gebhart/patrepeval huggingface dataset:
SLAng: A language for defining service level agreements (2004)

Application or web services are increasingly being used across organisational boundaries. Moreover, new services are being introduced at the network and storage level. Languages to specify interfaces for such services have been researched and transferred into industrial practice. We investigate end-to-end quality of service (QoS) and highlight that QoS provision has multiple facets and requires complex agreements between network services, storage services and middleware services. We introduce SLAng, a language for defining Service Level Agreements (SLAs) that accommodates these needs. We illustrate how SLAng is used to specify QoS in a case study that uses a web services specification to support the processing of images across multiple domains and we evaluate our language based on it.
Novel biological function of sialic acid (<i>N</i>‐acetylneuraminic acid) as a hydrogen peroxide scavenger (2004)

We have found that N-acetylneuraminic acid (NANA) consumes toxic hydrogen peroxide (H(2)O(2)) under physiological conditions. Close investigation of this finding revealed that NANA was oxidized by an equimolar amount of H(2)O(2) to provide its decarboxylated product, 4-(acetylamino)-2,4-dideoxy-D-glycero-D-galacto-octonic acid (ADOA). To date, there have been little data on this reaction, and its physiological significance has not been discussed. Examining the detoxification of H(2)O(2) in cultured cells with NANA, we were able to confirm that the cell death caused by H(2)O(2) was suppressed by NANA in a dose-dependent manner. These results revealed a novel role for NANA as a reactive oxygen scavenger. It is known that terminal NANA residues are removed by neuraminidase and that free NANA molecules are recycled or degraded by enzymes. We propose that released monomeric NANA is the potent defense molecule against oxidative damage.
Spatio-temporal Adaptive Pricing for Balancing Mobility-on-Demand Networks (2019)

Pricing in mobility-on-demand (MOD) networks, such as Uber, Lyft, and connected taxicabs, is done adaptively by leveraging the price responsiveness of drivers (supplies) and passengers (demands) to achieve such goals as maximizing drivers’ incomes, improving riders’ experience, and sustaining platform operation. Existing pricing policies only respond to short-term demand fluctuations without accurate trip forecast and spatial demand-supply balancing, thus mismatching drivers to riders and resulting in loss of profit. We propose CAPrice, a novel adaptive pricing scheme for urban MOD networks. It uses a new spatio-temporal deep capsule network (STCapsNet) that accurately predicts ride demands and driver supplies with vectorized neuron capsules while accounting for comprehensive spatio-temporal and external factors. Given accurate perception of zone-to-zone traffic flows in a city, CAPrice formulates a joint optimization problem by considering spatial equilibrium to balance the platform, providing drivers and riders/passengers with proactive pricing “signals.” We have conducted an extensive experimental evaluation upon over 4.0× 10 8 MOD trips (Uber, Didi Chuxing, and connected taxicabs) in New York City, Beijing, and Chengdu, validating the accuracy, effectiveness, and profitability (often 20% ride prediction accuracy and 30% profit improvements over the state-of-the-arts) of CAPrice in managing urban MOD networks.
AR and VR Applications Improve Engineering Collaboration, Personnel Optimization, and Equipment Accuracy for Separation Solutions (2019)

