, but also the amount of space (memory) needed. Without careful scheduling, the parallel execution on p processors can use a factor of p or larger more space than a sequential implementation of the same program. This paper first identifies a class of parallel schedules that are provably efficient in both time and space. For any computation with w units of work and critical path length d , and for any sequential schedule that takes space s 1 , we provide a parallel schedule that takes fewer than w/p + d steps on p processors and requires less than s 1 + p·d space. This matches the lower bound that we show, and significantly improves upon the best previous bound of s 1 ·p spaces for the common case where d « s 1 . The paper then describes a scheduler for implementing high-level languages with nested parallelism, that generates schedules in this class. During program execution, as the structure of the computation is revealed, the scheduler keeps track of the active tasks, allocates the tasks to the processors, and performs the necessary task synchronization. The scheduler is itself a parallel algorithm, and incurs at most a constant factor overhead in time and space, even when the scheduling granularity is individual units of work. The algorithm is the first efficient solution to the scheduling problem discussed here, even if space considerations are ignored.
Control of neuronal migration through rostral migration stream in mice (2010)

During the nervous system development, immature neuroblasts have a strong potential to migrate toward their destination. In the adult brain, new neurons are continuously generated in the neurogenic niche located near the ventricle, and the newly generated cells actively migrate toward their destination, olfactory bulb, via highly specialized migratory route called rostral migratory stream (RMS). Neuroblasts in the RMS form chains by their homophilic interactions, and the neuroblasts in chains continually migrate through the tunnels formed by meshwork of astrocytes, glial tube. This review focuses on the development and structure of RMS and the regulation of neuroblast migration in the RMS. Better understanding of RMS migration may be crucial for improving functional replacement therapy by supplying endogenous neuronal cells to the injury sites more efficiently.
Image formation in phase-shifting digital holography and applications to microscopy (2001)

We discuss image formation in phase-shifting digital holography by developing an analytical formulation based on the Fresnel-Kirchhoff diffraction theory. Image-plane position and imaging magnification are derived for general configurations in which a spherical reference is employed. The influences of discrete sampling of the resulting interference patterns by a CCD and numerical reconstruction on qualities of point images are investigated. Dependence of the point images on the ratio of the minimum fringe spacing to pixel pitch of the CCD is numerically analyzed. Two-point resolution and magnification are also investigated as a function of pixel numbers by a simulation using a one-dimensional model. In experiments magnified images of biological objects and a resolution target were reconstructed with the same quality as by conventional microscopy.
Estimation of the Effective Permeability in Magnetorheological Fluids (1999)

Magnetorheological (MR) fluids constitute examples of controllable ("smart") fluids, whose Theological properties vary in response to an applied magnetic field. These fluids typically consist of micron-sized, magnetizable particles dispersed in a nonpermeable carrier fluid. The essential characteristic of MR fluids is that they may be continuously and reversibly varied from a state of free flowing liquids in the absence of an applied magnetic field to that of stiff semi-solids in a moderate field. Understanding the magnetic properties of MR fluids is crucial to the design of MR fluid-based devices and it also provides valuable insight into the character of the microstructure responsible for their field-dependent rheology. Prediction of the overall magnetic properties of MR composites is a challenging task, however, due to the highly nonlinear and strongly spatially variable nature of the magnetization of the constituents. In this paper we propose a model for this behavior that is based on the mathematical theory of homogenization. We derive effective equations that govern the magnetic response of (periodically arranged) particle-chains through magnetic saturation. Comparisons of numerical results for these equations with experimental data show good agreement which suggests that our approach could be useful in the design of improved MR fluids.
Traces d'Interaction au sein d'un Environnement de Collaboration (2011)

National audience
Lifetime risk of suicide for affective disorder, alcoholism and schizophrenia (1998)

The lifetime suicide risk figures often quoted in the literature appear to be too high.
Omeprazole and H2-receptor antagonists in the acute treatment of duodenal ulcer, gastric ulcer and reflux oesophagitis: a meta-analysis. (1995)

