gebhart/patrepeval huggingface dataset:
Collagen I and III and their decorin modified surfaces studied by atomic force microscopy and the elucidation of their affinity toward positive apolipoprotein B-100 residue by quartz crystal microbalance (2011)

Collagen, the major component of extracellular matrix (ECM) and the most abundant protein in the human body, is implicated in the development of atherosclerosis. Collagen types I and III were immobilized on fused-silica capillary to investigate their shape, size and structure by atomic force microscopy (AFM). For comparison, collagen was also immobilized on a mica surface. Our studies demonstrated that not only does the adsorption pattern on the substrate vary with the type of collagen, but also the substrate material plays an important role in the fibril formation process. Decorin, which promotes the binding of low-density lipoprotein (LDL) particles with collagen, was investigated for its effect on the fibrillogenesis. On both substrate materials, addition of decorin clearly reduced the fibril diameter of collagen surfaces. Moreover, a quartz crystal microbalance (QCM)-based biosensor approach was applied to clarify and evaluate the affinity of different collagen coatings immobilized on a silicon dioxide sensor chip toward apolipoprotein B-100, the major protein of LDL. The results confirmed the importance of collagen type and their fibrillogenesis on the binding of the positive residues of apolipoprotein B-100 on negatively charged collagen surfaces.
Data from BCA101 Is a Tumor-Targeted Bifunctional Fusion Antibody That Simultaneously Inhibits EGFR and TGFβ Signaling to Durably Suppress Tumor Growth (2023)

&lt;div&gt;Abstract&lt;p&gt;The EGFR and TGFβ signaling pathways are important mediators of tumorigenesis, and cross-talk between them contributes to cancer progression and drug resistance. Therapies capable of simultaneously targeting EGFR and TGFβ could help improve patient outcomes across various cancer types. Here, we developed BCA101, an anti-EGFR IgG1 mAb linked to an extracellular domain of human TGFβRII. The TGFβ “trap” fused to the light chain in BCA101 did not sterically interfere with its ability to bind EGFR, inhibit cell proliferation, or mediate antibody-dependent cellular cytotoxicity. Functional neutralization of TGFβ by BCA101 was demonstrated by several &lt;i&gt;in vitro&lt;/i&gt; assays. BCA101 increased production of proinflammatory cytokines and key markers associated with T-cell and natural killer–cell activation, while suppressing VEGF secretion. In addition, BCA101 inhibited differentiation of naïve CD4&lt;sup&gt;+&lt;/sup&gt; T cells to inducible regulatory T cells (iTreg) more strongly than the anti-EGFR antibody cetuximab. BCA101 localized to tumor tissues in xenograft mouse models with comparable kinetics to cetuximab, both having better tumor tissue retention over TGFβ “trap.” TGFβ in tumors was neutralized by approximately 90% in animals dosed with 10 mg/kg of BCA101 compared with 54% in animals dosed with equimolar TGFβRII-Fc. In patient-derived xenograft mouse models of head and neck squamous cell carcinoma, BCA101 showed durable response after dose cessation. The combination of BCA101 and anti-PD1 antibody improved tumor inhibition in both B16-hEGFR–expressing syngeneic mouse models and in humanized HuNOG-EXL mice bearing human PC-3 xenografts. Together, these results support the clinical development of BCA101 as a monotherapy and in combination with immune checkpoint therapy.&lt;/p&gt;Significance:&lt;p&gt;The bifunctional mAb fusion design of BCA101 targets it to the tumor microenvironment where it inhibits EGFR and neutralizes TGFβ to induce immune activation and to suppress tumor growth.&lt;/p&gt;&lt;/div&gt;
Beam-stack search: integrating backtracking with beam search (2005)