Abstract With the most recent industry downturn still fresh in many minds, the oil and gas E&P sector is approaching this recovery with a commitment to long-term cost discipline. As a result, augmented reality (AR) and virtual reality (VR) technologies are being adopted by operators and service companies alike as a means of cost savings while driving operational efficiency. AR technologies employ enhanced visualization hardware, techniques, and methodologies to create new environments wherein digital and physical objects and their data coexist and interact with one another, enhancing the user experience of the real world (Kunkel and Soechti 2017). VR refers to the full immersion of the user intoand interaction with a completely digital environment. Together, these technologies form the core of immersive experience and a new paradigm in industrial interaction. Until recently, these technologies were primarily applied as enhanced entertainment products, most notably within the gaming industry. However, during the past several years, and thanks to the introduction of hands-free, head-mounted display (HMD) technologies, such as Microsoft® HoloLens™ and now HoloLens 2, AR and VR are migrating into the enterprise sector. While the oil field has not been as quick to integrate AR and VR as other sectors, such as medicine, defense, and aeronautics, operators and service providers alike have increased adoption overthe past 12 months. Motivated by a mandate to keep operating costs low and improve efficiencies in terms of field processes, operators have begun implementing AR/VR applications as collaborative problem-solving, planning, and design tools. For example, some operators are initiating ARconcepts to promote internal use development and prototyping for both oilfield applications and remote refinery inspections. Additionally, service companies are embracing the use of smart glasses and wearable technologies to help improve remote work and collaboration to help increase in-field safety and reduce downtime. As part of its strategy to help drive the oil and gas industry's digital transformation, one major service provider is developing AR/VR applications to create digital representations of physical oilfield assets on the Microsoft® HoloLens device. One area of focus is the planning, design, and deployment of solids control, fluid separation, and handling technologies for offshore drilling applications.
Novel Neuroprotective GSK-3β Inhibitor Restricts Tat-Mediated HIV-1 Replication (2013)

The implementation of new antiretroviral therapies targeting transcription of early viral proteins in postintegrated HIV-1 can aid in overcoming current therapy limitations. Using high-throughput screening assays, we have previously described a novel Tat-dependent HIV-1 transcriptional inhibitor named 6-bromoindirubin-3'-oxime (6BIO). The screening of 6BIO derivatives yielded unique compounds that show potent inhibition of HIV-1 transcription. We have identified a second-generation derivative called 18BIOder as an inhibitor of HIV-1 Tat-dependent transcription in TZM-bl cells and a potent inhibitor of GSK-3β kinase in vitro. Structurally, 18BIOder is half the molecular weight and structure of its parental compound, 6BIO. More importantly, we also have found a different GSK-3β complex present only in HIV-1-infected cells. 18BIOder preferentially inhibits this novel kinase complex from infected cells at nanomolar concentrations. Finally, we observed that neuronal cultures treated with Tat protein are protected from Tat-mediated cytotoxicity when treated with 18BIOder. Overall, our data suggest that HIV-1 Tat-dependent transcription is sensitive to small-molecule inhibition of GSK-3β.
Layered motion segmentation and depth ordering by tracking edges (2004)

This paper presents a new Bayesian framework for motion segmentation--dividing a frame from an image sequence into layers representing different moving objects--by tracking edges between frames. Edges are found using the Canny edge detector, and the Expectation-Maximization algorithm is then used to fit motion models to these edges and also to calculate the probabilities of the edges obeying each motion model. The edges are also used to segment the image into regions of similar color. The most likely labeling for these regions is then calculated by using the edge probabilities, in association with a Markov Random Field-style prior. The identification of the relative depth ordering of the different motion layers is also determined, as an integral part of the process. An efficient implementation of this framework is presented for segmenting two motions (foreground and background) using two frames. It is then demonstrated how, by tracking the edges into further frames, the probabilities may be accumulated to provide an even more accurate and robust estimate, and segment an entire sequence. Further extensions are then presented to address the segmentation of more than two motions. Here, a hierarchical method of initializing the Expectation-Maximization algorithm is described, and it is demonstrated that the Minimum Description Length principle may be used to automatically select the best number of motion layers. The results from over 30 sequences (demonstrating both two and three motions) are presented and discussed.
Dissociation of yeast hexokinase by hydrostatic pressure (1988)

