gebhart/patrepeval huggingface dataset:
Method for evaluation of stemming algorithms based on error counting (1996)

In most previous studies, the effectiveness of stemming algorithms has been compared by determining the retrieval performance for various experimental test collections. The present work assesses performance by counting the number of identifiable errors during the stemming of words from various text samples. This entails manual grouping of the words in each sample; software has been developed to facilitate this. After grouping, the words are stemmed and indices are then computed which represent the rate of understemming and overstemming. Results are presented for three stemmers (Lovins, Porter, and Paice/Husk), in each case using three distinct text samples. Although the results are not entirely clear cut, it appears that the Lovins stemmer is inferior to the other two in terms of general accuracy. The way in which the indices vary with the size of the text sample is also investigated. © 1996 John Wiley & Sons, Inc.
IP MULTIMEDIA SUBSYSTEM - NetCAPE: Enabling Seamless IMS Service Delivery across Heterogeneous Mobile Networks (2007)

An evolving wireless world is constantly providing users with a wider set of access technologies to choose from, each with different capabilities and properties. In this world, IMS as defined by 3GPP provides an enabling, standardized multimedia architecture that is access independent, hence, providing service convergence. This trend is accompanied by an increasing number of multimode terminals so that inter-access- system-service continuity gains relevance. This article presents the architectural framework of NetCAPE (networking context aware policy environment), which addresses the optimization of mobility management in such a heterogeneous environment while interacting with IMS applications to enable seamless service delivery across heterogeneous mobile networks; even as the mobility offered by the underlying network remains transparent to IMS applications. Although the focus is on 3GPP-based mobile networks, the framework also incorporates wired access technologies, hence, taking a further step toward fixed mobile convergence (FMC). First results are presented highlighting the improvements gained by applying NetCAPE concepts.
Cardiotrophin‐1 requires LIFRβ to promote survival of mouse motoneurons purified by a novel technique (1999)

The cytokines ciliary neurotrophic factor (CNTF) and leukemia inhibitory factor (LIF) signal through a receptor complex formed between two transmembrane proteins, gp130 and LIFRβ. In addition, CNTF also uses a ligand-binding component which is anchored to the cell membrane. In the case of cardiotrophin-1 (CT-1), LIFRβ is also required in cardiomyocytes, but this has not been proven in neurons, and published data suggest that motoneurons may use a different receptor complex. We used Lifrβ knockout mice to assess the requirement for this receptor component in the signal transduction of CT-1 in motoneurons. To study purified motoneurons from such mutants, we have developed a method allowing for isolation of highly purified mouse motoneurons. This protocol is based on the immunoaffinity purification of motoneurons using antibodies against the extracellular domain of the neurotrophin receptor, p75, followed by cell sorting using magnetic microbeads. We show that CNTF, LIF, and CT-1 are unable to promote the survival of motoneurons derived from homozygous Lifrβ−/− mutant embryos. Thus, LIFRβ is absolutely required to transduce the CT-1 survival signal in motoneurons. J Neurosci Res 55:119–126, 1999. © 1999 Wiley-Liss, Inc.
2-methoxyestradiol up-regulates death receptor 5 and induces apoptosis through activation of the extrinsic pathway. (2003)

2-Methoxyestradiol (2ME2), a natural metabolite of estradiol, is a potent antitumor and antiangiogenic agent. In vitro, 2ME2 inhibits the proliferation of a wide variety of cell lines and primary cultures, and in numerous models in vivo, it has been shown to be an effective inhibitor of tumor growth and angiogenesis. 2ME2 is currently in several Phase I and Phase II clinical trials under the name Panzem. Although various molecular targets have been proposed for this compound, the mechanism by which 2ME2 exerts its effects is still uncertain. This study shows that 2ME2 uses the extrinsic pathway for induction of apoptosis. 2ME2 treatment results in up-regulation of death receptor 5 (DR5) protein expression in vitro and in vivo and renders cells more sensitive to the cytotoxic activities of the DR5 ligand tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). 2ME2-induced apoptosis requires caspase activation and kinetic studies show the sequential activation of caspase-8, caspase-9, and caspase-3. Blockage of death receptor signaling by expression of dominant-negative Fas-associated death domain severely attenuates the ability of 2ME2 to induce apoptosis. Because 2ME2 administration has not manifested dose-limiting toxicity in the clinic, DR5 expression may serve as a surrogate marker for biological response.
PENICILLIN-BINDING PROTEINS AND THE MECHANISM OF ACTION OF BETA-LACTAM ANTIBIOTICS (1983)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
A Resilient, Untethered Soft Robot (2014)