This paper is a meta-analysis of 30 published, double-blind clinical trials comparing omeprazole with ranitidine or cimetidine for the treatment of duodenal ulcer, gastric ulcer and reflux oesophagitis. These studies compare the recommended doses of omeprazole with those for ranitidine and cimetidine, and the confidence intervals for the therapeutic gain show that the findings are highly reliable. The difference in healing rates favoured omeprazole over ranitidine in patients with duodenal ulcer after 2 weeks of treatment (15.2 percentage units; P < 0.001), and after 4 weeks of treatment in patients with gastric ulcer (9.9 percentage units; P = 0.005), or reflux oesophagitis (23 percentage units; P < 0.001). Similarly, omeprazole gave a 20.6 percentage units higher average healing rate than cimetidine in patients with duodenal ulcer after 2 weeks of treatment (P < 0.0001). Significantly more patients treated with omeprazole were free of symptoms at their first follow-up visit than patients treated with ranitidine or cimetidine.
Augmenting supervised neural networks with unsupervised objectives for large-scale image classification (2016)

Unsupervised learning and supervised learning are key research topics in deep learning. However, as high-capacity supervised neural networks trained with a large amount of labels have achieved remarkable success in many computer vision tasks, the availability of large-scale labeled images reduced the significance of unsupervised learning. Inspired by the recent trend toward revisiting the importance of unsupervised learning, we investigate joint supervised and unsupervised learning in a large-scale setting by augmenting existing neural networks with decoding pathways for reconstruction. First, we demonstrate that the intermediate activations of pretrained large-scale classification networks preserve almost all the information of input images except a portion of local spatial details. Then, by end-to-end training of the entire augmented architecture with the reconstructive objective, we show improvement of the network performance for supervised tasks. We evaluate several variants of autoencoders, including the recently proposed what-where autoencoder that uses the encoder pooling switches, to study the importance of the architecture design. Taking the 16-layer VGGNet trained under the ImageNet ILSVRC 2012 protocol as a strong baseline for image classification, our methods improve the validation-set accuracy by a noticeable margin.
Synthesis and characterization of quinone-substituted octaalkyl porphyrin monomers and dimers (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of quinone-substituted octaalkyl porphyrin monomers and dimersJonathan L. Sessler, Martin R. Johnson, Stephen E. Creager, James C. Fettinger, and James A. IbersCite this: J. Am. Chem. Soc. 1990, 112, 25, 9310–9329Publication Date (Print):December 1, 1990Publication History Published online1 May 2002Published inissue 1 December 1990https://doi.org/10.1021/ja00181a038RIGHTS & PERMISSIONSArticle Views678Altmetric-Citations122LEARN 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 InReddit PDF (2 MB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Molecular Cloning, Genomic Structure, and Expression Analysis of MUC20, a Novel Mucin Protein, Up-regulated in Injured Kidney (2004)

Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis in the world. Here, we identify a cDNA encoding a novel mucin protein, shown previously to be up-regulated in IgAN patients, from a human kidney cDNA library. This protein contains a mucin tandem repeat of 19 amino acids consisting of many threonine, serine, and proline residues and likely to be extensively O-glycosylated; thus, this gene was classified in the mucin family and named MUC20. The human MUC20 gene contains at least four exons and is localized close to MUC4 on chromosome 3q29. We found variations in repeat numbers in the mucin tandem domain, suggesting polymorphism of this region. Northern blot and reverse transcription-PCR analyses revealed that human MUC20 mRNA was expressed most highly in kidney and moderately in placenta, colon, lung, prostate, and liver. Immunohistochemical analysis of human kidney revealed that MUC20 protein was localized in the proximal tubules. Immunoblotting analysis of MUC20 proteins produced in Madin-Darby canine kidney and HEK293 cells indicated the localization of MUC20 protein in a membrane fraction and extensive posttranslational modification. Immunoelectron microscopy of MUC20-producing Madin-Darby canine kidney cells demonstrated that MUC20 protein was localized on the plasma membrane. Expression of MUC20 mRNA in a human kidney cell line was up-regulated by tumor necrosis factor-alpha, phorbol 12-myristate 13-acetate, or lipopolysaccharide. Two species of MUC20 mRNA (hMUC20-L and hMUC20-S), resulting from alternative transcription, were identified in human tissue, whereas only one variant was observed in mouse tissues. Mouse MUC20 mRNA was expressed in the epithelial cells of proximal tubules, and the expression increased dramatically with the progression of lupus nephritis in the kidney of MRL/MpJ-lpr/lpr mice. Moreover, the expression of mouse MUC20 was augmented in renal tissues acutely injured by cisplatin or unilateral ureteral obstruction. These characteristics suggest that the production of MUC20 is correlated with development and progression of IgAN and other renal injuries.
Developments in mud filtration technology in the sugarcane industry (2014)

