gebhart/patrepeval huggingface dataset:
Optical transients in the WASP survey (2010)

This thesis describes a search for transient phenomena using data from the&#13;\nWide Angle Search for Planets (WASP) observatories. With images taken of the&#13;\nsame region of sky every 15 minutes and a field-of-view of 974 degrees squared,&#13;\nthe WASP survey is ideal for identifying both short and long duration transients&#13;\nto a limiting magnitude of 16 in V. A high cadence wide-field survey of this type&#13;\nhas not been carried out before so provides a different method of sampling variable&#13;\npopulations and has the potential to identify previously unknown phenomena.&#13;\nAn algorithm to carry out a full untargeted search of the database was developed,&#13;\ntested and run on data from 2004, 2006, 2007 and 2008. False positives were&#13;\nrejected based on their proximity to similar magnitude stars, the tightness of the&#13;\nclustering of detections in sky coordinates, the focus of the images and the number&#13;\nof corroborating detections.&#13;\nOverall, 44 cataclysmic variable candidates, 144 extreme flare candidates, 63&#13;\nvariable star candidates and 57 transients of unknown type were identified. The cataclysmic&#13;\nvariable candidates showed similarities to the currently known population&#13;\nalthough some selection effects were uncovered. Of particular note were two new WZ&#13;\nSge systems, an eclipsing system with a period of 540 minutes and an object with&#13;\nan M-star spectrum and broad Balmer lines but no visible white dwarf. The flares&#13;\nare some of the largest ever observed on M-type stars. The largest of these released&#13;\n~1035erg in the V-band alone. A candidate flare was also identified on a G-type&#13;\nstar releasing 1.6×1037erg in the V-band. Alternatively, it may be unrelated to the&#13;\nG-star and could be a gamma ray burst or similar transient without a persistent&#13;\ncounterpart. A known supernova and two known novae were also identified.
Cytotoxic potential of ribonuclease and ribonuclease hybrid proteins. (1991)

Pancreatic RNase injected into Xenopus oocytes abolishes protein synthesis at concentrations comparable to the toxin ricin yet has no effect on oocyte protein synthesis when added to the extracellular medium. Therefore RNase behaves like a potent toxin when directed into a cell. To explore the cytotoxic potential of RNase toward mammalian cells, bovine pancreatic ribonuclease A was coupled via a disulfide bond to human transferrin or antibodies to the transferrin receptor. The RNase hybrid proteins were cytotoxic to K562 human erythroleukemia cells in vitro with an IC50 around 10(-7) M whereas greater than 10(-5) M native RNase was required to inhibit protein synthesis. Cytotoxicity requires both components of the conjugate since excess transferrin or ribonuclease inhibitors added to the medium protected the cells from the transferrin-RNase toxicity. Compounds that interfere with transferrin receptor cycling and compartmentalization such as ammonium chloride decreased the cytotoxicity of transferrin-RNase. After a dose-dependent lag period inactivation of protein synthesis by transferrin-RNase followed a first-order decay constant. In a clonogenic assay that measures the extent of cell death 1 x 10(-6) M transferrin-RNase killed at least 4 logs or 99.99% of the cells whereas 70 x 10(-6) M RNase was nontoxic. These results show that RNase coupled to a ligand can be cytotoxic. Human ribonucleases coupled to antibodies also may exhibit receptor-mediated toxicities providing a new approach to selective cell killing possibly with less systemic toxicity and importantly less immunogenicity than the currently employed ligand-toxin conjugates.
Gas flow and mixing in the airways (1994)

The dominant mechanism for the enhancement of gas transport along airways at high frequency is likely to lie in the coupling of the secondary motions caused by airway curvature with the oscillatory longitudinal flow. However, laboratory experiments and theoretical analyses have led only to an accurate simulation of the phenomena in idealized geometries, not in real lungs.
Proteolytic inactivation of the leukocyte C5a receptor by proteinases derived from Porphyromonas gingivalis (1996)