We describe a method for transforming beam search into a complete search algorithm that is guaranteed to find an optimal solution. Called beam-stack search, the algorithm uses a new data structure, called a beam stack, that makes it possible to integrate systematic backtracking with beam search. The resulting search algorithm is an anytime algorithm that finds a good, sub-optimal solution quickly, like beam search, and then backtracks and continues to find improved solutions until convergence to an optimal solution. We describe a memory-efficient implementation of beam-stack search, called divide-and-conquer beam-stack search, as well as an iterative-deepening version of the algorithm. The approach is applied to domain-independent STRIPS planning, and computational results show its advantages.
Campbell Diagram Computation for a Drillstring Immersed in Curved Wells (2019)

The drilling operations use a rotary slender structure introduced inside the drill well. The nonlinear dynamics with bit-bouncing, stick-slip phenomena, and pulsating mud flow may yield the premature wear and damage of drilling equipment and should be investigated to improve the reliability of drilling operations. This work presents the beam element formulation to model the drilling nonlinear dynamics. The well-pipe contacts are modeled by the radial elastic stops. The fluid–structure interactions are considered. The first step consists in computing the static position of structure to determine the contact points and calculate the preloaded state. These results are then considered to calculate the Campbell diagram. The potentially unstable speeds of rotation are identified. The results show that the modal coupling phenomena strongly occur for the three-dimensional well. The well-pipe contacts modify the modes in rotation, and the rotating fluid induces a strong deviation of the flexural mode curves.
Multi-state kinetics (2006)

The two-state model of Chapter 7 can be used as a basic building block for more complicated processes. When a system has more than two states, conversions between different pairs can occur, and then the kinetics reflects the aggregate behavior of those various transitions. The time course is no longer a simple exponential function, and in this chapter we will see how multi-state models lead to multi-exponential kinetics.
The Effect of Various Waste Materials’ Contents on the Attenuation Level of Anti-Radiation Shielding Concrete (2013)

Samples of concrete contain various waste materials, such as iron particulates, steel balls of used ball bearings and slags from steel industry were assessed for their anti-radiation attenuation coefficient properties. The attenuation measurements were performed using gamma spectrometer of NaI (Tl) detector. The utilized radiation sources comprised <sup>137</sup>Cs and ⁶⁰Co radioactive elements with photon energies of 0.662 MeV for <sup>137</sup>Cs and two energy levels of 1.17 and 1.33 MeV for the ⁶⁰Co. Likewise the mean free paths for the tested samples were obtained. The aim of this work is to investigate the effect of the waste loading rates and the particulate dispersive manner within the concrete matrix on the attenuation coefficients. The maximum linear attenuation coefficient (μ) was attained for concrete incorporates iron filling wastes of 30 wt %. They were of 1.12 ± 1.31×10<sup>-3</sup> for <sup>137</sup>Cs and 0.92 ± 1.57 × 10<sup>-3</sup> for ⁶⁰Co. Substantial improvement in attenuation performance by 20%-25% was achieved for concrete samples incorporate iron fillings as opposed to that of steel ball samples at different (5%-30%) loading rates. The steel balls and the steel slags gave much inferior values. The microstructure, concrete-metal composite density, the homogeneity and particulate dispersion were examined and evaluated using different metallographic, microscopic and measurement facilities.
Phase I expansion of S-222611, a reversible inhibitor of EGFR and HER2, in advanced solid tumors, including patients with brain metastases. (2015)