The pressure-induced dissociation of the isozymes P1 and P2 of hexokinase was investigated by studies of the spectral shift of the intrinsic protein fluorescence and by the fluorescence polarization of dansyl conjugates. The free energy of association of the monomers at atmospheric pressure, Katm, was -14.2 kcal mol-1 at 20 degrees C and -11.4 kcal mol-1 at 0 degrees C. The positive enthalpy indicates that the association of the monomers is entropy-driven, overcoming the negative enthalpy of hydration of the subunit interfaces. At 0 degrees C and 1 bar, glucose stabilizes the association by -1.1 kcal mol-1 and the binding of both adenosine 5'-(beta, gamma-methylenetriphosphate) (AMPPCP) and glucose by an even larger amount, -1.34 kcal mol-1. Paradoxically, adenosine 5'-triphosphate (ATP), or AMPPCP, in the absence of glucose destabilizes the association by +0.34 kcal mol-1, while adenosine 5'-diphosphate (ADP) stabilizes it by -0.6 kcal mol-1. Comparison of dV0, the apparent standard volume of association, at different pHs and temperatures indicates that its value (115-160 mL mol-1) is strongly dependent upon the ionization of a group at the subunit interface with a pK near neutrality. Under dissociating pressures, trypsin action results in permanent dissociation of the dimer, confirming earlier observations of Colowick by less direct methods. The P1 and P2 enzymes differ in Katm and dV0 and markedly so in the effects of salt upon the stability of the dimer.(ABSTRACT TRUNCATED AT 250 WORDS)
The REAnimation Low Immune Status Markers (REALISM) project: a protocol for broad characterisation and follow-up of injury-induced immunosuppression in intensive care unit (ICU) critically ill patients (2017)

Clinicaltrials.gov Registration number: NCT02638779. Pre-results.
Multibaseline stereo using a single-lens camera (2004)

In stereopsis, correspondence is a central problem that is known to suffer from several inherent difficulties. Single-lens stereo systems have brought a geometrical solution to some of the problems of stereopsis. The plenoptic camera is one of those systems that we found to simplify the process of depth recovery, but whose main limitation lies in its small baseline. For this particular reason, matches in the plenoptic camera are obtained more easily, however, this trades off against the accuracy with which they are recovered. In this paper, we show how its lack of accuracy due to a small baseline can be made up for to some extent, by using a multibaseline estimate in lieu of the commonly used equal-baseline estimate.
Transmission of IP over Ethernet over IEEE 802.16 Networks (2009)

This document describes the transmission of IPv4 over Ethernet, as well as IPv6 over Ethernet, in an access network deploying the IEEE 802.16 cellular radio transmission technology.The Ethernet on top of IEEE 802.16 is realized by bridging connections that IEEE 802.16 provides between a base station and its associated subscriber stations.Due to the resource constraints of radio transmission systems and the limitations of the IEEE 802.16 Media Access Control (MAC) functionality for the realization of an Ethernet, the transmission of IP over Ethernet over IEEE 802.16 may considerably benefit by adding IP-specific support functions in the Ethernet over IEEE 802.16 while maintaining full compatibility with standard IP over Ethernet behavior.
Characterization of five microRNA families in maize (2006)

In recent years, microRNAs (miRNAs) have polarized the interest of the scientific community as a new category of gene expression regulators, present in both plants and animals. Plant miRNAs are involved in processes such as plant development, organ identity, and stress response. Nonetheless, knowledge of their functions is still incomplete, and it is conceivable that further new processes in which they are involved will be discovered. For these reasons, structural and functional characterization of MIR genes, that are also in crop species such as Zea mays L., becomes instrumental in addressing genetic and molecular mechanisms controlling phenotype determination and phenotypic adaptation to growing conditions. The present study contributes to the characterization of five miRNA families in maize, from the determination of their expression pattern in different maize tissues and genotypes, to the identification of putative targets by bioinformatic means and subsequent experimental validation of three targets by modified 5' RACE experiments. Furthermore, 30 different MIR genes belonging to these five miRNA families were analysed by their attribution to maize chromosomes using oat-maize addition lines and by investigating their phylogenetic relationship with genes from other cereals. In particular, sequence homology was determined by the reciprocal best BLAST hit approach, to define groups of homologous genes between maize, rice, and sorghum.
[Fibronectin. Structure and functions associated to hemostasis. Review]. (2007)

Fibronectin is an adhesive glycoprotein present in a soluble form in plasma and in an insoluble form in the extracellular matrix of many tissues. The human plasma level of this protein is about 300 +/- 100 microg/mL. It is synthesized and secreted by a wide variety of cells, consequently is one of the components of greater distribution in the body that participates in the biochemical reactions of diverse physiological and pathological processes. Due to the presence of multifunctional domains in its structure, fibronectin interacts with diverse components of the coagulation and fibrinolysis. It may bind to collagen, fibrinogen, fibrin, heparin, factor XIII and platelets, among others, regulating processes of importance in hemostasis such as: platelet adhesion and aggregation, tissue remodelling during wound healing, and activation of fibrinolysis by the plasminogen activators.
SMART HIGHWAYS : TOO CLEVER TO SUCCEED? (1991)

