gebhart/patrepeval huggingface dataset:
Flame Stabilization and Multimode Heat Transfer in Inert Porous Media: A Numerical Study (1990)

Abstract This paper presents a numerical analysis of combustion and multimode heat transfer in inert porous media. The work is directly relevant to the understanding of premixed flame stabilization in porous radiant burners. The influence of the flame location, the radiative properties of the porous material, the solid thermal conductivity, and stoichiometry on the flame speed and stability are determined using a one-dimensional conduction, convection, radiation, and combustion model. The porous medium is allowed to emit, absorb, and scatter radiant energy, Non-local thermal equilibrium between the solid and gas is accounted for by introducing separate energy equations for the two phases. Heat release is described by a single-step, global reaction. The results indicate that stable combustion at elevated flame speeds can be maintained in two different spatial domains. Flame propagation near the edge of the porous layer is controlled mostly by solid-phase conduction; whereas, in the interior both solid conduction and radiation heal transfer are important. The radiative characteristics of the porous matrix such as the optical depth and scattering albedo were also shown to have a considerable effect on flame stability
Study on the Hydrophobic Fluorinated Amorphous Carbon(a-C:F) Film Deposited by DBD-PECVD (2009)

Fluorocarbon films were prepared by DBD-PECVD with C4F8 as discharging gas, which were characterized by Fourier transform infrared spectroscopy(FTIR),atomic force microscopy(AFM),contact angle measurements and profilometry.The effects of discharge pressure and deposition time on the film properties,such as deposition rates,RMS surface roughness,and a-C:F film hydrophobicity have been investigated.Results show that film deposition rate increases with increasing deposition pressure,with a maximum value of 193 nm·min-1.At lower deposition pressure,RMS value is below 1.0nm,at higher pressure,RMS valure will exceed 100 nm.All deposited fluorocarbon films show the hydrophobic surface properties,with a contact angle up to 137°.The surface roughness of a-C:F film will effect its hydrophobic properties in a remarkable extent.
Optimizing High-Throughput Metabolomic Biomarker Screening: A Study of Quenching Solutions to Freeze Intracellular Metabolism in CHO Cells (2012)

Metabolomics is a rapidly emerging tool for studying and optimizing both media and bioprocess development for culturing recombinant mammalian cells that are used in protein production processes. Quenching of the cells is crucial to fix their metabolic status at the time of sampling. Three precooled quenching solutions were tested for their ability to fix the metabolic activity of CHO cells: phosphate-buffered saline (PBS) (pH 7.4; 0.5°C), 60% methanol with 70 mM HEPES (pH 7.4; -20°C), and 60% methanol with 0.85% (w/v) ammonium bicarbonate (AMBIC) (pH 7.4; -20°C). The metabolic activity of the sampled CHO cells was assessed by determining the intracellular levels of ATP using a bioluminescence assay and selected metabolites with LC-MS/MS. We found the precooled PBS (pH 7.4; 0.5°C) to be the optimal quenching reagent for fixing intracellular metabolism. Importantly, the structural integrity of the cell membrane was maintained and highest yields were obtained for intracellular levels of ATP as well as for 18 out of 28 intracellular metabolites. In contrast to the previously reported studies, buffered methanol quenching was not applicable for suspension cultured CHO cells as cellular membrane integrity was affected. We recommend that the cells are quenched and washed simultaneously to keep the sampling time to a minimum and to prevent any further metabolic activity in the cells. We observed that additional washing steps are not required. Our analyses suggest that methanol as quenching solution, even in combination with a buffer substance, appears not suitable for quenching sensitive mammalian cells. The protocol we report herein is a simple cell sampling method that enables high-throughput metabolomic analyses and is suitable for a large number of samples.
Structure of the cold- and menthol-sensing ion channel TRPM8 (2017)

