gebhart/patrepeval huggingface dataset:
Exploring writhe in supercoiled minicircle DNA (2006)

Using λ-Int recombination in E. coli, we have generated milligram quantities of supercoiled minicircle DNA. Intramolecular Int recombination was efficient down to lengths ~254 bp. When nicked and religated in the presence of ethidium bromide, 339 bp minicircles adopted at least seven unique topoisomers that presumably correspond to ΔLk ranging from 0 to -6, which we purified individually. We used these minicircles, with unique ΔLk, to address the partition into twist and writhe as a function of ΔLk. Gel electrophoresis and atomic force microscopy revealed progressively higher writhe conformations in the presence of 10 mM CaCl(2) or MgCl(2). From simplistic calculations of the bending and twisting energies, we predict the elastic free energy of supercoiling for these minicircles to be lower than if the supercoiling was partitioned mainly into twist. The predicted writhe corresponds closely with that which we observed experimentally in the presence of divalent metal ions. However, in the absence of divalent metal ions only limited writhe was observed, demonstrating the importance of electrostatic effects on DNA structure, when the screening of charges on the DNA is weak. This study represents a unique insight into the supercoiling of minicircle DNA, with implications for DNA structure in general.
Peroxisome-proliferator-activated receptor δ mediates the effects of long-chain fatty acids on post-confluent cell proliferation (2000)

Nutritional long-chain fatty acids control adipose tissue mass by regulating the number and the size of adipocytes. It is now established that peroxisome-proliferator-activated receptors (PPARs) play crucial functions in the control of gene expression and the level of cell differentiation. PPARgamma, which is activated by specific prostanoids, is a key factor in activating terminal differentiation and adipogenesis. We have recently demonstrated that PPARdelta, once activated by fatty acids, drives the expression of a limited set of genes, including that encoding PPARgamma, thereby inducing adipose differentiation. Thus far, the mechanism of action of fatty acids in the control of preadipocyte proliferation has remained unknown. We show here that PPARdelta is directly implicated in fatty acid-induced cell proliferation. Ectopic expression of PPARdelta renders 3T3C2 cells capable of responding to treatment with long-chain fatty acids by a resumption of mitosis, and this effect is limited to a few days after confluence. This response is restricted to PPARdelta activators and, for fatty acids, takes place within the range of concentrations found to trigger differentiation of preadipocytes both in vitro and in vivo. Furthermore, the use of a mutated inactive PPARdelta demonstrated that transcriptional activity of the nuclear receptor is required to mediate fatty acid-induced proliferation. These data demonstrate that PPARdelta, as a transcription factor, is directly implicated in fatty acid-induced proliferation, and this could explain the hyperplastic development of adipose tissue that occurs in high-fat-fed animals.
Bioaccessibility of inorganic arsenic species in raw and cooked Hizikia fusiforme seaweed (2004)

Abstract Samples of Hizikia fusiforme edible seaweed, a commercially available dried food with high concentrations of total arsenic (t‐As) and inorganic arsenic (i‐As), both raw and cooked (boiling at 100 °C, 20 min), were selected for the bioaccessibility study. Cooking caused a significant reduction in the concentrations of t‐As (30–43%) and i‐As (46–50%), despite which the i‐As contents in the cooked product were high (42.7–44.6 µg g −1 seaweed). An in vitro gastrointestinal digestion (pepsin, pH 2, and pancreatin–bile extract, pH 7) was applied to the seaweed to estimate arsenic bioaccessibility (maximum soluble concentration in gastrointestinal medium) of t‐As, i‐As, arsenic(III) and arsenic(V). The influence of the gastric and intestinal stages of the in vitro digestion method was evaluated. The gastric stage is the key stage in the solubilization of both t‐As and i‐As. The bioaccessible i‐As in raw seaweed (54.0–66.5%) increases after cooking (78.3–84.4%), a fact that is considered to be of interest because this is the usual form in which this seaweed is ingested. Speciation of the i‐As in the bioaccessible fraction revealed a different arsenic(III)/arsenic(V) relationship in the product when raw or cooked. When raw, the majority species was arsenic(III) after either the gastric or the gastrointestinal stage, whereas in the cooked product it depended on the batch analysed, with bioaccessible arsenic(III) contents of 7.1–25.4 µg g −1 of dried seaweed, which represents 5–17% of the i‐As tolerable daily intake. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Synthesis and Characterization of Zwitterionic Polymer Brush Functionalized Hydrogels with Ionic Responsive Coefficient of Friction (2020)