The anaerobic bacterium Porphyromonas gingivalis has been implicated as a primary causative agent in adult periodontitis. Several proteinases are produced by this bacterium, and it is suggested that they contribute to virulence and to local tissue injury resulting from infection by P. gingivalis. Cysteine proteinases with specificities to cleave either Arg-X or Lys-X peptide bonds (i.e., gingipains) have been characterized as predominant enzymes associated with vesicles shed from the surface of this bacterium. It has recently been demonstrated that these proteinases are capable of degrading the blood complement component C5, resulting in the generation of biologically active C5a. By using an affinity-purified rabbit antibody raised against residues 9 to 29 of the C5a receptor (C5aR; CD88), we demonstrate that noncysteinyl proteinases associated with vesicles obtained from P. gingivalis cleave the C5aR on human neutrophils. Proteolytic attack of the C5aR by enzymes from the P. gingivalis vesicles was inhibited by TPCK (tolylsullonyl phenylalanyl chloromethyl ketone), PMSF (phenylmethylsulfonyl fluoride), and dichloroisocoumarin, suggesting that serine proteinases are primarily responsible for this degradative activity. The purified vesicle proteinase Lys-gingipain but not Arg-gingipain also cleaved the N-terminal region of the C5aR on the human neutrophils. Lys-gingipain activity was essentially resistant to these inhibitors but was inhibited by TLCK (Nalpha-p-tosyl-L-lysine chloromethyl ketone) and iodoacetamide. A synthetic peptide that mimics the N-terminal region of C5aR (residues 9 to 29; PDYGHY DDKDTLDLNTPVDKT) was readily cleaved by chymotrypsin but not by trypsin, despite the presence of two potential trypsin (i.e., lysyl-X) cleavage sites. The specific sites of cleavage in the C5aR 9-29 peptide were determined by mass spectroscopy for both chymotrypsin and Lys-gingipain digests. This analysis demonstrated that the C5aR peptide is susceptible to cleavage at both potential Lys-gingipain sites (i.e., between residues 17 and 18 [K-D] and 28 and 29 [K-T]) and at two chymotrypsin sites (between residues 14 and 15 [Y-D] and 20 and 21 [L-D]), respectively. These studies suggest that P. gingivalis contains at least two enzymes capable of cleaving the C5aR, Lys-gingipain and a second nontryptic serine proteinase that is distinct from either Arg- or Lys-gingipain.
DESIGN METHOD OF UNIFORM LOADING SYSTEM USING AIRBAGS IN STRUCTURE TEST (2012)

Aiming at a new structural loading type by airbags,the paper establishes the mechanical model of airbag loading system and discusses some key points,showing that,the surface tension of airbags should be eliminated in the direction of large curvature of the loading surface,but the elimination of surface tension is not necessary in the direction of small curvature.To reduce the experimental cost and facilitate experimental observation,surface tension is restrained by boundary isolation rather than the traditional way of metal containers.Then a corresponding discipline of loading control is designed as well as an approach of system verification.The feasibility of airbag loading system has been demonstrated by a model test example of aircraft fuselage frame.
Bioorthogonal chemical tagging of protein cholesterylation in living cells (2011)

We report the first chemical probe for bioorthogonal chemical tagging of post-translationally cholesterylated proteins with an azide in living cells. This enables rapid multiplexed fluorescence detection and affinity labelling of protein cholesterylation, as exemplified by Sonic hedgehog protein, opening up new approaches for the de novo identification of cholesterylated proteins.
Hydrogen-Induced Ostwald Ripening at Room Temperature in a Pd Nanocluster Film (2008)

The structural and morphological changes occurring in an ensemble of vapor deposited palladium nanoclusters have been studied after several hydrogenation cycles with x-ray diffraction, extended x-ray-absorption fine structure spectroscopy, Rutherford backscattering spectrometry, and STM. Initial hydrogenation increased the cluster size, a result that is attributed to hydrogen-induced Ostwald ripening. This phenomenon originates from the higher mobility of palladium atoms resulting from the low sublimation energy of the palladium hydride as compared to that of the palladium metal. The universality of this phenomenon makes it important for the application of future nanostructured hydrogen storage materials.
Structure of the Eukaryotic Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand (2006)

Riboswitches are untranslated regions of messenger RNA, which adopt alternate structures depending on the binding of specific metabolites. Such conformational switching regulates the expression of proteins involved in the biosynthesis of riboswitch substrates. Here, we present the 2.9 angstrom-resolution crystal structure of the eukaryotic Arabidopsis thaliana thiamine pyrophosphate (TPP)-specific riboswitch in complex with its natural ligand. The riboswitch specifically recognizes the TPP via conserved residues located within two highly distorted parallel "sensor" helices. The structure provides the basis for understanding the reorganization of the riboswitch fold upon TPP binding and explains the mechanism of resistance to the antibiotic pyrithiamine.
Craniovertebral Junction Realignment for the Treatment of Basilar Invagination With Syringomyelia: Preliminary Report of 12 Cases (2005)

Twelve selected patients, eight males and four females aged 14 to 50 years, with syringomyelia associated with congenital craniovertebral bony anomalies including basilar invagination and fixed atlantoaxial dislocation, and associated Chiari I malformation in eight, were treated by atlantoaxial joint manipulation and restoration of the craniovertebral region alignment between October 2002 and March 2004. Three patients had a history of trauma prior to the onset of symptoms. Spastic quadriparesis and ataxia were the most prominent symptoms. The mean duration of symptoms was 11 months. The atlantoaxial dislocation and basilar invagination were reduced by manual distraction of the facets of the atlas and axis, stabilization by placement of bone graft and metal spacers within the joint, and direct atlantoaxial fixation using an inter-articular plate and screw method technique. Following surgery all patients showed symptomatic improvement and restoration of craniovertebral alignment during follow up from 3 to 20 months (mean 7 months). Radiological improvement of the syrinx could not be evaluated as stainless steel metal plates, screws, and spacers were used for fixation. Manipulation of the atlantoaxial joints and restoring the anatomical craniovertebral alignments in selected cases of syringomyelia leads to remarkable and sustained clinical recovery, and is probably the optimum surgical treatment.
Depth Reconstruction and Computer-Aided Polyp Detection in Optical Colonoscopy Video Frames (2016)