2511 Background: S-222611 is an oral, reversible ErbB tyrosine kinase inhibitor of EGFR and HER2 with potent pre-clinical activity. MTD was not reached during dose-escalation, even at the maximum dose of 1600mg QD. PK and efficacy data supported a daily dose of 800mg. A further cohort has been treated to further explore safety and efficacy. Methods: Subjects with advanced solid tumors expressing EGFR and/or overexpressing HER2 were enrolled. S-222611 was administered until disease progression or unacceptable toxicity. Results: 76 patients (33 male/43 female; median age 62 years [range 31-81], ECOG PS 0/1/2: 24/51/1), were included in this expansion phase, including breast (27), esophago-gastric (30), head & neck (12) and renal (7). Dose reduction was required because of adverse events in 11 patients (14%); the most frequent of such being diarrhea and elevated bilirubin. Only 2 patients discontinued treatment due to drug-related adverse events. Of the 41 patients with HER2-positive cancers (26 breast, 13 esophago-gastric, 2 head & neck), 1 complete response (gastric-esophageal junction cancer) and 5 partial responses (4 breast cancer, 1 gastric cancer) were observed; all these patients had received prior HER2-directed therapy. Prolonged stable disease ( ≥ 6 months) was observed in 3 additional patients with breast cancer. 6 of the 25 breast patients had brain metastases, in whom 1 intracranial response and 2 prolonged SD ( ≥ 6mo) were observed. In the EGFR+ve/HER2-ve cohort (n = 35), no RECIST responses were seen, however 4 patients had prolonged stable disease ( ≥ 6mo). Conclusions: S-222621 was well tolerated at a dose of 800mg once daily. Anti-tumour activity, including shrinkage of brain metastases, was evident in a heavily pre-treated population of patients with HER2-positive breast and esophago-gastric cancers. Clinical trial information: 2009-017817-31.
Channel outage performance of QPSK and pi /4-DQPSK in a multipath fading environment (2003)

Channel outage probabilities for QPSK and pi /4-DQPSK are evaluated in a Gaussian profiled multipath fading channel with additive white noise by computer simulation. Assuming a minimum acceptable bit error rate of 10/sup -5/, it is found that even with a very small normalised delay spread d'=0.05, the channel outage probability is greater than 10/sup -3/. Using 4-branch switched diversity this can be reduced such that channel outage is less than 10/sup -5/ with d'<0.2 (QPSK) or 0.13 ( pi /4-DQPSK).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Differential RNA-Dependent ATPase Activities of Four rRNA Processing Yeast DEAD-Box Proteins (2009)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionDifferential RNA-Dependent ATPase Activities of Four rRNA Processing Yeast DEAD-Box ProteinsIvelitza Garcia and Olke C. UhlenbeckCite this: Biochemistry 2009, 48, 4, 810Publication Date (Web):January 7, 2009Publication History Received12 November 2008Published online7 January 2009Published inissue 3 February 2009https://pubs.acs.org/doi/10.1021/bi802088ghttps://doi.org/10.1021/bi802088gcorrectionACS PublicationsCopyright © 2009 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views507Altmetric-Citations-LEARN 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 PDF (14 KB) Get e-AlertscloseSUBJECTS:Fungi Get e-Alerts
Monitoring electrochemical methanol oxidation and CO coverage using Pt deposited SPR sensor platform (2021)

In order to apply the surface plasmon resonance (SPR) sensing to the study of heterogeneous catalytic reactions, in addition to the metals and dielectrics that the SPR platform already has, a layer or particle that can additionally act as a catalyst is required. The Au layer (50 nm thick) was formed by sputter deposition on the polycarbonate (PC) grating surface of the original DVD-R structure, and the Pt layer was additionally formed by electrochemical deposition. As-prepared Au-covered PC grating exhibits the sensing sensitivity of 973.95 nm/RIU and a figure of merit (FOM) of 69.17. Even after electrochemical Pt deposition, it still showed high sensing sensitivity of 956.57 nm/RIU and FOM of 55.96. In particular, the methanol oxidation and CO coverage on the Pt surface, which are one of the major reactions of the polymer electrolyte membrane fuel cells (PEMFCs), were monitored using Pt deposited SPR sensor. As a result, as the applied potential for methanol oxidation increased and the CO coverage increased, the SPR sensor showed a blue-shift trend. This is probably due to the process of dehydrogenation of methanol (CH3OH) molecules to CO and CO2, and the replacing process the water on the Pt surface with CO.
Monolingual Distributional Similarity for Text-to-Text Generation (2012)