A pneumatically powered, fully untethered mobile soft robot is described. Composites consisting of silicone elastomer, polyaramid fabric, and hollow glass microspheres were used to fabricate a sufficiently large soft robot to carry the miniature air compressors, battery, valves, and controller needed for autonomous operation. Fabrication techniques were developed to mold a 0.65-meter-long soft body with modified Pneu-Net actuators capable of operating at the elevated pressures (up to 138 kPa) required to actuate the legs of the robot and hold payloads of up to 8 kg. The soft robot is safe to interact with during operation, and its silicone body is innately resilient to a variety of adverse environmental conditions including snow, puddles of water, direct (albeit limited) exposure to flames, and the crushing force of being run over by an automobile.
Large metal ion-centered template reactions. Uranyl complex of cyclopentakis(2-iminoisoindoline) (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLarge metal ion-centered template reactions. Uranyl complex of cyclopentakis(2-iminoisoindoline)Victor W. Day, Tobin J. Marks, and William A. WachterCite this: J. Am. Chem. Soc. 1975, 97, 16, 4519–4527Publication Date (Print):August 1, 1975Publication History Published online1 May 2002Published inissue 1 August 1975https://pubs.acs.org/doi/10.1021/ja00849a012https://doi.org/10.1021/ja00849a012research-articleACS PublicationsRequest reuse permissionsArticle Views533Altmetric-Citations119LEARN 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
A photoreactive derivative of radiolabeled GM1 ganglioside: preparation and use to establish the involvement of specific proteins in GM1 uptake by human fibroblasts in culture (1989)

A new procedure was used to synthesize a derivative of ganglioside GM1 containing a photoreactive nitrophenyl azide group at the end of the fatty acyl moiety, using deAc-deAcyl-GM1 obtained by deacetylation of the sialic acid and deacylation of the ceramide portion of GM1. This deAc-deAcyl-GM1 was first acylated at the long chain base amino group with 12-aminododecanoic acid, which has the amino group protected by a fluorenyl residue, and tritium labeled at the sialic acid amino group with [3H]acetic anhydride of very high specific radioactivity. The fluorenyl group removed by ammonia treatment was substituted by a nitrophenyl azide group. Cultured human fibroblasts were exposed to mixtures of radioactive photolabeled GM1 and cold natural GM1 (1:10 by mol) for different times and then illuminated and the radioactive protein patterns studied by SDS-PAGE. After 2h of exposure, the photolabeled GM1 was stably associated to the cells and underwent almost no metabolic processing, behaving exactly as the underivatized natural GM1. Under these conditions very few proteins became radioactive: one, of about 30 kDa, interacted with the ganglioside molecules inserted into the outer membrane layer; three, in the region of 46 kDa, interacted with the portion of associated ganglioside able to be released by trypsin treatment. Thus, it is evident that the ganglioside binding to fibroblasts and insertion into the outer layer of the plasma membrane involve few individual proteins.(ABSTRACT TRUNCATED AT 250 WORDS)
Fabrication of nanoplate resonating structures via micro-masonry (2014)

International audience
DMAP-Catalyzed [3 + 2] and [4 + 2] Cycloaddition Reactions between [60]Fullerene and Unmodified Morita–Baylis–Hillman Adducts in the Presence of Ac2O (2013)

One-step DMAP-catalyzed [3 + 2] and [4 + 2] cycloaddition reactions between C(60) and unmodified Morita-Baylis-Hillman adducts in the presence of Ac(2)O have been developed for the easy preparation of cyclopentene- and cyclohexene-fused [60]fullerene derivatives. When the MBH adducts bear an alkyl group, two different reaction pathways could be controlled selectively depending on the conditions.
Crude extracts of bacterially expressed dsRNA can be used to protect plants against virus infections (2003)

Our approach provides an alternative to genetic transformation of plant species with dsRNA-expressing constructs capable to interfere with plant viruses. The main advantage of this mode of dsRNA production is its simplicity and its extremely low cost compared with the requirements for regenerating transgenic plants. This approach provides a reliable and potential tool, not only for plant protection against virus diseases, but also for the study of gene silencing mechanisms in plant virus infections.
Nanobelts as nanocantilevers (2003)

Semiconducting oxide nanobelts of ZnO have been sectioned and manipulated, for microelectromechanical systems, using an atomic force microscopy probe. Structurally modified nanobelts demonstrate potential for nanocantilever based technologies. With dimensions ∼35–1800 times smaller than conventional cantilevers, the nanocantilevers are expected to have improved physical, chemical, and biological sensitivity for scanning probe microscopy and sensor applications.
Stable Formation of Compositionally Unique Stress Granules in Virus-Infected Cells (2010)