Freeze-thaw poly(vinyl alcohol) hydrogels (PVA-H) offer great potential for several biomedical applications due to their biomimetic mechanical properties and biocompatibility. Despite these advantages, the use of PVA-H for load bearing applications has been limited due to poor performance in boundary lubrication compared to natural tissue such as articular cartilage. Recently, zwitterionic polymer brushes have been shown to act as effective boundary lubricants on rigid substrates; however, to the best of our knowledge, the synergistic effects of zwitterionic brushes coupled with the biomimetic fluid load support exhibited by hydrogels have not been reported. We report here on our investigation involving the synthesis and characterization of two unique types of polymer brush functionalized PVA hydrogels. The zwitterionic polymers that were compared contained either [2-(methacryloyloxy)ethyl]dimethyl-3-sulfopropylammonium hydroxide, PMEDSAH, or 2-methacryloyloxyethylphosphorylcholine, PMPC, repeating units. Both hydrogels coated with zwitterionic polymers were found to be cytocompatible. We report further on micrometer-scale surface properties via water contact angle goniometry, surface roughness measurements, and scanning electron microscopy. Finally, the impact of brush functionalization on the mechanics of the tribologically enhanced gels is reported with comparison to natural articular cartilage within the context of Hertzian contact theory.
Preventive and Prophylactic Mechanisms of Action of Pomegranate Bioactive Constituents (2013)

Pomegranate fruit presents strong anti-inflammatory, antioxidant, antiobesity, and antitumoral properties, thus leading to an increased popularity as a functional food and nutraceutical source since ancient times. It can be divided into three parts: seeds, peel, and juice, all of which seem to have medicinal benefits. Several studies investigate its bioactive components as a means to associate them with a specific beneficial effect and develop future products and therapeutic applications. Many beneficial effects are related to the presence of ellagic acid, ellagitannins (including punicalagins), punicic acid and other fatty acids, flavonoids, anthocyanidins, anthocyanins, estrogenic flavonols, and flavones, which seem to be its most therapeutically beneficial components. However, the synergistic action of the pomegranate constituents appears to be superior when compared to individual constituents. Promising results have been obtained for the treatment of certain diseases including obesity, insulin resistance, intestinal inflammation, and cancer. Although moderate consumption of pomegranate does not result in adverse effects, future studies are needed to assess safety and potential interactions with drugs that may alter the bioavailability of bioactive constituents of pomegranate as well as drugs. The aim of this review is to summarize the health effects and mechanisms of action of pomegranate extracts in chronic inflammatory diseases.
Fermented cereal with specific bifidobacteria normalizes bowel movements in elderly nursing home residents. A randomized, controlled trial. (2007)

It is possible to normalize bowel movements in frail nursing home.
Antigen presentation in allergic sensitization (1996)

IgE antibodies, when cross-linked by allergen on the surface of effector cells such as mast cells and basophils, are known to be directly responsible for immediate type hypersensitivity reactions. In addition, IgE may be involved in other, indirect, mechanisms, fundamental to the pathogenesis of allergic diseases, such as enhancement of the antigen capturing capacity of antigen presenting cells. IgE mediated antigen presentation could lead to a continuous activation of the immune system by very low concentrations of allergen. As a result, Th2 cell populations may expand and may induce more B cells to switch to IgE production. Subsequently, the overproduction of IgE and Th2 cells in a patient may explain the clinical observation that certain allergic patients deteriorate from sensitivity to a single group of allergens to sensitivity to multiple groups of allergens. Therefore, control of IgE production is not only important for the treatment of allergic symptoms, but may also regulate deterioration of allergy via the mechanism of CD23/IgE mediated allergen presentation by naive B cells. The role that monocytes, which have recently been found to express Fc epsilon RI, play in the pathogenesis of allergy, remains speculative. We hypothesize that their role may be to remove IgE from the circulation and re-direct the immune response from naive B cells. IgG antibodies which cannot be used for antigen uptake by B cells also direct the immune response to monocytes.
Steroids from the Gorgonian Isis hippuris (2005)

