gebhart/patrepeval huggingface dataset:
Study of Delay Drift in GNSS-R Altimetry (2014)

Differently to the case of a conventional spaceborne nadir-looking mono-static radar altimeter, where the fly-around time of the pulses remains basically constant (assuming an almost circular orbit around an almost spherical Earth), the bistatic geometry of GNSS-R with the transmitter and the receiver embarked on different satellites imprints a significant temporal variation to the delays of the direct and reflected signals. Within a GNSS-R-based spaceborne ocean altimeter using the PARIS concept, such temporal variation in the delay has to be compensated for with the objective to finely adjust the delay of the direct signal to permanently match with that of the reflected signal according to some a priori model of the geometry. The impact of the residual delay drift on the accuracy and the precision of the range observations is assessed here.
Water Plays Multifunctional Roles in the Intervening Formation of Secondary Organic Aerosols in Ozonolysis of Limonene: A Valence Photoelectron Spectroscopy and Density Functional Theory Study (2023)

Although water may affect aqueous aerosol chemistry, how it intervenes in the formation of secondary organic aerosols (SOAs) at the molecular level remains elusive. Ozonolysis of limonene is one of the most important sources of indoor SOAs. Here, we report the valence electronic properties of limonene aerosols and SOAs derived from limonene ozonolysis (Lim-SOAs) via aerosol vacuum ultraviolet photoelectron spectroscopy, with a focus on the effects of water on Lim-SOAs. The first vertical ionization energy of limonene aerosols is measured to be 8.79 ± 0.07 eV. While water significantly increases the total photoelectron yield of Lim-SOAs, three photoelectron features attributable to Lim-SOAs each exhibit distinct dependence on the fraction of water in aerosols, implying that different formation pathways and molecular origins are involved in the formation of Lim-SOAs. Combined with density functional theory calculation and mass spectrometry measurements, this study reveals that water, particularly the water dimer, enhances the formation of Lim-SOAs by altering the ozonolysis energetics and pathways by intervening in its Criegee chemistry, acting as both a catalyst and a reactant. The atmospheric implication is discussed.
Practical Syntheses of N-Acetyl (E)-β-Arylenamides (2013)

A facile and practical method for the preparation of (<i>E</i>)-β-arylenamides [(<i>E</i>)-<i>N</i>-(1-arylprop-1-en-2-yl]acetamides] has been developed by reductive acetylation of the corresponding oximes with iron(II) acetate as the reducing reagent. Employment of hexamethylphosphoramide as the solvent was found to be critical for the high <i>E</i>/<i>Z</i> selectivity. The methodology has been applied in efficient syntheses of a key chiral intermediate of tamsulosin by asymmetric hydrogenation.
Model-Driven Discovery (2015)

If observed facts of undoubted accuracy will not fit any of the alternatives it leaves open, the system itself is in need of reconstruction– Talcott Parsons
Novel Targeted Therapies for Eosinophil-Associated Diseases and Allergy (2014)

Eosinophil-associated diseases often present with life-threatening manifestations and/or chronic organ damage. Currently available therapeutic options are limited to a few drugs that often have to be prescribed on a lifelong basis to keep eosinophil counts under control. In the past 10 years, treatment options and outcomes in patients with clonal eosinophilic and other eosinophilic disorders have improved substantially. Several new targeted therapies have emerged, addressing different aspects of eosinophil expansion and inflammation. In this review, we discuss available and currently tested agents as well as new strategies and drug targets relevant to both primary and secondary eosinophilic diseases, including allergic disorders.
A New Indanone from the Marine Cyanobacterium Lyngbya majuscula That Inhibits Hypoxia-Induced Activation of the VEGF Promoter in Hep3B Cells (2000)

A new indanone (1) has been isolated from the filamentous marine cyanobacterium Lyngbya majuscula, and its structure determined spectroscopically. Vascular endothelial growth factor (VEGF) is an important regulator of tumor angiogenesis. Compound 1 inhibits hypoxia-induced activation of the VEGF gene promoter in Hep3B human liver tumor cells, in vitro.
N ‐ tert ‐Butoxycarbonyl‐ L ‐Leucinal (2003)