Stress granules are sites of mRNA storage formed in response to a variety of stresses, including viral infections. Here, the mechanisms and consequences of stress granule formation during poliovirus infection were examined. The results indicate that stress granules containing T-cell-restricted intracellular antigen 1 (TIA-1) and mRNA are stably constituted in infected cells despite lacking intact RasGAP SH3-domain binding protein 1 (G3BP) and eukaryotic initiation factor 4G. Fluorescent in situ hybridization revealed that stress granules in infected cells do not contain significant amounts of viral positive-strand RNA. Infection does not prevent stress granule formation in response to heat shock, indicating that poliovirus does not block de novo stress granule formation. A mutant TIA-1 protein that prevents stress granule formation during oxidative stress also prevents formation in infected cells. However, stress granule formation during infection is more dependent upon ongoing transcription than is formation during oxidative stress or heat shock. Furthermore, Sam68 is recruited to stress granules in infected cells but not to stress granules formed in response to oxidative stress or heat shock. These results demonstrate that stress granule formation in poliovirus-infected cells utilizes a transcription-dependent pathway that results in the appearance of stable, compositionally unique stress granules.
Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2 (2011)

RosettaDock has been increasingly used in protein docking and design strategies in order to predict the structure of protein-protein interfaces. Here we test capabilities of RosettaDock 3.2, part of the newly developed Rosetta v3.2 modeling suite, against Docking Benchmark 3.0, and compare it with RosettaDock v2.3, the latest version of the previous Rosetta software package. The benchmark contains a diverse set of 116 docking targets including 22 antibody-antigen complexes, 33 enzyme-inhibitor complexes, and 60 'other' complexes. These targets were further classified by expected docking difficulty into 84 rigid-body targets, 17 medium targets, and 14 difficult targets. We carried out local docking perturbations for each target, using the unbound structures when available, in both RosettaDock v2.3 and v3.2. Overall the performances of RosettaDock v2.3 and v3.2 were similar. RosettaDock v3.2 achieved 56 docking funnels, compared to 49 in v2.3. A breakdown of docking performance by protein complex type shows that RosettaDock v3.2 achieved docking funnels for 63% of antibody-antigen targets, 62% of enzyme-inhibitor targets, and 35% of 'other' targets. In terms of docking difficulty, RosettaDock v3.2 achieved funnels for 58% of rigid-body targets, 30% of medium targets, and 14% of difficult targets. For targets that failed, we carry out additional analyses to identify the cause of failure, which showed that binding-induced backbone conformation changes account for a majority of failures. We also present a bootstrap statistical analysis that quantifies the reliability of the stochastic docking results. Finally, we demonstrate the additional functionality available in RosettaDock v3.2 by incorporating small-molecules and non-protein co-factors in docking of a smaller target set. This study marks the most extensive benchmarking of the RosettaDock module to date and establishes a baseline for future research in protein interface modeling and structure prediction.
Volumetric measurements of bacterial cells and extracellular polymeric substance glycoconjugates in biofilms (2004)

In this study an enrichment culture developed from activated sludge was used to investigate the architecture of fully hydrated multispecies biofilms. The assessment of biofilm structure and volume was carried out using confocal laser scanning microscopy (CLSM). Bacterial cell distribution was determined with the nucleic acid-specific stain SYTO 60, whereas glycoconjugates of extracellular polymeric substances (EPS) were stained with the Alexa-488-labeled lectin of Aleuria aurantia. Digital image analysis was employed for visualization and quantification of three-dimensional CLSM data sets. The specific volumes of the polymeric and cellular biofilm constituents were quantified. In addition, gravimetric measurements were done to determine dry mass and thickness of the biofilms. The data recorded by the CLSM technique and the gravimetric data were then compared. It was shown that the biofilm thicknesses determined with both methods agree well for slow-growing heterotrophic and chemoautotrophic biofilms. In addition, for slow-growing biofilms, the volumes and masses calculated from CLSM and the biomass calculated from gravimetric measurements were also comparable. For fast-growing heterotrophic biofilms cultivated with high glucose concentrations the data sets fit to a lesser degree, but still showed the same common trend. Compared with traditional gravimetric measurements, CLSM allowed differential recording of multiple biofilm parameters with subsequent three-dimensional visualization and quantification. The quantitative three-dimensional results recorded by CLSM are an important basis for understanding, controlling, exploiting, and modeling of biofilms.
Prevention of Endothelial Cell Injury by Activated Protein C: The Molecular Mechanism(s) and Therapeutic Implications (2004)

