gebhart/patrepeval huggingface dataset:
Accuracy enhancement using spectral postprocessing for differential equations and integral equations (2009)

Abstract. It is demonstrated that spectral methods can be used to improve the accuracy of numerical solutions obtained by some lower order methods. More precisely, we can use spectral methods to postprocess numerical solutions of initial value differential equations. After a few number of iterations (say 3 to 4), the errors can decrease to a few orders of magnitude less. The iteration uses the Gauss-Seidel type strategy, which gives an explicit way of postprocessing. Numerical examples for ODEs, Hamiltonian system and integral equations are provided. They all indicate that the spectral processing technique can be a very useful way in improving the accuracy of the numerical solutions. In particular, for a Hamiltonian system accuracy is only one of the issues; some other conservative properties are even more important for large time simulations. The spectral postprocessing with the coarse-mesh symplectic initial guess can not only produce high accurate approximations but can also save a significant amount of computational time over the standard symplectic schemes.
Is information-centric multi-tree routing feasible? (2013)

We have argued that an information-centric network should natively support publish/subscribe event notification in addition to on-demand content delivery. We have also argued that both primitives could use the same forwarding information base and, furthermore, that both primitives can easily support addresses that are more expressive than simple hierarchical names. In this paper we present a concrete routing scheme that realizes this: "push" as well as "pull" communication; anycast as well as multicast; and descriptor-based (as opposed to name-based) addressing. The scheme is founded on multiple tree covers that can be arranged and composed hierarchically following the structure of network domains. On each tree, the scheme combines addresses so as to reduce forwarding state. We demonstrate the feasibility and scalability of the scheme through simulations on Internet-scale workloads in realistic network settings.
LTE UE Energy Saving by Applying Carrier Aggregation in a HetNet Scenario (2013)

In this work it is examined if downlink Carrier Aggregation (CA) can be used to save UE energy. A dual-receiver LTE release 10 UE is compared with a single-receiver LTE release 8 UE. The models are based on scaling of an existing LTE release 8 UE power model. The energy consumption of the UEs is examined in a Heterogeneous Network scenario consisting of macro and small cells. The unexpected conclusion is that CA UEs can save energy, compared to LTE release 8 UEs, if they, depending on cell load, experience a throughput gain of 20 %. However if the UE throughput is unaltered the energy consumption can increase up to 20 %.
Imprinted tumor suppressor genes ARHI and PEG3 are the most frequently down‐regulated in human ovarian cancers by loss of heterozygosity and promoter methylation (2008)

Loss of expression of the growth-inhibitory imprinted genes ARHI and PEG3 through promoter methylation, LOH, and other mechanisms may stimulate clonogenic growth and contribute to the pathogenesis of a majority of ovarian cancers.
Inhibition of osteoclastogenesis and inflammation by phosvitin and phosvitin hydrolysate via NF-κB and MAPK pathways in RAW 264.7 cells (2021)

Phosvitin (PV) is an egg protein. Our recent study showed both phosvitin and phosvitin hydrolysate (PVH) could promote osteoblast differentiation in osteoblast cells. The objective of the study was to investigate the effects of PV and PVH on osteoclastogenesis and possible signalling pathways in RAW264.7 cells. Both PV and PVH inhibited osteoclastogenesis (fewer tartrate-resistant acid phosphatase (TRAP) positive cells and lower TRAP activity), reduced levels of transcription factors, c-Fos and NFATc1 (nuclear factor of activated T-cells, cytoplasmic 1), and suppressed inflammatory biomarkers TNF-α (tumor necrosis factor alpha), MCP-1 (monocyte chemoattractant protein 1), RANTES (regulated on activation, normal T cell expressed and secreted), and inducible nitric oxide synthase. The inhibitory effects of PV and PVH on RAW264.7 cells differentiation were likely mediated through p38, c-Jun N-terminal kinases (JNK) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathways. These results indicated that PV and PVH might inhibit bone resorption activities.
Performance Assessment of Linear State Estimators Using Synchrophasor Measurements (2016)