Transient receptor potential melastatin (TRPM) cation channels are polymodal sensors that are involved in a variety of physiological processes. Within the TRPM family, member 8 (TRPM8) is the primary cold and menthol sensor in humans. We determined the cryo-electron microscopy structure of the full-length TRPM8 from the collared flycatcher at an overall resolution of ~4.1 ångstroms. Our TRPM8 structure reveals a three-layered architecture. The amino-terminal domain with a fold distinct among known TRP structures, together with the carboxyl-terminal region, forms a large two-layered cytosolic ring that extensively interacts with the transmembrane channel layer. The structure suggests that the menthol-binding site is located within the voltage-sensor-like domain and thus provides a structural glimpse of the design principle of the molecular transducer for cold and menthol sensation.
Screening for Dimethylarginine Dimethylaminohydrolase Inhibitors Reveals Ebselen as a Bioavailable Inactivator (2011)

Dimethylarginine dimethylaminohydrolase (DDAH) is an endogenous regulator of nitric oxide production and represents a potential therapeutic target. However, only a small number of biologically useful inhibitors have been reported, and many of these are substrate analogs. To seek more diverse scaffolds, we developed a high-throughput screening (HTS) assay and queried two small libraries totaling 2446 compounds. The HTS assay proved to be robust, reproducible and scalable, with Z' factors ≥ 0.78. One inhibitor, ebselen, is structurally divergent from substrate and was characterized in detail. This selenazole covalently inactivates DDAH in vitro and in cultured cells. The rate constant for inactivation of DDAH (44,000 ± 2,400 M(-1)s(-1)) is greater than those reported for any other target, suggesting this pathway is an important aspect of ebselen's total pharmacological effects.
Predicting the <i>Cis−Trans</i> Dichloro Configuration of Group 15−16 Chelated Ruthenium Olefin Metathesis Complexes: A DFT and Experimental Study (2009)

Gradient-corrected (BP86) and hybrid (M06-L) density functional calculations were used to study the relative stability of cis and trans-dichloro X-chelated benzylidene ruthenium complexes (X = O, S, Se, N, P). Calculations in the gas phase differed from experimental results, predicting the trans-dichloro configuration as being more stable in every case. The addition of Poisson-Boltzmann (PBF) continuum approximation (dichloromethane) corrected the disagreement and afforded energies consistent with experimental results. Novel N, Se, and P chelated ruthenium olefin metathesis complexes were synthesized to evaluate calculation predictions. These findings reinforce the importance of including solvent corrections in DFT calculations of ruthenium metathesis catalysts and predict that stronger sigma donors as chelating atoms tend to electronically promote the unusual and less active cis-dichloro configuration.
Evaluation and comparison of clustering algorithms in analyzing es cell gene expression data (2002)

Many clustering algorithms have been used to analyze microarray gene expression data. Given embryonic stem cell gene expression data, we applied several indices to evaluate the performance of clustering algorithms, including hierarchical clustering, k-means, PAM and SOM. The indices were homogeneity and separation scores, silhouette width, redundant score (based on redundant genes), and WADP (testing the robustness of clustering results after small perturbation). The results showed that the ES cell dataset posed a challenge for cluster analysis in that the clusters generated by different methods were only partially consistent. Using this data set, we were able to evaluate the advantages and weaknesses of algorithms with respect to both internal and external quality measures. This study may provide a guideline on how to select suitable clustering algorithms and it may help raise relevant issues in the extraction of meaningful biological information from microarray expression data. Keywords cluster analysis; gene expression; microarray; mouse embryonic stem cell
Digital methods of offset compensation in 90nm CMOS operational amplifiers (2013)

This paper deals with comparison of two discrete methods for digital trimming of the input offset voltage in operation amplifiers designed in 90nm CMOS technology. Two different topologies based on the binary weighed ladder, one using successive approximation register (SAR) and the other employing a simple counter, were compared. Furthermore, a correction circuit was proposed and used to form the mean offset voltage and increase the probability that its value after trimming process will be near zero. Finally, achieved results and improvements are discussed.
Continuous-wave mid-infrared laser sources based on difference frequency generation (2007)

We report on recent developments of widely tunable, continuous-wave (CW) laser sources based on difference-frequency generation (DFG) in nonlinear optical materials. The state-of-the-art of CW DFG technology will be reviewed. Applications of the DFG-based laser source to high-resolution molecular spectroscopy and trace gas detection will be presented. New development trends of DFG will be discussed.
TLS-N: Non-repudiation over TLS Enabling - Ubiquitous Content Signing for Disintermediation. (2017)