Abstract N ‐ tert ‐butoxycarbonyl‐ L ‐leucinal product: N ‐ tert ‐Butoxycarbonyl‐ L ‐leucinal: Boc‐ L ‐leucinal intermediate: Boc‐ L ‐leucine N ‐methyl‐O‐methycarboxamide
Assessment of tumour viability in human lung cancer xenografts with texture-based image analysis (2015)

The proposed image analysis-based tumour viability assessment resulted in a high agreement with expert annotations. By providing extraction of detailed information of the tumour microenvironment, the automated method can be used in preclinical research settings. The method could also have implications in cancer diagnostics, cancer outcome prognostics and prediction.
Bovine and mouse serum beta inhibitors of influenza A viruses are mannose-binding lectins. (1990)

Normal bovine and mouse sera contain a component, termed beta inhibitor, that inhibits the infectivity and hemagglutinating activity of influenza A viruses of the H1 and H3 subtypes. To investigate the nature of the interaction of beta inhibitors with influenza A viruses we isolated a mutant of the virus Mem71H-BelN (H3N1) that could grow in the presence of bovine serum. The mutant virus was resistant to hemagglutination inhibition by mouse serum as well as by bovine serum and had undergone changes in the receptor-binding and the antigenic properties of its hemagglutinin (HA) molecule. Sequence analysis of the HA genes of parent and mutant viruses revealed a single nucleotide change in the mutant, resulting in the substitution Thr----Asn at residue 167 of the HA1 chain of HA. This change leads to loss of the potential glycosylation site Asn-165-Val-166-Thr-167 at the tip of the HA spike, which in viruses of the H3 subtype is known to bear a high-mannose (type II) carbohydrate side chain N-linked to Asn-165. The association of beta inhibitor resistance with loss of this carbohydrate side chain suggested that beta inhibitors may be lectins. In support of this hypothesis, treatment of the beta inhibitor-sensitive parent virus Mem71H-BelN with periodate converted it to the resistant state. Furthermore, the inhibitory activity of both bovine and mouse sera for the parental virus was abrogated by D-mannose. We conclude that the beta inhibitors in bovine and mouse sera are mannose-binding lectins that inhibit hemagglutination and neutralize virus infectivity by binding to carbohydrate at the tip of the HA spike, blocking access of cell-surface receptors to the receptor-binding site on HA.
Microencapsulated IL-12 Drives Genital Tract Immune Responses to Intranasal Gonococcal Outer Membrane Vesicle Vaccine and Induces Resistance to Vaginal Infection with Diverse Strains of Neisseria gonorrhoeae (2022)

An experimental gonococcal vaccine consisting of outer membrane vesicles (OMVs) and microsphere (ms)-encapsulated interleukin-12 (IL-12 ms) induces Th1-driven immunity, with circulating and genital antibodies to Neisseria gonorrhoeae, after intravaginal (i.vag.) administration in female mice, and generates resistance to vaginal challenge infection. Because i.vag. administration is inapplicable to males and may not be acceptable to women, we determined whether intranasal (i.n.) administration would generate protective immunity against N. gonorrhoeae. Female and male mice were immunized i.n. with gonococcal OMVs plus IL-12 ms or blank microspheres (blank ms). Responses to i.n. immunization were similar to those with i.vag. immunization, with serum IgG, salivary IgA, and vaginal IgG and IgA antigonococcal antibodies induced when OMVs were administered with IL-12 ms. Male mice responded with serum IgG and salivary IgA antibodies similarly to female mice. Gamma interferon (IFN-γ) production by CD4<sup>+</sup> T cells from iliac lymph nodes was elevated after i.n. or i.vag. immunization with OMVs plus IL-12 ms. Female mice immunized with OMVs plus IL-12 ms by either route resisted challenge with N. gonorrhoeae to an equal extent, and resistance generated by i.n. immunization extended to heterologous strains of N. gonorrhoeae. Detergent-extracted OMVs, which have diminished lipooligosaccharide, generated protective immunity to challenge similar to native OMVs. OMVs from mutant N. gonorrhoeae, in which genes for Rmp and LpxL1 were deleted to eliminate the induction of blocking antibodies against Rmp and diminish lipooligosaccharide endotoxicity, also generated resistance to challenge infection similar to wild-type OMVs when administered i.n. with IL-12 ms. <b>IMPORTANCE</b> We previously demonstrated that female mice can be immunized intravaginally with gonococcal outer membrane vesicles (OMVs) plus microsphere (ms)-encapsulated interleukin-12 (IL-12 ms) to induce antigonococcal antibodies and resistance to genital tract challenge with live Neisseria gonorrhoeae. However, this route of vaccination may be impractical for human vaccine development and is inapplicable to males. Because intranasal immunization has previously been shown to induce antibody responses in both male and female genital tracts, we have evaluated this route of immunization with gonococcal OMVs plus IL-12 ms. In addition, we have refined the composition of gonococcal OMVs to reduce the endotoxicity of lipooligosaccharide and to eliminate the membrane protein Rmp, which induces countereffective blocking antibodies. The resulting vaccine may be more suitable for ultimate translation to human application against the sexually transmitted infection gonorrhea, which is becoming increasingly resistant to treatment with antibiotics.
A random walk algorithm to estimate a lower bound of the star discrepancy (2022)