This article details the problem of system-optimal vs. user-optimal equilibrium in traffic systems. Traffic engineers in charge of an intelligent system may have to broadcast false information in order to achieve a system-optimal solution. If the public learns that information communicated to them lacks credibility, they might try to outguess the system, defeating its purpose
Sensitive and specific enzyme-linked immunosorbent assay for urokinase-type plasminogen activator and its application to plasma from patients with breast cancer. (1988)

An enzyme-linked immunosorbent assay (ELISA) was developed for the measurement of human urokinase-type plasminogen activator (u-PA) in plasma and serum. Microtiter plates were coated with a monoclonal antibody and incubated with standard or sample. Bound u-PA was quantitated with polyclonal antibodies conjugated with biotin, followed by avidin-peroxidase. The assay was 10 times as sensitive as previously reported immunoassays, the detection limit being approximately 1 pg u-PA in a volume of 100 microliter, with a linear dose-response up to 15 pg u-PA. The assay detected active u-PA and its inactive proenzyme form equally well, and the recovery of both forms was higher than 90% in plasma. It also detected u-PA complexed with plasminogen activator inhibitor type 1. Various structurally related proteins, including t-PA, were tested, but no reaction was observed with proteins other than u-PA and its amino-terminal fragment. The intra-assay and interassay coefficients of variation for determination of u-PA in plasma were 7.6% and 8.4%, respectively. The ELISA was used to measure the concentration of u-PA in plasma from 34 healthy donors and 92 patients with breast cancer with a varying extent of disease. The mean value for the healthy donors was 1.1 +/- 0.3 ng/ml (SD) of u-PA in plasma. This value is substantially lower than those previously reported. The mean value for the patients with breast cancer was 1.3 +/- 0.4 ng/ml. This moderate increase was statistically significant at the 1% level. Approximately one quarter of the patients had plasma u-PA concentrations above the range observed for the healthy controls. There was a positive correlation between the mean u-PA plasma concentration and the extent of disease in different groups of patients.
Thought about development of traditional Chinese medicine industry (2002)

Objective: To analyze the current situation of traditional Chinese medicine industry and raise suggestions for its modernization and internationalization. Methods: The fields of present situation, existing problems and exerting orientations were analysized and discussed. Results and conclusion: There is solid ground for the modernization and internationalization of traditional Chinese medicine industry, and there still exists certain deficiencies. Realizing the modernization and internationalization of traditional Chinese medicine industry is out of question by strengthening elementary and applied study, especially study on chemistry, pharmacodynamics and quality standards of traditional Chinese medicine,and emphasizing propaganda of traditional Chinese medicine.
Plasmin generation dependent on α-enolase-type plasminogen receptor is required for myogenesis (2003)

Plasmin is a potent extracellular protease specialized in the degradation of fibrin (fibrinolysis). Active plasmin is generated by proteolytic activation of the zymogen plasminogen (Plg) by urokinase-type plasminogen activator (uPA) and tissue-type plasminogen activator (tPA). Alpha-enolase constitutes a receptor for plasminogen on several leukocyte cell types, serving to localize and promote plasminogen activation pericellularly. However, a role for a -enolase-type plasminogen receptor (PlgR) in myogenesis has never been demonstrated. In this study, we show that C2C12 mouse myoblasts express PlgR, being its expression greatly induced during the differentiation process. A monoclonal antibody against PIgR MAb 11G1, with cell surface-generated plasmin inhibitory abilities, was able to fully abrogate C2C12 myoblast fusion and differentiation in vitro. Moreover, both plasmin activity and PlgR expression were significantly induced in regenerating skeletal muscle in vivo, either in experimentally-injured muscle or in the dystrophic muscle of mdx mouse (an animal model of human Duchenne muscular dystrophy, DMD). The mdx muscle presents better regeneration capacities and less fibrosis than the human DMD muscle; therefore, the increase in PlgR/plasmin activity in mdx muscle suggests an important contribution of the fibrinolytic system in mdx regeneration. This study constitutes the first indication of alpha-enolase-type plasminogen receptor as an important component of skeletal myogenesis, by concentrating and enhancing plasmin generation on the cell surface.
Identification of Ebp1 as a component of cytoplasmic<i>bcl</i>-<i>2</i>mRNP (messenger ribonucleoprotein particle) complexes (2006)