Dirt collected with sugarcane is processed and separated from the juice in the sugar factory by filtration equipment for return to the cane fields. New technologies over the past decade have enabled performance improvements to be obtained for this key unit operation. Filter mud product still contains a reasonable amount of sugar and the transportation of high moisture mud product has considerable cost. Australia’s traditional approach has been to use Rotary Vacuum Filters for processing and separating mud and other impurities from juice, but in recent years there has been interest in reducing sugar losses and transportation costs through utilisation of new technologies such as Horizontal Bed Filters, Vacuum Belt Press Filters, Membrane Press Filters and Centrifuges. Increasingly, these alternative equipment are being installed in new factories. This chapter describes the general principles of mud filtration theory and mud conditioning followed by a detailed description and review of the various filtration technologies and analysis of the relative merits associated with the equipment.
Highly diastereoselective synthesis of densely functionalized cyclopentanoids by intramolecular azomethine imine cycloadditions in sugar templates (1997)

Conversion of a sugar to a δ,Îµ-unsaturated aldehyde, and subsequent condensation of the aldehyde moiety with BnNHNHCO2Et, yields the respective azomethine imine intermediate dipole which adds intramolecularly to the existing double bond, thus generating a bicyclic adduct with high diastereoselectivity.
Asymmetric hydroformylation of styrene catalyzed by platinum complexes of chiral diphosphites with atropisomeric terminal moieties (2001)

To study the nature of steric and electronic effects of diphosphites, a novel diphosphite was synthesized and tested with regard of its catalytic performance in the hydroformylation of styrene catalyzed by platinum complexes. The novel ligand 3 was prepared by the reaction of enantiomerically pure pentane-2,4-diol with (S)-2-chloro-5,5',6,6',7,7',8,8'-octahydro-dinaphtho[2,1-d:1',2'-f][1,3,2]dioxaphosphepine based on H 8 -BINOL (H 8 -BINOL = 5,5',6,6',7,7',8,8'-octahydro-1,1'-bi-2-naphthol). For a comparative study, the BINOL (1,1'-bi-2-naphthol) based analogue 4 of 3 has also been synthesized. The highest chemoselectivity to aldehyde (71%) and regioselectivity to branched aldehyde (85%) with an enantiomer excess (ee) of 86% was obtained with the platinum(II)-SnCl 2 catalytic system associated with (2S,4S)-bis(S)-3.Key words: asymmetric hydroformylation, chirality, homogeneous catalysis, P ligands, platinum.
MICROCALORIMETRIC STUDIES ON GERMINATIONS OF CEREALS (1952)

Experiments have been performed on seedlings of many species of cultivated plants with a new Tian-Calvet microcalorimeter installed at the University of Montreal. The characteristic elements of the curve of thermogenesis are first described on wheat germinations and their variations discussed in function of temperature, preliminary dehydration, substances in solution in the soaking liquid: salts, alcohol, auxins, etc. Then comparisons are made between germinative thermogeneses of oats, rye, barley, corn, flax, tomatoes, etc., showing the numerous possible applications of microcalorimetry in plant studies and agronomy.
Report of the Secretary-Treasurer for the Year 1932-33 (1933)

Journal Article Report of the Secretary-Treasurer for the Year 1932–33 Get access C. S. Paine C. S. Paine Search for other works by this author on: Oxford Academic Google Scholar Journal of American History, Volume 20, Issue 2, September 1933, Pages 239–246, https://doi.org/10.2307/1896992 Published: 01 September 1933
Application of a diffusion‐erosion model to alluvial channels which degrade due to base‐level lowering (1988)

Abstract The applicability of a diffusion‐erosion model that predicts transient longitudinal profiles of degrading alluvial channels has already been demonstrated in laboratory experiments, and is here applied to some field examples. By fitting simulated longitudinal profiles to measured ones for several streams (with discharge 0.04< Q 5 <680 m 3 s −1 ) diffusion‐erosion coefficients, K , were determined which are well correlated to discharge and drainage area. Headward knickpoint migration which results from base‐level lowering was also treated through the diffusion‐erosion model. Theoretically, the distance of a knickpoint from the mouth of a tributary should be proportional to the square root of the time that elapsed since the base‐level was lowered. Field observations are in accordance with these theoretical considerations. Use of the model is discussed for prediction of erosion and for assessment of the age of alluvial fault scarps crossed by streams.
Improved Method for Use of Chelation to Free Stuck Pipe and Enhance Treatment of Lost Returns (2007)