Six new polyoxygenated steroids, hippuristerones J-L (1-3), hippuristerols E-F (4, 5), and a novel gorgosteroid, 1alpha,3beta,5beta,11alpha-tetrahydroxygorgostan-6-one (6), were isolated from the gorgonian Isis hippuris. The structures of these metabolites were elucidated by extensive spectroscopic analyses and comparison of the NMR data with those of related steroids.
“Peudo” Late Potentials Unmasked by Spectrocardiography (1996)

We present a patient with chronic obstructive pulmonary disease and sustained ventricular tachycardia in the setting of unstable coronary artery disease. Signal-averaged ECG (SAECG), inadvertently performed during an atrial tachycardia with 2:1 atrioventricular (AV) block, was abnormal by time-domain analysis, but was normal by a relatively new frequency analysis technique of the entire QRS (spectrocardiography). The patient was noninducible for sustained ventricular arrhythmias. Following cardioversion to sinus rhythm, SAECG was normal by time-domain analysis and spectrocardiography. This technique may show promise in the management of patients who are at risk for sustained ventricular arrhythmias, particularly those who cannot be evaluated by time-domain analysis.
Profile synthesis in multicomponent glass optical fibers (1977)

It is proposed that the concentration profiles of the components of a multicomponent glass be specified independently in order to synthesize an optical fiber having several optimized transmission characteristics. Assuming a linear relationship between concentration and refractive index, we show how the synthesis procedure operates for ternary glasses and illustrate the method by computing the concentration profiles required to realize a SiO(2)-GeO(2)-P(2)O(5) fiber with minimum modal dispersion over a wide range of wavelengths ( partial differentialalpha/ partial differentiallambda = 0).
Plasmonic Microbubble Dynamics in Binary Liquids (2020)

The growth of surface plasmonic microbubbles in binary water/ethanol solutions is experimentally studied. The microbubbles are generated by illuminating a gold nanoparticle array with a continuous wave laser. Plasmonic bubbles exhibit ethanol concentration-dependent behaviors. For low ethanol concentrations (<i>f</i><sub>e</sub>) of ≲67.5%, bubbles do not exist at the solid-liquid interface. For high <i>f</i><sub>e</sub> values of ≳80%, the bubbles behave as in pure ethanol. Only in an intermediate window of 67.5% ≲ <i>f</i><sub>e</sub> ≲ 80% do we find sessile plasmonic bubbles with a highly nontrivial temporal evolution, in which as a function of time three phases can be discerned. (1) In the first phase, the microbubbles grow, while wiggling. (2) As soon as the wiggling stops, the microbubbles enter the second phase in which they suddenly shrink, followed by (3) a steady reentrant growth phase. Our experiments reveal that the sudden shrinkage of the microbubbles in the second regime is caused by a depinning event of the three-phase contact line. We systematically vary the ethanol concentration, laser power, and laser spot size to unravel water recondensation as the underlying mechanism of the sudden bubble shrinkage in phase 2.
Modeling, Design, and Validation of Magnetic Hysteresis Motors (2019)

The use of hysteresis motors nowadays is limited to few niche-focused applications. Nevertheless, their intrinsic features make them ideal for next-generation high-speed machinery. Hysteresis motors are highly nonlinear and their behavior is heavily influenced by the initial magnetization state of the rotor active part. As such, the exploitation of hysteresis machine technology requires a reliable method to assess the torque capability, both numerically and experimentally. This paper proposes a finite-element model for the design of hysteresis motors. In this tool, rotor hysteresis is described through the vector generalization of the Jiles-Atherton model. For validation purposes, a prototype is defined based on a specific application. The torque of this prototype is experimentally characterized for different electrical loadings and rotor speeds. Subsequently, this output is measured after rotor magnetization at different levels. It is demonstrated that the initial condition of the rotor active part can be exploited in synchronous conditions to improve the machine output torque.
Energy Efficient User Association for Cloud Radio Access Networks (2016)