The 3'-UTR (untranslated region) of bcl-2 mRNA contains an ARE (AU-rich element) that potentially regulates the stability of bcl-2 mRNA in a cell specific fashion. Previous studies have demonstrated that multiple proteins interact with bcl-2 mRNA in HL-60 (human leukaemia-60) cells, potentially contributing to the overexpression of Bcl-2 protein. Treatment of HL-60 cells with taxol or okadaic acid has been shown to induce destabilization of bcl-2 mRNA, which was associated with decreased binding of trans-acting factors to bcl-2 mRNA. Nucleolin has been identified as one of the bcl-2 mRNA-binding proteins [Sengupta, Bandyopadhyay, Fernandes and Spicer (2004) J. Biol. Chem. 279, 10855-10863]. In an effort to identify additional bcl-2 mRNA-binding proteins, two polypeptides of approx. 45 kDa and 60 kDa were isolated from HL-60 cells by ARE(bcl-2) (transcripts that contain bcl-2 AREs) RNA affinity chromatography. These proteins were identified as the human proliferation associated protein, Ebp1, and human DRBP76 (double stranded RNA-binding protein 76) respectively, by MALDI (matrix-assisted laser-desorption ionization)-MS. RNA electrophoretic mobility shift assays indicated that recombinant Ebp1 binds to ARE(bcl-2) RNA but not to the group 1 ARE present in GM-CSF (granulocyte macrophage-colony stimulating factor) mRNA in vitro. Antibody supershift assays demonstrated that Ebp1 is present in protein-ARE(bcl-2) RNA complexes formed with cytosolic HL-60 extracts. The interaction of Ebp1 with bcl-2 mRNA in HL-60 cells was also demonstrated by RNA co-immunoprecipitation assays. This interaction was not detected in extracts of taxol-treated HL-60 cells. Immunoprecipitation assays further revealed that Ebp1 co-precipitates with nucleolin from HL-60 cytoplasmic extracts. The observation that co-precipitation was decreased when extracts were treated with RNase suggests that Ebp1 and nucleolin are present in the same bcl-2 mRNP (messenger ribonucleoprotein particle) complexes. RNA-decay assays further demonstrated that Ebp1 decreased the rate of decay of beta-globin-ARE(bcl-2) transcripts in HL-60 cell extracts. Collectively, these results indicate a novel function for Ebp1 in contributing to the regulation of bcl-2 expression in HL-60 cells.
Trajectory-based differential expression analysis for single-cell sequencing data (2020)

Trajectory inference has radically enhanced single-cell RNA-seq research by enabling the study of dynamic changes in gene expression. Downstream of trajectory inference, it is vital to discover genes that are (i) associated with the lineages in the trajectory, or (ii) differentially expressed between lineages, to illuminate the underlying biological processes. Current data analysis procedures, however, either fail to exploit the continuous resolution provided by trajectory inference, or fail to pinpoint the exact types of differential expression. We introduce tradeSeq, a powerful generalized additive model framework based on the negative binomial distribution that allows flexible inference of both within-lineage and between-lineage differential expression. By incorporating observation-level weights, the model additionally allows to account for zero inflation. We evaluate the method on simulated datasets and on real datasets from droplet-based and full-length protocols, and show that it yields biological insights through a clear interpretation of the data.
PC‐3 cells with enhanced androgen receptor signaling: A model for clonal selection in prostate cancer (2004)

These studies provide new evidence that the androgen-signaling axis can be sensitized in prostate cancer cells, and have important implications for the analysis and interpretation of AR structure and function in in vitro cell systems.