Abstract In many Monte Carlo applications, one can substitute the use of pseudorandom numbers with quasirandom numbers and achieve improved convergence. This is because quasirandom numbers are more uniform that pseudorandom numbers. The most common measure of that uniformity is the star discrepancy. Moreover, the main error bound in quasi-Monte Carlo methods, called the Koksma–Hlawka inequality, has the star discrepancy in the formulation. A difficulty with this bound is that computing the star discrepancy is very costly. The star discrepancy can be computed by evaluating a function called the local discrepancy at a number of points. The supremum of these local discrepancy values is the star discrepancy. If we have a point set in <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:msup> <m:mrow> <m:mo stretchy="false">[</m:mo> <m:mn>0</m:mn> <m:mo>,</m:mo> <m:mn>1</m:mn> <m:mo stretchy="false">]</m:mo> </m:mrow> <m:mi>s</m:mi> </m:msup> </m:math> {[0,1]^{s}} with N members, we need to compute the local discrepancy at <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:msup> <m:mi>N</m:mi> <m:mi>s</m:mi> </m:msup> </m:math> {N^{s}} points. In fact, computing star discrepancy is NP-hard. In this paper, we will consider an approximate algorithm for a lower bound on the star discrepancy based on using a random walk through some of the <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:msup> <m:mi>N</m:mi> <m:mi>s</m:mi> </m:msup> </m:math> {N^{s}} points. This approximation is much less expensive that computing the star discrepancy, but still accurate enough to provide information on convergence. Our numerical results show that the random walk algorithm has the same convergence rate as the Monte Carlo method, which is <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mi>O</m:mi> <m:mrow> <m:mo stretchy="false">(</m:mo> <m:msup> <m:mi>N</m:mi> <m:mrow> <m:mo>-</m:mo> <m:mfrac> <m:mn>1</m:mn> <m:mn>2</m:mn> </m:mfrac> </m:mrow> </m:msup> </m:mrow> </m:mrow> </m:math> {O(N^{-\frac{1}{2}}} ).
A Geological Model for the Origin of Fluid Compositional Gradients in a Large Saudi Arabian Oilfield: An Investigation by Two-Dimensional Gas Chromatography (GC × GC) and Asphaltene Chemistry (2015)

The heavy oil rim of a large Saudi Arabian oilfield has been shown to be in vertical and lateral equilibrium, matching predictions of the gravity term from the Flory–Huggins–Zuo equation of state for asphaltenes in the form of 5.2 nm clusters of the Yen–Mullins model. The large (10×) vertical gradient of asphaltene concentration over a very large perimeter (≫10 km) of the oilfield provided a stringent test of this equation-of-state fit. Two-dimensional gas chromatography (GC × GC) and stable isotope analysis (δ D and δ 13C) were used to determine the consistency of the liquid-phase components with equilibration and the effects of biodegradation or thermal maturity on the observed asphaltene gradient. These analyses confirm homogeneity of equilibrated liquid-phase components of similar chemical character and equilibrated asphaltene isotopes. Biodegradation is minimal and there is no maturity variation among the samples. Thus, the large asphaltene gradient did not result from these secondary processes and is not a remnant from how the reservoir was charged with crude oil. The results are consistent with original findings that the oil column is equilibrated. Thermodynamic equilibration over such large distances (>10 km) requires convective currents and provides constraints on fluid dynamic processes in reservoirs. A simple one-dimensional (1-D) three-component single-phase model is introduced to account for asphaltene accumulation by way of convective currents established from a diffusive gas front at the top of the oil column.
Factors Limiting the Quantitative Use of Mud-Logging Data (1993)