We present a computer-aided detection algorithm for polyps in optical colonoscopy images. Polyps are the precursors to colon cancer. In the US alone, more than 14 million optical colonoscopies are performed every year, mostly to screen for polyps. Optical colonoscopy has been shown to have an approximately 25% polyp miss rate due to the convoluted folds and bends present in the colon. In this work, we present an automatic detection algorithm to detect these polyps in the optical colonoscopy images. We use a machine learning algorithm to infer a depth map for a given optical colonoscopy image and then use a detailed pre-built polyp profile to detect and delineate the boundaries of polyps in this given image. We have achieved the best recall of 84.0% and the best specificity value of 83.4%.
APRIL and BCMA promote human multiple myeloma growth and immunosuppression in the bone marrow microenvironment (2016)

Here we show that overexpression or activation of B-cell maturation antigen (BCMA) by its ligand, a proliferation-inducing ligand (APRIL), promotes human multiple myeloma (MM) progression in vivo. BCMA downregulation strongly decreases viability and MM colony formation; conversely, BCMA overexpression augments MM cell growth and survival via induction of protein kinase B (AKT), MAPK, and nuclear factor (NF)-κB signaling cascades. Importantly, BCMA promotes in vivo growth of xenografted MM cells harboring p53 mutation in mice. BCMA-overexpressing tumors exhibit significantly increased CD31/microvessel density and vascular endothelial growth factor compared with paired control tumors. These tumors also express increased transcripts crucial for osteoclast activation, adhesion, and angiogenesis/metastasis, as well as genes mediating immune inhibition including programmed death ligand 1, transforming growth factor β, and interleukin 10. These target genes are consistently induced by paracrine APRIL binding to BCMA on MM cells, which is blocked by an antagonistic anti-APRIL monoclonal antibody hAPRIL01A (01A). 01A is cytotoxic against MM cells even in the presence of protective bone marrow (BM) myeloid cells including osteoclasts, macrophages, and plasmacytoid dendritic cells. 01A further decreases APRIL-induced adhesion and migration of MM cells via blockade of canonical and noncanonical NF-κB pathways. Moreover, 01A prevents in vivo MM cell growth within implanted human bone chips in SCID mice. Finally, the effect of 01A on MM cell viability is enhanced by lenalidomide and bortezomib. Taken together, these data delineate new molecular mechanisms of in vivo MM growth and immunosuppression critically dependent on BCMA and APRIL in the BM microenvironment, further supporting targeting this prominent pathway in MM.
Hedera: dynamic flow scheduling for data center networks (2010)

Today's data centers offer tremendous aggregate bandwidth to clusters of tens of thousands of machines. However, because of limited port densities in even the highest-end switches, data center topologies typically consist of multi-rooted trees with many equal-cost paths between any given pair of hosts. Existing IP multipathing protocols usually rely on per-flow static hashing and can cause substantial bandwidth losses due to long-term collisions.In this paper, we present Hedera, a scalable, dynamic flow scheduling system that adaptively schedules a multi-stage switching fabric to efficiently utilize aggregate network resources. We describe our implementation using commodity switches and unmodified hosts, and show that for a simulated 8,192 host data center, Hedera delivers bisection bandwidth that is 96% of optimal and up to 113% better than static load-balancing methods.
The World Spider Catalog (2000)

Submitted by Sandra Pereira (srpereira@ufrrj.br) on 2019-05-07T13:23:56Z No. of bitstreams: 1 2011 - Rafael Prezzi Indicatti.pdf: 855417 bytes, checksum: c447f2c33b8662a3edffa1c19c57f575 (MD5)
RNA Interference: From Basic Research to Therapeutic Applications (2009)

An efficient mechanism for the sequence-specific inhibition of gene expression is RNA interference. In this process, double-stranded RNA molecules induce cleavage of a selected target RNA (see picture). This technique has in recent years developed into a standard method of molecular biology. Successful applications in animal models have already led to the initiation of RNAi-based clinical trials as a new therapeutic option.Only ten years ago Andrew Fire and Craig Mello were able to show that double-stranded RNA molecules could inhibit the expression of homologous genes in eukaryotes. This process, termed RNA interference, has developed into a standard method of molecular biology. This Review provides an overview of the molecular processes involved, with a particular focus on the posttranscriptional inhibition of gene expression in mammalian cells, the possible applications in research, and the results of the first clinical studies.
Origin of Enhanced Stem Cell Growth and Differentiation on Graphene and Graphene Oxide (2011)