Abstract This paper describes how intentionally increasing the permeability of a non-aqueous fluid (NAF) filter cake can enhance treatments to free differentially stuck pipe and recover from lost returns. NAFs are well known for their ability to deposit thin, low-permeability filter cakes that reduce the risk of differential sticking. Yet, differential sticking still occurs and techniques to free the pipe have largely been ineffective. In addition, lost returns in NAF continue to be one of the industry's most difficult and expensive problems to solve. The operator has developed an improved technique to increase the permeability of a NAF filter cake. The technique involves locally soaking the cake using a combination treatment that first conditions the cake and then removes a significant amount of the weighting material. Laboratory experiments have shown the technique can increase cake permeability by more than 850 fold. There are at least two applications for this treatment. In the first, a pill is spotted across pipe segments (e.g., drill collars) believed to be differentially stuck. By increasing the cake permeability, pressure is allowed to penetrate the cake underneath the pipe, allowing it to more easily become free. Dissolving barite also reduces the shear strength of the filter cake, which may also facilitate freeing stuck pipe. A second application is to enhance the performance of high fluid loss lost circulation material (LCM) treatments after NAF has damaged the fracture face permeability. Increased permeability enhances loss of the LCM carrier fluid and development of the immobile mass required to stop the growth of the fracture induced during lost returns. Formation integrity can then be rebuilt using rock mechanics-based techniques.
Accelerating cross-project knowledge collaboration using collaborative filtering and social networks (2005)

Vast numbers of free/open source software (F/OSS) development projects use hosting sites such as Java.net and Source-Forge.net.These sites provide each project with a variety of software repositories (e.g.repositories for source code sharing, bug tracking, discussions, etc.) as a media for communication and collaboration.They tend to focus on supporting rich collaboration among members in each project.However, a majority of hosted projects are relatively small projects consisting of few developers and often need more resources for solving problems.In order to support crossproject knowledge collaboration in F/OSS development, we have been developing tools to collect data of projects and developers at SourceForge, and to visualize the relationship among them using the techniques of collaborative filtering and social networks.The tools help a developer identify "who should I ask?" and "what can I ask?" and so on.In this paper, we report a case study of applying the tools to F/OSS projects data collected from SourceForge and how effective the tools can be used for helping cross-project knowledge collaboration.
Common idiotypic determinant associated with human antibodies to hepatitis B surface antigen. (1983)

Anti-Id antisera generated to purified anti-HBs isolated from two different individuals recognized a common idiotype. This idiotype was detected in purified anti-Hbs preparations from three individuals and also in anti-HBs-positive sera obtained from six hemophilic patients. The ability of both HBsAg and a virus-derived HBsAg native polypeptide to inhibit the idiotype-anti-idiotype reaction suggested that the anti-HBs idiotype was associated with the antibody-combining site.
'Minimal' DNA-intercalating agents as anti-tumour drugs: 2-styrylquinoline analogues of amsacrine. (1987)

A series of analogues of amsacrine have been prepared by replacing the acridine with a variety of other chromophores, in a search for 'minimal' DNA-intercalating anti-tumour agents which might show superior distributive properties as a consequence of lower levels of binding to cellular macromolecules. 2-Styrylquinoline derivatives did show in vivo anti-leukaemic activity, but none of the compounds was superior to amsacrine itself.
TCP performance in WCDMA-based cellular wireless IP networks (2002)

The performance of TCP (transmission control protocol) is evaluated for downlink data transmission in a cellular WCDMA (wideband code division multiple access) network where variable rate transmission is supported at the RLC (radio link control)/MAC (medium access control) level. A simple rate search procedure (based on the number of simultaneous TCP connections and the channel condition) is proposed for the RLC/MAC level transmission rate selection for downlink data transmission. The dynamic rate variation is assumed to be achieved by using single-code transmission with variable spreading factor, where the spreading factor varies inversely with the transmission rate. A novel 'mean-sense' approach to calculate intercell interference in such an environment is developed assuming homogeneous traffic load (in terms of active TCP connections) in different cells. The impact of the different physical layer, RLC/MAC layer and TCP parameters on the end-to-end throughput performance are investigated by simulating the system dynamics under multiple concurrent TCP connections.