Activated protein C (APC), a natural anticoagulant, is formed from protein C by the action of thrombin bound to thrombomodulin on the endothelial cell surface. APC regulates the coagulation system by inactivating the activated form of factors V and VIII in the presence of protein S. Tumor necrosis factor-alpha (TNF-alpha) plays critical roles in the development of disseminated intravascular coagulation, acute respiratory distress syndrome and shock in sepsis by inducing endothelial cell damage through activation of neutrophils. APC reduces the pulmonary endothelial cell injury and hypotension in rats administered endotoxin (ET) by inhibiting TNF-alpha production through inhibition of its transcription. Furthermore, APC reduces the ischemia/reperfusion-induced renal injury and the stress-induced gastric mucosal injury in rats. Inhibition by APC of the endothelial cell damage inhibited the decrease in the endothelial production of prostacyclin in vivo. These therapeutic effects could not be attributed to its anticoagulant effects, but to inhibition of TNF-alpha production. APC inhibits ET-induced TNF-alpha production in vitro in human monocytes by inhibiting activation of NFkappaB and AP-1 by inhibiting degradation of IkappaB and mitogen-activated protein kinase pathways, respectively. Recombinant APC was reported to reduce the mortality of patients with severe sepsis. These observations strongly suggest that APC might be involved not only in regulation of the coagulation system, but in regulation of inflammatory responses by preventing endothelial cell injury. Furthermore, APC reduced the spinal cord injury induced by compression-trauma or ischemia/reperfusion by inhibiting TNF-alpha production in rats, suggesting that APC may be a potential therapeutic agent for spinal cord injury in which only limited therapeutic measures are currently available.
Identification of cell culture conditions to control N‐glycosylation site‐occupancy of recombinant glycoproteins expressed in CHO cells (2009)

The effect of different cell culture conditions on N-glycosylation site-occupancy has been elucidated for two different recombinant glycoproteins expressed in Chinese hamster ovary (CHO) cells, recombinant human tissue plasminogen activator (t-PA) and a recombinant enzyme (glycoprotein 2-GP2). Both molecules contain a N-glycosylation site that is variably occupied. Different environmental factors that affect the site-occupancy (the degree of occupied sites) of these molecules were identified. Supplementing the culture medium with additional manganese or iron increased the fraction of fully occupied t-PA (type I t-PA) by approximately 2.5-4%. Decreasing the cultivation temperature from 37 to 33 degrees C or 31 degrees C gradually increased site-occupancy of t-PA up to 4%. The addition of a specific productivity enhancer, butyrate, further increased site-occupancy by an additional 1% under each cultivation temperature tested. In addition, the thyroid hormones triiodothyronine and thyroxine increased site-occupancy of t-PA compared to control conditions by about 2%. In contrast, the addition of relevant nucleoside precursor molecules involved in N-glycan biosynthesis (e.g., uridine, guanosine, mannose) either had no effect or slightly reduced site-occupancy. For the recombinant enzyme (GP2), it was discovered that culture pH and the timing of butyrate addition can be used to control N-glycan site-occupancy within a specific range. An increase in culture pH correlated with a decrease in site-occupancy. Similarly, delaying the timing for butyrate addition also decreased site-occupancy of this molecule. These results highlight the importance of understanding how cell culture conditions and media components can affect the product quality of recombinant glycoproteins expressed in mammalian cell cultures. Furthermore, the identification of relevant factors will enable one to control product quality attributes, specifically N-glycan site-occupancy, within a specific range when applied appropriately.
Analysis of gaseous toxic industrial compounds and chemical warfare agent simulants by atmospheric pressure ionization mass spectrometry (2006)

The suitability of atmospheric pressure chemical ionization mass spectrometry as sensing instrumentation for the real-time monitoring of low levels of toxic compounds is assessed, especially with respect to public safety applications. Gaseous samples of nine toxic industrial compounds, NH3, H2S, Cl2, CS2, SO2, C2H4O, HBr, C6H6 and AsH3, and two chemical warfare agent simulants, dimethyl methylphosphonate (DMMP) and methyl salicylate (MeS), were studied. API-MS proves highly suited to this application, with speedy analysis times (<30 seconds), high sensitivity, high selectivity towards analytes, good precision, dynamic range and accuracy. Tandem MS methods were implemented in selected cases for improved selectivity, sensitivity, and limits of detection. Limits of detection in the parts-per-billion and parts-per-trillion range were achieved for this set of analytes. In all cases detection limits were well below the compounds' permissible exposure limits (PELs), even in the presence of added complex mixtures of alkanes. Linear responses, up to several orders of magnitude, were obtained over the concentration ranges studied (sub-ppb to ppm), with relative standard deviations less than 3%, regardless of the presence of alkane interferents. Receiver operating characteristic (ROC) curves are presented to show the performance trade-off between sensitivity, probability of correct detection, and false positive rate. A dynamic sample preparation system for the production of gas phase analyte concentrations ranging from 100 pptr to 100 ppm and capable of admixing gaseous matrix compounds and control of relative humidity and temperature is also described.