This paper aims to assess the performance of linear state estimation (SE) processes of power systems relying on synchrophasor measurements. The performance assessment is conducted with respect to two different families of SE algorithms, i.e., static ones represented by weighted least squares (WLS) and recursive ones represented by Kalman filter (KF). To this end, this paper firstly recalls the analytical formulation of linear WLS state estimator (LWLS-SE) and Discrete KF state estimator (DKF-SE). We formally quantify the differences in the performance of the two algorithms. The validation of this result, together with the comprehensive performance evaluation of the considered state estimators, is carried out using two case studies, representing distribution (IEEE 123-bus test feeder) and transmission (IEEE 39-bus test system) networks. As a further contribution, this paper validates the correctness of the most common process model adopted in DKF-SE of power systems.
PHOTOBIOSTIMULATION BY LIGHT-INDUCED CYTOSOLIC CALCIUM OSCILLATIONS (1996)

We discuss light-induced stimulation of biological activity in terms of crytosolic calcium ion concentration oscillations triggered by visible or infrared irradiation of the cells. In the visible region, endogenous or exogenous photosensitizers lead to the formation of reactive oxygen species (ROS) which stimulate the redox activity of the respiratory chain (RC). However, there is competition between photosensitization and intramolecular electronic-vibrational energy transfer from an endogenous photosensitizer to an enzyme of the RC, bringing this enzyme into an inactive configuration and thereby paralyzing the RC. Moreover, there is competition between stimulation of the redox activity of the RC by the ROS and a slower reaction of the enzymes of the RC with the ROS which again paralyzes the RC. The paralysis of the RC plays a dominant rôle in the case of ROS overproduction between reactivation of the ATPase ion pumps in the cell membranes and inhibition of the enzymes of the RC resulting from vibrational overtone excitation. Vibrational heating leading to similar effects may also be achieved by infrared laser-induced multiphoton excitation. Because of the negative influence of the competing processes, optimal irradiation conditions must be achieved to obtain photobiostimulation.
Corneal minimal visible lesion thresholds for 20 μm laser radiation (2007)

To support refinement of the ANSI Maximum Permissible Exposure safety limits, a series of experiments were conducted in vivo on Dutch Belted rabbit corneas to determine corneal minimum visible lesion thresholds for 2.0 microm continuous-wave laser irradiation. Single pulse radiant exposures were made at specified pulse durations of 0.1, 0.25, 0.5, 1.0, 2.0, and 4.0 s for spot 1/e(2) diameters of 1.17 mm and 4.02 mm. Threshold lesions were defined as the presence of a superficial surface whitening one hour after irradiation. Temperature measurements indicated that threshold peak temperatures were dependent on spot size and exposure duration. The exposure duration dependence of threshold average radiant exposure was described by an empirical power law equation: threshold radiant exposure[J/cm(2)]=a x exposure duration[s](b).
Abstract 5063: Predicting target driven toxicity for small molecule inhibitors to aid in drug development (2022)

Abstract Adverse events and toxicity concerns account for roughly 50% of clinical trial failures and the majority of drug withdrawals. A large part of these toxicity effects can be explained by a drug’s molecular target, known off targets or a drug’s lack of specificity. Therefore, the understanding of a target’s potential toxicity is crucial in the drug development process, potentially informing therapeutic hypotheses and/or chemical design. Here, we introduce a machine learning model to predict a gene’s likelihood to result in patient toxicity when inhibited, independent of chemical compound information. We used information on drug approvals, discontinuations and withdrawals from the FDA to define “toxic” and “safe” targets, to be used as training data. Our model leveraged preclinical, gene-specific features that can be easily collected such as tissue expression, pathway involvement, and loss of function data, and achieves significant predictive performance (ROC = 0.80). We validated our model’s ability to discriminate between successful and unsuccessful drug candidates based on their predicted target toxicity. Furthermore, our model was able to predict differences in toxicity between gene isoforms, which were in agreement with published in vivo evidence, further highlighting its ability to be applied to guide drug development and lead optimization. By applying our model, the prediction of target-specific toxicity can guide drug screenings, prioritize candidates and avoid costly and dangerous drug failures. Citation Format: Manuel Garcia-Quismondo, Mukti Parikh, Neel Madhukar, Coryandar Gilvary. Predicting target driven toxicity for small molecule inhibitors to aid in drug development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5063.
Acoustic propagation in aperiodic transition layers and waveguides (1980)