Previous work on paraphrase extraction and application has relied on either parallel datasets, or on distributional similarity metrics over large text corpora. Our approach combines these two orthogonal sources of information and directly integrates them into our paraphrasing system’s log-linear model. We compare different distributional similarity feature-sets and show significant improvements in grammaticality and meaning retention on the example text-to-text generation task of sentence compression, achieving stateof-the-art quality. 1
Determinants in Nonstructural Protein 4A of Dengue Virus Required for RNA Replication and Replication Organelle Biogenesis (2021)

Dengue virus (DENV) constitutes one of the most important arboviral pathogens affecting humans. The high prevalence of DENV infections, which cause more than 20,000 deaths annually, and the lack of effective vaccines or direct-acting antiviral drugs make it a global health concern. DENV genome replication occurs in close association with the host endomembrane system, which is remodeled to form the viral replication organelle that originates from endoplasmic reticulum (ER) membranes. To date, the viral and cellular determinants responsible for the biogenesis of DENV replication organelles are still poorly defined. The viral nonstructural protein 4A (NS4A) can remodel membranes and has been shown to associate with numerous host factors in DENV-replicating cells. In the present study, we used reverse and forward genetic screens and identified sites within NS4A required for DENV replication. We also mapped the determinants in NS4A required for interactions with other viral proteins. Moreover, taking advantage of our recently developed polyprotein expression system, we evaluated the role of NS4A in the formation of DENV replication organelles. Together, we report a detailed map of determinants within NS4A required for RNA replication, interaction with other viral proteins, and replication organelle formation. Our results suggest that NS4A might be an attractive target for antiviral therapy. <b>IMPORTANCE</b> DENV is the most prevalent mosquito-borne virus, causing around 390 million infections each year. There are no approved therapies to treat DENV infection, and the only available vaccine shows limited efficacy. The viral nonstructural proteins have emerged as attractive drug targets due to their pivotal role in RNA replication and establishment of virus-induced membranous compartments, designated replication organelles (ROs). The transmembrane protein NS4A, generated by cleavage of the NS4A-2K-4B precursor, contributes to DENV replication by unknown mechanisms. Here, we report a detailed genetic interaction map of NS4A and identify residues required for RNA replication and interaction between NS4A-2K-4B and NS2B-3 as well as NS1. Importantly, by means of an expression-based system, we demonstrate the essential role of NS4A in RO biogenesis and identify determinants in NS4A required for this process. Our data suggest that NS4A is an attractive target for antiviral therapy.
On Regularization and Robustness of Deep Neural Networks (2018)

Despite their success, deep neural networks suffer from several drawbacks: they lack robustness to small changes of input data known as examples and training them with small amounts of annotated data is challenging. In this work, we study the connection between regularization and robustness by viewing neural networks as elements of a reproducing kernel Hilbert space (RKHS) of functions and by regularizing them using the RKHS norm. Even though this norm cannot be computed, we consider various approximations based on upper and lower bounds. These approximations lead to new strategies for regularization, but also to existing ones such as spectral norm penalties or constraints, gradient penalties, or adversarial training. Besides, the kernel framework allows us to obtain margin-based bounds on adversarial generalization. We study the obtained algorithms for learning on small datasets, learning adversarially robust models, and discuss implications for learning implicit generative models.
Dataset on nicotine-free, nontransgenic tobacco (Nicotiana tabacum l.) edited by CRISPR-Cas9 (2019)

This dataset in brief is related to the research letter entitled “Nicotine-free, nontransgenic tobacco (Nicotiana tabacum l.) edited by CRISPR-Cas9” [1]. Cured tobacco products with a significantly reduced nicotine content helps people to overcome their nicotine addiction. Here we summarize additional data and method descriptions of the generation process of a nicotine-free, nontransgenic tobacco plant. This included the cloning, transformation and regeneration of transgenic tobacco plants, followed by the analysis of the nicotine content and genomic modifications caused by CRISPR-Cas9 mediated gene editing. Subsequently, nicotine-free plants were screened for loss of T-DNA cassette, i.e. nontransgenity. Finally, a metabolic footprint was recorded by 1H NMR analysis.
Experimental determination of dynamic parameters of robotic arms (1993)