Cloud radio access network (C-RAN) and massive multiple-input multiple-output (MIMO) are recognized as two key technologies for the fifth-generation mobile networks. In this paper, we consider the energy efficiency-based user association problem in massive MIMO empowered C-RAN, where multiple antennae are clustered at each remote radio head (RRH). We first obtain the deterministic equivalent expression of the energy efficiency, and then propose three user association algorithms, named nearest-based user association (NBUA), single-candidate RRH user association (SCRUA), and multi-candidate RRHs user association (MCRUA), respectively. In NBUA and SCRUA, each user is associated with only one RRH, and in MCRUA, multiple RRHs can serve the same user. In our algorithms, the impact of the power consumption of fronthaul links and antennas is considered by allowing inefficient RRHs to be turned into sleep mode. We provide the numerical comparisons of the proposed algorithms and a state-of-the-art baseline, which associates each user with the nearest RRH. The results show that our proposed algorithms achieve higher energy efficiency than the baseline algorithm. The proposed MCRUA algorithm achieves a good balance between spectral and energy efficiency, and the performance gain is more significant when the number of users is large.
Multiwalled Carbon Nanotubes Drive the Activity of Metal@oxide Core–Shell Catalysts in Modular Nanocomposites (2012)

Rational nanostructure manipulation has been used to prepare nanocomposites in which multiwalled carbon nanotubes (MWCNTs) were embedded inside mesoporous layers of oxides (TiO(2), ZrO(2), or CeO(2)), which in turn contained dispersed metal nanoparticles (Pd or Pt). We show that the MWCNTs induce the crystallization of the oxide layer at room temperature and that the mesoporous oxide shell allows the particles to be accessible for catalytic reactions. In contrast to samples prepared in the absence of MWCNTs, both the activity and the stability of core-shell catalysts is largely enhanced, resulting in nanocomposites with remarkable performance for the water-gas-shift reaction, photocatalytic reforming of methanol, and Suzuki coupling. The modular approach shown here demonstrates that high-performance catalytic materials can be obtained through the precise organization of nanoscale building blocks.
The Rough Draft (2021)

The story so far. . . After several days of work, you have: <li> • a correctly formatted scaffold that address all reviewer criteria </li> <li> • illustrations that give the gist of the project</li> <li> • a list of citations from your literature search </li>
Multivalent Glycosylated Carbon Nanostructures: Efficient Inhibitors of Emergent Viruses Infection (2021)

The infection of humans by lethal pathogens such as Ebola and other related viruses such as Zika and Dengue viruses has not been properly addressed so far. The entry of these viruses to the host cell takes place through several receptors including DC-SIGN, so that multivalent glycoconjugates are considered as good candidates to inhibit the viral infection process. In particular, we have focused on fullerene C60 and other carbon nanostructures as biocompatible platforms for the multivalent presentation of carbohydrates. The antiviral activity of these compounds in an Ebola pseudotyped infection model reached IC50 values in the subnanomolar range in the case of tridecafullerenes appended with 120 mannoses. SWCNTs, MWCNTs and SWCNHs have also been employed as viruses mimicking nanocarbon platforms for the multivalent presentation of carbohydrates. In particular, MWCNTs functionalized with glycofullerenes have been shown as potent inhibitors of Ebola virus infection. In order to get enhanced multivalency in biocompatible systems, tridecafullerenes appended with up to 360 1,2-mannobiosides have been synthesized using a strain promoted cycloaddition of azides to alkynes (SPAAC) strategy. These systems have been tested against ZIKV and DENV infection, showing an inhibitory activity in the picomolar range.
Mobile Human Airbag System for Fall Protection Using MEMS Sensors and Embedded SVM Classifier (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> This paper introduces a mobile human airbag system designed for fall protection for the elderly. A Micro Inertial Measurement Unit (<formula formulatype="inline"> <tex Notation="TeX">$\mu$</tex></formula>IMU) of 56 mm<formula formulatype="inline"> <tex Notation="TeX">$\,\times\,$</tex></formula>23 mm<formula formulatype="inline"> <tex Notation="TeX">$\,\times\,$</tex></formula>15 mm in size is built. This unit consists of three dimensional MEMS accelerometers, gyroscopes, a Bluetooth module and a Micro Controller Unit (MCU). It records human motion information, and, through the analysis of falls using a high-speed camera, a lateral fall can be determined by gyro threshold. A human motion database that includes falls and other normal motions (walking, running, etc.) is set up. Using a support vector machine (SVM) training process, we can classify falls and other normal motions successfully with a SVM filter. Based on the SVM filter, an embedded digital signal processing (DSP) system is developed for real-time fall detection. In addition, a smart mechanical airbag deployment system is finalized. The response time for the mechanical trigger is 0.133 s, which allows enough time for compressed air to be released before a person falls to the ground. The integrated system is tested and the feasibility of the airbag system for real-time fall protection is demonstrated. </para>
Development of the arbitrarily primed-representational difference analysis method and chromosomal mapping of isolated high throughput rat genetic markers (1999)