An internet user wanting to share observed content is typically restricted to primitive techniques such as screenshots, web caches or share button-like solutions. These acclaimed proofs, however, are either trivial to falsify or require trust in centralized entities (e.g., search engine caches). This motivates the need for a seamless and standardized internet-wide non-repudiation mechanism, allowing users to share data from news sources, social websites or financial data feeds in a provably secure manner. Additionally, blockchain oracles that enable data-rich smart contracts typically rely on a trusted third party (e.g., TLSNotary or Intel SGX). A decentralized method to transfer web-based content into a permissionless blockchain without additional trusted third party would allow for smart contract applications to flourish. In this work, we present TLS-N, the first TLS extension that provides secure non-repudiation and solves both of the mentioned challenges. TLS-N generates non-interactive proofs about the content of a TLS session that can be efficiently verified by third parties and blockchain based smart contracts. As such, TLS-N increases the accountability for content provided on the web and enables a practical and decentralized blockchain oracle for web content. TLS-N is compatible with TLS 1.3 and adds a minor overhead to a typical TLS session. When a proof is generated, parts of the TLS session (e.g., passwords, cookies) can be hidden for privacy reasons, while the remaining content can be verified.
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology (2008)

DNA topoisomerases are a diverse set of essential enzymes responsible for maintaining chromosomes in an appropriate topological state. Although they vary considerably in structure and mechanism, the partnership between topoisomerases and DNA has engendered commonalities in how these enzymes engage nucleic acid substrates and control DNA strand manipulations. All topoisomerases can harness the free energy stored in supercoiled DNA to drive their reactions; some further use the energy of ATP to alter the topology of DNA away from an enzyme-free equilibrium ground state. In the cell, topoisomerases regulate DNA supercoiling and unlink tangled nucleic acid strands to actively maintain chromosomes in a topological state commensurate with particular replicative and transcriptional needs. To carry out these reactions, topoisomerases rely on dynamic macromolecular contacts that alternate between associated and dissociated states throughout the catalytic cycle. In this review, we describe how structural and biochemical studies have furthered our understanding of DNA topoisomerases, with an emphasis on how these complex molecular machines use interfacial interactions to harness and constrain the energy required to manage DNA topology.
Use of Sterol Mutants as Probes for Sterol Functions in the Yeast,<i>Saccharomyces cerevisiae</i> (1999)

(1999). Use of Sterol Mutants as Probes for Sterol Functions in the Yeast, Saccharomyces cerevisiae. Critical Reviews in Biochemistry and Molecular Biology: Vol. 34, No. 6, pp. 399-404.
Omni-directional rain sensor utilizing scattered light reflection by water particle on automotive windshield glass (2011)

Omni-directional rain sensor utilizing scattered light detection reflected by rain or moisture on windshield glass is realized, while conventional rain sensor senses disturbances at point or line on windshield glass along light path. Modulated light from light source is emitted without directional pattern, and light block fixture is placed between light source and photodiode to prevent direct propagation to photodiode. Water particle on windshield glass behaved as scattering medium, and it relayed light signal from light source to photodiode over light block fixture. This sensing mechanism eliminated any optical elements such as lens, while this expanded sensing area in 2 dimensions in contrast to conventional narrow sensing spot or line pattern. Time division sensing algorithm was used to discriminate raining intensity in 7 steps to apply as rain sensor in automobile. Experiments using simulated rain facility showed possibility as rain sensor for automotive application.
Unusual Morphologic Features of Uterine Leiomyomas Treated with Gonadotropin Releasing Hormone Agonists: Massive Lymphoid Infiltration and Vasculitis (2003)

This report describes 2 unusual morphologic features of leiomyomas in patients who had been treated preoperatively with gonadotropin-releasing hormone (GnRH) agonists. In 1 case there was extensive and widespread infiltration of the leiomyoma by numerous small mature lymphocytes, in keeping with a leiomyoma with massive lymphoid infiltration. In the other leiomyoma there were fibrin and foamy histiocytes within the walls of many arterioles, in keeping with a vasculitis. These 2 features, massive lymphoid infiltration and vasculitis, have rarely been described in association with GnRH agonists. Since GnRH agonists are increasingly being used in the management of uterine leiomyomas, pathologists should be aware of these unusual morphologic features in order to avoid diagnostic confusion.
Somatic hypermutation in antoimmune thyroid disease (1998)