Abstract This paper focuses on the quality of mud logging data and the need for improving the quality. Included examples clearly demonstrate that traditional mud logging data suffers from errors and poor quality which limits its quantitative use, for instance in drill bit optimisation or modelling work. Special concern is paid to the accuracy of the depth, the rate of penetration and the surface weight on bit. It is concluded that there is a significant potential for improving the accuracy of these variables.
Adversarial Objectness Gradient Attacks in Real-time Object Detection Systems (2020)

Real-time object detection is one of the key applications of deep neural networks (DNNs) for real-world mission-critical systems. While DNN-powered object detection systems celebrate many life-enriching opportunities, they also open doors for misuse and abuse. This paper presents a suite of adversarial objectness gradient attacks, coined as TOG, which can cause the state-of-the-art deep object detection networks to suffer from untargeted random attacks or even targeted attacks with three types of specificity: (1) object-vanishing, (2) object-fabrication, and (3) object-mislabeling. Apart from tailoring an adversarial perturbation for each input image, we further demonstrate TOG as a universal attack, which trains a single adversarial perturbation that can be generalized to effectively craft an unseen input with a negligible attack time cost. Also, we apply TOG as an adversarial patch attack, a form of physical attacks, showing its ability to optimize a visually confined patch filled with malicious patterns, deceiving well-trained object detectors to misbehave purposefully. We report our experimental measurements using three benchmark datasets (PASCAL VOC, MS COCO, and INRIA) on models from three dominant detection algorithms (YOLOv3, SSD, and Faster R-CNN). The results demonstrate serious adversarial vulnerabilities and the compelling need for developing robust object detection systems. The source code is available at https://github.com/git-disl/TOG.
Quaternized Starch-Based Composite Nanoparticles for siRNA Delivery to Tumors (2021)

RNA interference (RNAi) therapy has emerged as a promising cancer therapy platform; however, there is an ongoing need for a safe and effective delivery carrier for siRNA. The present study demonstrates for the first time the systemic in vivo delivery of nanosized complexes of quaternized starch (Q-starch) and siRNA to effectively target cancer in a murine model. Our results show that Q-starch/siRNA composite nanoparticle complexes are safe for systemic administration, with no evident toxicities. Encouragingly, the results demonstrate their cellular uptake in the tumor and 63% gene silencing post intratumor injection. Moreover, a biodistribution study reveals favorable accumulation of the composite nanoparticles in the tumor site post systemic administration. The gene-silencing results are encouraging, although not sufficient for therapeutic application, and raise the need to further investigate the potential of Q-starch/siRNA complexes in terms of gene-silencing efficiency and of tumor targeting and stability following systemic administration. Overall, our composite nanoparticles show promising potential for RNAi delivery to tumor sites, with their accumulation in the lungs suggesting that there may be particular merit in investigating the use of Q-starch/siRNA complexes to treat lung cancer.
Cost-effective and eco-friendly leaf-based bio-adsorbent for methyl blue dye adsorption: thermodynamics, kinetics, isotherms, and phytotoxicity (2023)

Abstract The elimination of textile dye from wastewater is an ecological and environmental barrier to continued industrial expansion. The current study aims to analyse the anionic methyl blue (MB) dye's ability to bind to the Artocarpus heterophyllus leaf powder (AHLP) and assess its capacity to eliminate the dye from an aqueous solution. The Fourier transform infrared spectroscopy (FT-IR), Scanning electron microscopy (SEM), X-ray diffraction (XRD), and zero-point charge (pHzpc) analyses were utilised to characterise the leaf powder (adsorbent). The adsorption efficiency was evaluated through various conditions, including solution pH (3-10), dye concentration (20-50 mg.L-1), AHLP dosage (1.50-8.0 g.L-1), contact time (0-90 min), and temperature (300-323 K). The maximum dye adsorption efficiency (91.10%) was achieved within 45 min, using 3.0 g.L-1 adsorbent dose in 20 mg.L-1 MB solution at pH 4.0 and 300 K temperature. The adsorption mechanism was congruent with the pseudo-second-order model (R2 &gt; 0.99) and the Langmuir model (R2 = 1.0). Several thermodynamic parameters, like enthalpy change (∆H o ), Gibbs free energy change (∆G o ), and entropy change (∆S o ) were analysed to identify the spontaneity and exothermic nature of the adsorption. Besides, the phytotoxicity trials on Cicer arietinum seeds revealed 0%, 80%, 87%, and 100% germination in the experimental MB solution, treated MB solution, MB-loaded AHLP, and fresh water, respectively, confirming the non-toxicity of both the treated MB solution and MB-loaded AHLP adsorbent. Therefore, the AHLP adsorbent might be a potential material for wastewater management due to its several advantages, like cost-free, abundant, easy to prepare, fast and high efficiency, and eco-friendly.
Surface modification of polypyrrole via affinity peptide: quantification and mechanism (2012)