Wave propagation in inhomogeneous media is studied by a new method, the ’’cutting-out’’ Jessel’s method. Emphasis is on transition layers, where both the sound velocity and density variations are taken into account. Several classes of layers are studied and impedance matching by a smooth dioptre is described. By using the analogy between inhomogeneous media and waveguides, this property of impedance matching has been extended to connecting horns, thus leading to the definition of a new family : the aperiodic horns.
Tyrosine Phosphorylation of Tub and Its Association with Src Homology 2 Domain-containing Proteins Implicate Tub in Intracellular Signaling by Insulin (1999)

A mutation in the tub gene leads to maturity-onset obesity, insulin resistance, and progressive retinal and cochlear degeneration in mice. tub is a member of a growing family of genes that encode proteins of unknown function that are remarkably conserved across species. The absence of obvious transmembrane domain(s) or signal sequence peptide motif(s) suggests that Tub is an intracellular protein. Additional sequence analysis revealed the presence of putative tyrosine phosphorylation motifs and Src homology 2 (SH2)-binding sites. Here we demonstrate that in CHO-IR cells, transfected Tub is phosphorylated on tyrosine in response to insulin and insulin-like growth factor-1 and that in PC12 cells, insulin but not EGF induced tyrosine phosphorylation of endogenous Tub. In vitro, Tub is phosphorylated by purified insulin receptor kinase as well as by Abl and JAK 2 but not by epidermal growth factor receptor and Src kinases. Furthermore, upon tyrosine phosphorylation, Tub associated selectively with the SH2 domains of Abl, Lck, and the C-terminal SH2 domain of phospholipase Cgamma and insulin enhanced the association of Tub with endogenous phospholipase Cgamma in CHO-IR cells. These data suggest that Tub may function as an adaptor protein linking the insulin receptor, and possibly other protein-tyrosine kinases, to SH2-containing proteins.
Epididymal Lipocalin-Type Prostaglandin D2 Synthase: Identification Using Mass Spectrometry, Messenger RNA Localization, and Immunodetection in Mouse, Rat, Hamster, and Monkey1 (2002)

This study identified prostaglandin D2 synthase (PGDS) in murine epididymal fluid using a proteomic approach combining two-dimensional (2D) gel electrophoresis and mass spectrometry (MS). The caudal epididymal fluid was collected by retroperfusion, and proteins were separated by 2D gel electrophoresis followed by matrix-assisted laser desorption ionization MS analyses after trypsin digestion. The identification was based on the protein-specific peptide map as well as on sequence information generated by nano-electrospray ionization MS/MS. By in situ hybridization, the mRNA was detected in caput, corpus, and cauda, but it was not detected in the initial segment. The PGDS protein was mostly detected in the corpus and cauda by Western blot analysis and immunohistochemistry using a specific polyclonal antibody. In caudal fluid, PGDS was distributed among several isoforms (pI range, 6.5-8.8), suggesting that this protein undergoes posttranslational modification of its primary sequence. After N-glycanase digestion, the molecular mass decreased from 20-25 to 18.5 kDa, its theoretical mass. The PGDS was also detected in the epididymis of rat, hamster, and cynomolgus monkey from the caput to the cauda. In conclusion, MS is a powerful and accurate technique that allows unambiguous identification of the murine epididymal PGDS. The protein is 1) present throughout the epididymis, except in the initial segment, with an increasing luminal concentration from distal caput to cauda; 2) a major protein in caudal fluid; 3) an N-glycosylated, highly polymorphic protein; and 4) conserved during evolution.
Gas Phase Reactivity of Carboxylates with N-Hydroxysuccinimide Esters (2014)

N-hydroxysuccinimide (NHS) esters have been used for gas-phase conjugation reactions with peptides at nucleophilic sites, such as primary amines (N-terminus, ε-amine of lysine) or guanidines, by forming amide bonds through a nucleophilic attack on the carbonyl carbon. The carboxylate has recently been found to also be a reactive nucleophile capable of initiating a similar nucleophilic attack to form a labile anhydride bond. The fragile bond is easily cleaved, resulting in an oxygen transfer from the carboxylate-containing species to the reagent, nominally observed as a water transfer. This reactivity is shown for both peptides and non-peptidic species. Reagents isotopically labeled with O(18) were used to confirm reactivity. This constitutes an example of distinct differences in reactivity of carboxylates between the gas phase, where they are shown to be reactive, and the solution phase, where they are not regarded as reactive with NHS esters.
SCM optical multiple-access network with cascaded optical modulators (1993)