Autoimmune thyroid disease is one of the most common autoimmune diseases. There is typically patient antibody (Ab) reactivity to one or more of the antigens thyroglobulin (Tg), thyroid peroxidase (TPO) and the thyroid simulating hormone receptor (TSHr). With the advent of combinatorial library technology, there has been an enormous increase in the number of sequences from Ab to Tg and TPO. The repertoire of both Tg and TPO Ab is restricted and indicates the importance of somatic hypermutation in the development of the high affinity Ab response. However, there are still too few sequences to determine patterns in which the mutation occurs, which residues are introduced during substitution and how individual substitutions affect the affinity of the Ab. Ab to the TSHr are of far greater pathological significance than those to Tg and TPO, but the current repertoire of Ab to the TSHr has yet to include the high affinity IgG Ab characteristic of patient serum Ab. Instructive analysis of the role of somatic hypermutation in the development of TSHr Ab therefore still awaits the isolation of the pathologically active repertoire. Despite this, the Ab response in thyroid autoimmunity remains one of the best characterised of human autoimmune diseases.
Nanostructured selenium for preventing biofilm formation on polycarbonate medical devices (2012)

Biofilms are a common cause of persistent infections on medical devices as they are easy to form and hard to treat. The objective of this study was for the first time to coat selenium (a natural element in the body) nanoparticles on the surface of polycarbonate medical devices (such as those used for medical catheters) and to examine their effectiveness at preventing biofilm formation. The size and distribution of selenium coatings were characterized using scanning electron microscopy and atomic force microscopy. The strength of the selenium coating on polycarbonate was assessed by tape-adhesion tests followed by atomic absorption spectroscopy. Results showed that selenium nanoparticles had a diameter of 50-100 nm and were well distributed on the polycarbonate surface. In addition, more than 50% of the selenium coating survived the tape-adhesion test as larger nanoparticles had less adhesion strength to the underlying polycarbonate substrate than smaller selenium nanoparticles. Most significantly, the results of this in vitro study showed that the selenium coatings on polycarbonate significantly inhibited Staphylococcus aureus growth to 8.9% and 27% when compared with an uncoated polycarbonate surface after 24 and 72 h, respectively. Importantly, this was accomplished without using antibiotics but rather with an element (selenium) that is natural to the human body. Thus, this study suggests that coating polymers (particularly, polycarbonate) with nanostructured selenium is a fast and effective way to reduce bacteria functions that lead to medical device infections. © 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 100A: 3205-3210, 2012.
Evaluation of BAUER High Pressure Breathing Air P-2 Purification System (1991)

The Navy Experimental Diving Unit (NEDU) tested the BAUER P-2 High Pressure, Breathing Air Purification System from 16 July 1991 to 19 July 1991. The purpose of this test was to determine if the P-2 Air Purification System functioned as specified and was suitable for use by the U.S. Navy. Additionally, if the system passed the test criteria a recommendation would be made to add it to the Approved for Navy Use (ANU) list. The BAUER P-2 Purification System met the manufacturer's specifications for quantity of air processed with a quality which met U.S. Navy purity standards. The design and engineering were determined to be adequate. The BAUER P-2 Air purification System is considered suitable for use with U.S. Navy divers high pressure breathing air compressors.
Reactivity of 3d Transition Metal Cations in Diethylene Glycol Solutions. Synthesis of Transition Metal Ferrites with the Structure of Discrete Nanoparticles Complexed with Long-Chain Carboxylate Anions (2002)

Study of the reactivity of 3d transition metal cations in diethylene glycol solutions revealed several key features that made it possible to develop a new method for synthesis of the nanocrystalline transition metal ferrites. The 3-7 nm particles of [MFe2O4]n[O2CR]m, where M = Mn, Fe, Co, Ni, and Zn, ligated on their surface with long-chain carboxylate anions, have been obtained in an isolated yield of 75-90%. The key features are the following. Complexation of the first-row transition metal cations with diethylene glycol at a presence of alkaline hydroxide is sufficient to enable control over the rate of their hydrolysis. The reaction of hydrolysis leads to the formation of metal oxide nanocrystals in colloidal solution. The nanoparticles growth is terminated by an added long-chain carboxylic acid, which binds to their surface and acts as a capping ligand. The isolated nanocrystalline powders are stable against agglomeration and highly soluble in nonpolar organic solvents.
HEPA/Vaccine Plan for Indoor Anthrax Remediation (2005)