Linkage mapping of quantitative trait loci requires analysis of a large number of animals. Although genetic markers isolated by representational difference analysis (RDA) and its modifications meet the needs, the number of these markers has been limited. In the present study, we established the arbitrarily primed (AP)-RDA method to isolate virtually an unlimited number of the high throughput genetic markers. A representation of the genome, an AP-amplicon, was prepared by AP-PCR with a single primer or with a combination of primers using genomic DNA of the ACI/N (ACI) or BUF/Nac (BUF) rat as a template. By subtracting the AP-amplicon of ACI from that of BUF, a total of 40 polymorphic and independent markers were isolated in seven series of AP-RDA using a single primer. Two series of AP-RDA with primer combination yielded seven additional independent markers. All of the markers gave clear positive/negative signals by hybridization of a filter where AP-amplicons from F2 rats of ACI and BUF were dot-blotted at a high density without any concentration or purification. All of the 47 independent markers were mapped to unique chromosomal positions by linkage analysis, even though some arbitrary primers had very similar sequences. The markers were also informative between other strains of rats. Simultaneous hybridization of multiple filters made it possible to genotype a large number of rats simultaneously for multiple genetic loci. The AP-RDA method promises isolation of a large number of high throughput genetic markers in any species and is expected to facilitate linkage mapping of subtle quantitative trait loci.
Stimulation of Sex Pheromone Production in Corn Earworm Moths by Injection of Extracts of Heads of Males of the Caribbean Fruit Fly (1998)

Peter E. A. Teal, Stimulation of Sex Pheromone Production in Corn Earworm Moths by Injection of Extracts of Heads of Males of the Caribbean Fruit Fly, The Florida Entomologist, Vol. 81, No. 1 (Mar., 1998), pp. 98-104
Driving Cellular Plasticity and Survival Through the Signal Transduction Pathways of Metabotropic Glutamate Receptors (2005)

Metabotropic glutamate receptors (mGluRs) share a common molecular morphology with other G protein-linked receptors, but there expression throughout the mammalian nervous system places these receptors as essential mediators not only for the initial development of an organism, but also for the vital determination of a cell's fate during many disorders in the nervous system that include amyotrophic lateral sclerosis, Parkinson's disease, Alzheimer's disease, Huntington's disease, Multiple Sclerosis, epilepsy, trauma, and stroke. Given the ubiquitous distribution of these receptors, the mGluR system impacts upon neuronal, vascular, and glial cell function and is activated by a wide variety of stimuli that includes neurotransmitters, peptides, hormones, growth factors, ions, lipids, and light. Employing signal transduction pathways that can modulate both excitatory and inhibitory responses, the mGluR system drives a spectrum of cellular pathways that involve protein kinases, endonucleases, cellular acidity, energy metabolism, mitochondrial membrane potential, caspases, and specific mitogen-activated protein kinases. Ultimately these pathways can converge to regulate genomic DNA degradation, membrane phosphatidylserine (PS) residue exposure, and inflammatory microglial activation. As we continue to push the envelope for our understanding of this complex and critical family of metabotropic receptors, we should be able to reap enormous benefits for both clinical disease as well as our understanding of basic biology in the nervous system.
Concurrent Infection of Young Calves With Eimeria bovis and coronavirus (1991)

Over a period of 3 summers, 21 colostrum-fed Holstein bull calves, 1-3 days of age, were selected to form 7 replicates, each consisting of 3 calves. The project was conducted during the summer because screen-testing of calves indicated a higher likelihood during warm months of obtaining calves without evidence of coronavirus infection.