The conducting polymer, polypyrrole (PPy), is an exciting substrate for basic research to study cell behavior in the presence of exogenous electric fields and has potential for clinical application as a coating for neural electrodes. However, typical surface modification approaches (e.g., copolymerization of pyrrole and pyrrole derivatives, post-polymerization modification, doping with functional biomolecules) reduce the electrical conductivity and hence the utility of the material. In previous work, a 12 amino acid peptide, T59, was evolved to bind to PPy and provide a novel means of surface modification that does not reduce the bulk conductivity. In the current study, we have used equilibrium binding assays and force spectroscopy to determine that the affinity of T59 to PPy is 92.6 ± 21.4 nM, with a maximum surface density of 5.1 ± 1.7 femtomoles per cm<sup>2</sup> by equilibrium binding assay, and that the off-rate of this binding pair is 2.5 s<sup>-1</sup>, with a calculated on-rate of 2.6 × 10<sup>7</sup> M<sup>-1</sup> s<sup>-1</sup>. This suggests that T59 possesses a high affinity for PPy with binding that occurs in a rapid equilibrium. We also present evidence in support of a proposed mechanism of binding for T59 to PPy; an association of an aspartic acid (D8) and the delocalized positive charge on the backbone of oxidized PPy is indicated as the key interaction. Understanding the binding parameters and mechanism of this novel bio/synthetic interface is important as we try to understand how best to employ PPy-based materials.
Progress in the detection of neoplastic progress and cancer by Raman spectroscopy (2000)

Early detection of cancer is important because of the improved survival rates when the cancer is treated early. We study the application of NIR Raman spectroscopy for detection of dysplasia because this technique is sensitive to the small changes in molecular invasive in vivo detection using fiber-optic probes. The result of an in vitro study to detect neoplastic progress of esophageal Barrett's esophageal tissue will be presented. Using multivariate statistics, we developed three different linear discriminant analysis classification models to predict tissue type on the basis of the measured spectrum. Spectra of normal, metaplastic and dysplasia tissue could be discriminated with an accuracy of up to 88 percent. Therefore Raman spectroscopy seems to be a very suitable technique to detect dysplasia in Barrett's esophageal tissue.
Supplemental Figure S3 from Histone Deacetylase HDAC8 Promotes Insulin Resistance and β-Catenin Activation in NAFLD-Associated Hepatocellular Carcinoma (2023)

&lt;p&gt;HDAC8 promotes insulin resistance.&lt;/p&gt;
Wear Reduction Method for Frictionally Fast Feeding Piezoactuator (2006)

A new wear reduction method, which is based on a static friction without slipping, is developed for a frictionally fast feeding piezoactuator. This method is required for overcoming the problems related to the scattering of particles due to the use of a contact type actuator. Furthermore, wear reduction result in a frictionally driving actuator with a long-term stability for various applications, such as the electron beam inspection in the next-generation semiconductor industry.
Development of a Simulator for Stochastic Deployment of Wireless Sensor Networks (2009)

This paper presents an open framework and detailed procedures for creating simulators that address application-specific deployment of Wireless Sensor Network (WSN). The presented framework and developed models are combined in a deployment simulator. The simulator assists decision-makers in selecting among different WSN deployment alternatives. The outlined software framework serves as a blueprint for creating deployment simulators that take into account application specific factors and may be used for optimization of WSN stochastic deployments.
Charge Stripping Reaction (CSR) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.