The authors propose a novel optical multiple-access network with cascaded optical intensity modulators using subcarrier multiplexing (SCM). This network is free from beat noise because each node shares signal light from one transmitter laser diode (LD) with the other nodes. The properties involved in intermodulation distortion due to cascade connection of the optical modulators were analyzed, and the applicability of this network to a video monitoring system was investigated. Results indicate that a wide-area monitoring system with 260-km transmission distance and 52 video terminals is possible with the proposed network.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Furnace gas-phase chemistry of silicon oxynitridation in N2O (1996)

During furnace N2O-based silicon oxynitride growth, the total concentration of NOx species varies strongly with the flow rate of N2O. At low flow rates the N2O decomposes at least partially in the cooler region of the furnace near the gas inlet. This results in lower than expected NOx (x=1,2) concentrations in the oxidizing ambient. At high flow rates, the exothermic decomposition of N2O can heat the inlet region of the furnace, resulting in decomposition at a temperature above the nominal furnace temperature and higher than expected NOx concentrations. These effects can lead to a substantial variation in the concentration of N in the oxynitride as a function of N2O flow.
Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs (2012)

A combinatorial genetic perturbation strategy was applied to interrogate the yeast kinome on a genome-wide scale. We assessed the global effects of gene overexpression or gene deletion to map an integrated genetic interaction network of synthetic dosage lethal (SDL) and loss-of-function genetic interactions (GIs) for 92 kinases, producing a meta-network of 8700 GIs enriched for pathways known to be regulated by cognate kinases. Kinases most sensitive to dosage perturbations had constitutive cell cycle or cell polarity functions under standard growth conditions. Condition-specific screens confirmed that the spectrum of kinase dosage interactions can be expanded substantially in activating conditions. An integrated network composed of systematic SDL, negative and positive loss-of-function GIs, and literature-curated kinase-substrate interactions revealed kinase-dependent regulatory motifs predictive of novel gene-specific phenotypes. Our study provides a valuable resource to unravel novel functional relationships and pathways regulated by kinases and outlines a general strategy for deciphering mutant phenotypes from large-scale GI networks.
Role of vasopressin in diabetes mellitus-induced changes in medullary transport proteins involved in urine concentration in Brattleboro rats (2004)

In rats with streptozotocin-induced diabetes mellitus for 10-20 days, we showed that the abundance of the major medullary transport proteins involved in the urinary concentrating mechanism, urea transporter (UT-A1), aquaporin-2 (AQP2), and the Na+-K+-2Cl- cotransporter (NKCC2/BSC1), is increased, despite the ongoing osmotic diuresis. To test whether vasopressin is necessary for these diabetes mellitus-induced changes in UT-A1, AQP2, or NKCC2/BSC1, we studied Brattleboro rats because they lack vasopressin. Brattleboro rats were given vasopressin (2.4 microg/day via osmotic minipump) for 5 or 12 days. At 5 days, vasopressin increased AQP2 protein abundance but decreased UT-A1 abundance compared with untreated Brattleboro rats. At 12 days, vasopressin increased the abundance of both UT-A1 and AQP2 proteins but did not alter NKCC2/BSC1. Next, untreated Brattleboro rats were made diabetic for 10 days by injecting them with streptozotocin (40 mg/kg). Diabetes mellitus increased the abundance of AQP2 and NKCC2/BSC1 proteins, but UT-A1 protein abundance did not increase. Third, vasopressin-treated Brattleboro rats were made diabetic with streptozotocin for 10 days. In vasopressin-treated Brattleboro rats, diabetes mellitus increased UT-A1, AQP2, and NKCC2/BSC1 protein abundances. Vasopressin significantly increased UT-A1 phosphorylation in vasopressin-treated diabetic Brattleboro rats but not in the other groups of Brattleboro rats. We conclude that 1) administering vasopressin to Brattleboro rats for 12 days, but not for 5 days, increases UT-A1 protein abundance and 2) vasopressin is necessary for the increase in UT-A1 protein in diabetic rats but is not necessary for the increase in AQP2 or NKCC2 proteins.
Exposure to leachates from post-consumer plastic and recycled rubber causes stress responses and mortality in a copepod Limnocalanus macrurus (2021)