The culture of bone marrow derived mesenchymal stem cells (MSCs), as well as the control of its differentiation toward different tissue lineage, is a very important part of tissue engineering, where cells are combined with artificial scaffold to regenerate tissues. Graphene (G) and graphene oxide (GO) sheets are soft membranes with high in-plane stiffness and can potentially serve as a biocompatible, transferable, and implantable platform for stem cell culture. While the healthy proliferation of stem cells on various carbon platforms has been demonstrated, the chemical role of G and GO, if any, in guiding uncommitted stem cells toward differentiated cells is not known. Herein, we report that the strong noncovalent binding abilities of G allow it to act as a preconcentration platform for osteogenic inducers, which accelerate MSCs growing on it toward the osteogenic lineage. The molecular origin of accelerated differentation is investigated by studying the binding abilities of G and GO toward different growth agents. Interestingly, differentiation to adipocytes is greatly suppressed on G because insulin, which is a key regulator for the synthesis of fatty acids, is denatured upon π-π adsorption on G; in contrast, GO does not interfere with adipogenesis due to electrostatic binding with insulin. The different binding interactions and their subsequent influence on stem cell growth and differentiation are ascribed to different degrees of π-π stacking and electrostatic and hydrogen bonding mediated by G and GO.
The importance of nanoparticle shape in cancer drug delivery (2014)

Pioneering studies on nanoparticles show that nonspherical shapes show great promise as cancer drug delivery vectors. Filamentous or worm-like micelles together with other rare morphologies such as needles or disks may become the norm for next-generation drug carriers, though at present, traditional spherical micelles remain the dominant shape of nanocarriers described in the literature due to synthesis and testing difficulties. The few reports that do exist describing nonspherical nanoparticles show a number of favorable properties that should encourage more efforts to develop facile and versatile nanoparticle synthesis methodologies with the flexibility to create different shapes, tunable sizes and adaptable surface chemistries. In addition, the authors note that there is a current lack of understanding into the factors governing (and optimizing) the inter-relationships of size, surface characteristics and shapes of many nanoparticles proposed for use in cancer therapy.
On Bayesian new edge prediction and anomaly detection in computer networks (2019)

Monitoring computer network traffic for anomalous behaviour presents an important security challenge. Arrivals of new edges in a network graph represent connections between a client and server pair not previously observed, and in rare cases these might suggest the presence of intruders or malicious implants. We propose a Bayesian model and anomaly detection method for simultaneously characterising existing network structure and modelling likely new edge formation. The method is demonstrated on real computer network authentication data and successfully identifies some machines which are known to be compromised.
Fatty acid synthesis by the liver perfused with deuterated and tritiated water (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFatty acid synthesis by the liver perfused with deuterated and tritiated waterManohar Wadke, Henri Brunengraber, John M. Lowenstein, J. J. Dolhun, and G. P. ArsenaultCite this: Biochemistry 1973, 12, 14, 2619–2624Publication Date (Print):July 3, 1973Publication History Published online1 May 2002Published inissue 3 July 1973https://pubs.acs.org/doi/10.1021/bi00738a011https://doi.org/10.1021/bi00738a011research-articleACS PublicationsRequest reuse permissionsArticle Views149Altmetric-Citations59LEARN 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
An ambulatory dyskinesia monitor (2000)

This method provides an accurate, objective means for dyskinesia assessment, and compares favourably with established methods currently used.
Kinase Inhibitor Selectivity Profiling Using Differential Scanning Fluorimetry (2011)

Fast, robust, and inexpensive screening methods are the heart of drug discovery processes. Moreover, it is useful to have access to several established assay formats, for validation purposes. If a targeted protein is an enzyme, the logical and widely used approach is the direct measurement of the effect of the added ligands on its activity. A variety of enzymatic assay formats have been successfully applied for inhibitor screening of protein kinases. However, enzymatic assays require an active enzyme with a known substrate and often time-consuming assay optimization. Several alternative approaches have been recently developed that detect binding of ligands to proteins. This chapter overviews and provides the experimental protocol of the successful application of differential scanning fluorimetry (DSF) in our laboratory for fast and robust screening of medium-sized (<10,000) inhibitor libraries. DSF monitors the thermal stabilization of the native protein structure upon ligand binding. It allows selectivity profiling of any protein kinase without prior knowledge of either substrate or activity of the kinase under investigation. Comparative studies revealed that generated data is highly reproducible and correlates well with the results from other ligand binding methodologies, direct binding constants as well as enzymatic assays.