We developed a mathematical model to compare 2 indoor remediation strategies in the aftermath of an outdoor release of 1.5 kg of anthrax spores in lower Manhattan. The 2 strategies are the fumigation approach used after the 2001 postal anthrax attack and a HEPA/vaccine plan, which relies on HEPA vacuuming, HEPA air cleaners, and vaccination of reoccupants. The HEPA/vaccine approach leads to few anthrax cases among reoccupants if applied to all but the most heavily contaminated buildings, and recovery is much faster than under the decades-long fumigation plan. Only modest environmental sampling is needed. A surge capacity of 10,000 to 20,000 Hazmat workers is required to perform remediation within 6 to 12 months and to avoid permanent mass relocation. Because of the possibility of a campaign of terrorist attacks, serious consideration should be given to allowing or encouraging voluntary self-service cleaning of lightly contaminated rooms by age-appropriate, vaccinated, partially protected (through masks or hoods) reoccupants or owners.
Coeliac Disease <i>The Presence in Wheat of a Factor Having a Deleterious Effect in Cases of Coeliac Disease</i> (1953)

Summary Attention is drawn to the different effects of different kinds of cereals and starches on patients with coeliac disease. The effect of wheat flour is unfavourable while that of wheat starch is harmless. The harmful effect is produced by a still unknown substance and not by starch. The substance in question is provisionally called the “wheat factor.” The effect of this factor is judged according to its ability to produce or aggravate anorexia, vomiting, diarrhoea and steatorrhoea. Several conclusions as to the significance of this factor are presented.
Conserved Motifs within Hepatitis C Virus Envelope (E2) RNA and Protein Independently Inhibit T Cell Activation (2015)

T cell receptor (TCR) signaling is required for T-cell activation, proliferation, differentiation, and effector function. Hepatitis C virus (HCV) infection is associated with impaired T-cell function leading to persistent viremia, delayed and inconsistent antibody responses, and mild immune dysfunction. Although multiple factors appear to contribute to T-cell dysfunction, a role for HCV particles in this process has not been identified. Here, we show that incubation of primary human CD4+ and CD8+ T-cells with HCV RNA-containing serum, HCV-RNA containing extracellular vesicles (EVs), cell culture derived HCV particles (HCVcc) and HCV envelope pseudotyped retrovirus particles (HCVpp) inhibited TCR-mediated signaling. Since HCVpp's contain only E1 and E2, we examined the effect of HCV E2 on TCR signaling pathways. HCV E2 expression recapitulated HCV particle-induced TCR inhibition. A highly conserved, 51 nucleotide (nt) RNA sequence was sufficient to inhibit TCR signaling. Cells expressing the HCV E2 coding RNA contained a short, virus-derived RNA predicted to be a Dicer substrate, which targeted a phosphatase involved in Src-kinase signaling (PTPRE). T-cells and hepatocytes containing HCV E2 RNA had reduced PTPRE protein levels. Mutation of 6 nts abolished the predicted Dicer interactions and restored PTPRE expression and proximal TCR signaling. HCV RNA did not inhibit distal TCR signaling induced by PMA and Ionomycin; however, HCV E2 protein inhibited distal TCR signaling. This inhibition required lymphocyte-specific tyrosine kinase (Lck). Lck phosphorylated HCV E2 at a conserved tyrosine (Y613), and phospho-E2 inhibited nuclear translocation of NFAT. Mutation of Y613 restored distal TCR signaling, even in the context of HCVpps. Thus, HCV particles delivered viral RNA and E2 protein to T-cells, and these inhibited proximal and distal TCR signaling respectively. These effects of HCV particles likely aid in establishing infection and contribute to viral persistence.
Development of Sensing and Computing Enhanced Passive RFID Tags Using the Wireless Identification and Sensing Platform (2009)

Development of Sensing and Computing Enhanced Passive RFID Tags Using the Wireless Identification and Sensing Platform