Effects of household post-consumer plastics and tyre rubber on a Baltic Sea copepod Limnocalanus macrurus were assessed. Fragments of commercial recycled low-density polyethylene vegetable bags and rubber originating from recycled car tyres were incubated in seawater, and the copepods were exposed to the filtrate of the water. L. macrurus experienced erratic swimming behaviour and increased mortality in the filtrate of unwashed vegetable bags, containing elevated concentrations of alcohols, organic acids and copper. Responses of the antioxidant defence system (ADS) were recorded in copepods exposed to rubber treatments containing high concentrations of zinc. Significant responses in the ADS enzymes indicate that reactive oxygen species (ROS) formation was exceeding the detoxification capacity of the ADS which may further lead to prolonged state of oxidative stress. Observed effects of exposure on the biochemical level coincide with impaired swimming activity of the copepods, indicating possible irreversible cellular responses leading to behavioural changes and mortality.
An introduction to entrepreneurship (2021)

While often associated with start-up formation, entrepreneurship is considered a fundamental and transformat ional shi ft in how one interacts with and views the world. As championed by Prof. Stevenson and Prof. Eisenmann at the Harvard Business School, "Entrepreneurship is the pursuit of opportunity beyond resources controlled," and this definition embodies the guiding forces critical for success.
Electrochemical Detection of Hydrogen Peroxide Based on Graphene Oxide/Prussian Blue Modified Glassy Carbon Electrode (2012)

Prussian blue (PB) and graphene oxide (GO) were synthesized and characterized by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy among others. The synthesized Prussian blue and graphene oxide were used in the modification of glass carbon electrodes for the chemical detection of hydrogen peroxide at pH 3, 5.12 and 7.4. Cyclic and square wave voltammetry of GC-PB and GC-GO-PB electrodes show significant cathodic and anodic detection of hydrogen peroxide predominantly at pH 5.12 and 7.4 indicating one electron transfer reaction at the electrode surface.
New Hybrid Latexes from a Soybean Oil-Based Waterborne Polyurethane and Acrylics via Emulsion Polymerization (2007)

A series of new waterborne polyurethane (PU)/acrylic hybrid latexes have been successfully synthesized by the emulsion polymerization of acrylic monomers (butyl acrylate and methyl methacrylate) in the presence of a soybean oil-based waterborne PU dispersion using potassium persulfate as an initiator. The waterborne PU dispersion has been synthesized by a polyaddition reaction of toluene 2,4-diisocyanate and a soybean oil-based polyol (SOL). The resulting hybrid latexes, containing 15-60 wt % SOL as a renewable resource, are very stable and exhibit uniform particle sizes of 125 +/- 20 nm as determined by transmittance electronic microscopy. The structure, thermal, and mechanical properties of the resulting hybrid latex films have been investigated by Fourier transform infrared spectroscopy, solid state 13C NMR spectroscopy, dynamic mechanical analysis, extraction, and mechanical testing. Grafting copolymerization of the acrylic monomers onto the PU network occurs during the emulsion polymerization, leading to a significant increase in the thermal and mechanical properties of the resulting hybrid latexes. This work provides a new way of utilizing renewable resources to prepare environmentally friendly hybrid latexes with high performance for coating applications.
Nucleosides. Part 3.1Synthesis of 2-N-Substituted 1-β-D-Arabinofuranosylisocytosine Derivatives by The Reaction of 2′,5′-Dichloro-2′,5′-Dideoxyuridine with Amines (1985)

Abstract Reaction of 2′,5′-dichloro-2′,5′-dideoxyuridine (1) with ammonia and benzylamine afforded the corresponding 2-N-substituted 1-(5-chloro-5-deoxy-β-D-arabinofuranosyl)-isocytosine derivatives (2 and 10). Reaction of 1 with ammonia, methylamine, cyclohexylamine, and benzylamine followed by treatment with methanolic sodium methoxide gave the corresponding 2-N-substituted 1-(2,5-anhydro-β-D-arabino-furanosyl)isocytosine derivatives (6, 11, and 12).
Effects of albumin and Ringer’s lactate on production of lung cytokines and hydrogen peroxide after resuscitated hemorrhage and endotoxemia in rats (2003)

We conclude that resuscitation with albumin may have utility in reducing ventilator-induced lung injury after hemorrhagic shock, but not after endotoxic shock. These findings suggest that the mechanisms leading to ventilator-induced lung injury after hemorrhage differ from those after endotoxemia.