Abstract This article presents a practical method for determining the dynamic parameters of robotic arms. The two unique features of the method are that it determines the friction parameters along with the inertia and mass parameters and that it does not require the measurement of joint accelerations. The method is demonstrated experimentally by determining the dynamic parameters of a closed‐chain direct‐drive arm. The precision of the determined parameter was verified in the context of computed torquebased controllers. Statistical analysis also shows that the estimated values are reliable. © 1993 John Wiley &amp; Sons, Inc.
Larvicidal Potential and Phytochemical Analysis of Garcinia mangostana Extracts on Controlling of Culex pipiens Larvae (2022)

The present study assessed the larvicidal action of Garcinia mangostana pericarp against Culex pipiens larvae.Hexane extract was prepared from the fruit.The secondary metabolites were identified using phytochemical analysis and gas chromatography-mass spectrometry (GC-MS).The cytotoxic effect was also evaluated using normal human umbilical endothelial cells (HUV-EC).The larvicidal assay was performed on the third instar stage as recommended by WHO.The phytochemical analysis showed the presence of alkaloids, sterols, and phenolic compounds.The GC-MS analysis revealed the presence of 5 compounds, of which α-Copaene constituted 61.95% of the extract.The hexane extract showed good larvicidal activity, with an LC 50 = 33.9μg mL -1 and LC 90 = 64.1 µg/mL at 24 h post exposure.The midgut sections of treated larvae showed morphological alterations such as microvilli damage, loss of nuclei, and peritrophic membrane degeneration.The extract also showed high cytotoxic activity against HUV-EC cells, with an LC 50 of 19.8 µg/mL.The results indicated that G. mangostana has larvicidal activity against Cx.pipiens larvae.Further investigation can be done to confirm the larvicidal potential of this plant against different genus and species of mosquitoes.
Joint microseismic event location with uncertain velocity (2013)

We study the problem of the joint location of seismic events using an array of receivers. We show that locating multiple seismic events simultaneously is advantageous compared to the more traditional approaches of locating each event independently. Joint location, by design, includes estimating an uncertainty distribution on the absolute position of the events. From this can be deduced the distribution on the relative position of one event with respect to others. Many quantities of interest, such as fault sizes, fracture spacing or orientation, can be directly estimated from the joint distribution of seismic events. Event relocation methods usually update only the target event, while keeping the reference events fixed. Our joint approach can be used to update the locations of all events simultaneously. The joint approach can also be used in a Bayesian sense as prior information in locating a new event.
Obtaining an Array of Closely Packed Mesoscale Spheres Using Dielectrophoresis Forces for Optical Super-Resolution Microscopy (2022)

We reported on the proof of the concept of dielectric mesoscale particle array-based cover glass for optical super-resolution microscopy. The limited field of view is a limitation of ultra-high resolution microscopy based on single mesoscale particles. Using the forces of dielectrophoresis, we placed an ordered mesoscale spheres array over the sample and overcame this limitation using. A dielectrophoresis force acted on the mesoscale sphere electric dipole, which has set the particle into the forward motion due to an induced dipole moment formed in the volume of such particle placed in an inhomogeneous alternating electric field. The latex spheres were placed into the gap between the electrodes of the measuring cell. After the application of an electric field, the microspheres were grouped into arrays of densely spaced particles. The preliminary experiments confirmed the possibility of organizing an array of densely packed mesoscale particles under the action of dielectrophoresis force. The results obtained can be used for various applications in ultra-high resolution microscopy with extended functionality.