gebhart/patrepeval huggingface dataset:
Mass Spectrometric Analysis of Cytosine Methylation by Base-Specific Cleavage and Primer Extension Methods (2008)

The analysis of epigenetic changes in genomic DNA has seen an exponentially increasing interest over the last years. Within the field of epigenetics DNA methylation patterns have become of particular interest to the scientific community. The covalent addition of a methyl group to cytosine bases in the CpG dinucleotide sequence holds particular analytical advantages. Working with DNA as an analyte molecule is robust and samples are unproblematic to collect and handle. Also changes in DNA methylation are a dynamic process and the resulting patterns are tightly associated to disease. This combination of robust technical performance and disease-specific methylation patterns might enable DNA methylation as a powerful biomarker in the future. The increased interest has triggered exciting new findings which ultimately show that epigenetic regulation of gene expression is not a binary system. On the contrary, especially the quantitative measure DNA methylation has greatly contributed to the areas of gene regulation, developmental biology, and translational medicine. Performing quantitative methylation measurements in large scale used to be impaired by the limitations of measurement technologies. They either suffered from limited throughput, limited accuracy, high cost, or a combination of those. Here we introduce a new technique that combines candidate gene amplification with base-specific cleavage or primer extension methods and MALDI-TOF mass spectrometric analysis to overcome the described limitations.
Dual Electrospray Ion Source for Electron-Transfer Dissociation on a Hybrid Linear Ion Trap−Orbitrap Mass Spectrometer (2007)

A dual electrospray ionization source (ESI) has been modified to simultaneously produce cations and anions, one from each emitter, for performing rapid electron-transfer dissociation (ETD) ion/ion reactions on a hybrid linear ion trap-orbitrap mass spectrometer. Unlike the pulsed dual ESI sources that were used to generate ETD reagent ions, this source separates the emitters in space, rather than time, by physically switching which one is in front of the atmospheric inlet. The new arrangement allows for substantially enhanced spray stability and decreased switching times (<or=30 ms), allowing for more tandem-MS spectra per unit time. Herein, we demonstrate the stability of the ETD anion population and the ability to identify several c- and z-type product ions from multiply protonated peptide cations.
The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition (2018)

Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding and no net change in affinities. This phenomenon-termed enthalpy/entropy (H/S) compensation-hinders efforts in biomolecular design, and its incidence-often a surprise to experimentalists-makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/ S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting-and, perhaps, avoiding or exploiting-this phenomenon in biophysical systems.
ISway: a sensitive, valid and reliable measure of postural control (2012)

Based on these results, we recommend a subset of the most sensitive, reliable, and valid ISway measures to characterize posture control in PD: 1) JERK, 2) RMS amplitude and mean velocity from the time-domain measures, and 3) centroidal frequency as the best frequency measure, as valid and reliable measures of balance control from ISway.
Robust Multi-resolution Pedestrian Detection in Traffic Scenes (2013)

The serious performance decline with decreasing resolution is the major bottleneck for current pedestrian detection techniques. In this paper, we take pedestrian detection in different resolutions as different but related problems, and propose a Multi-Task model to jointly consider their commonness and differences. The model contains resolution aware transformations to map pedestrians in different resolutions to a common space, where a shared detector is constructed to distinguish pedestrians from background. For model learning, we present a coordinate descent procedure to learn the resolution aware transformations and deformable part model (DPM) based detector iteratively. In traffic scenes, there are many false positives located around vehicles, therefore, we further build a context model to suppress them according to the pedestrian-vehicle relationship. The context model can be learned automatically even when the vehicle annotations are not available. Our method reduces the mean miss rate to 60% for pedestrians taller than 30 pixels on the Caltech Pedestrian Benchmark, which noticeably outperforms previous state-of-the-art (71%).
Epidemiology of aplastic anemia: a prospective multicenter study (2008)

The incidence of aplastic anemia in Barcelona is low but the case fatality rate is high. Advanced age and severe disease at the time of diagnosis were associated with decreased survival.
Smart Wearable Band for Stress Detection (2015)

Sometimes mental stress needs to be control as it results in different dangerous suffering. Timely mental stress detection can help to prevent stress related health problems. The aim of this paper is to design an IoT base wearable, cost effective and low power smart band for health care that detect mental stress based on skin conductance. This band can monitor user's mental stress continuously and transmit the stress related data wirelessly to user's smart phone. It not only help the users in better understanding their stress patterns but also provide the physician with reliable data for a much better treatment. Inputs to this device are various signals from different sensors. By intelligently analyzing the correlation between these signals using machine learning algorithm, this band predicts that whether the subject is suffering from stress or not.
Fission-fusion systems: hybrid, symbiotic and augean (1975)

The achievement of controlled fusion will make available excess neutrons which can be used in various ways in combined fission-fusion power cycles. The various schemes are here classified as hybrid–in which heavy-element fission occurs in the fusion blanket; symbiotic–in which fissile material is bred in the absence of fission events; and augean–in which the neutron surplus is used to transmute fission reactor waste products. The earliest work in this field, unpublished and originally classified secret, is reviewed. Recent studies of hybrid systems based on subcritical thermal and sub-critical fast-fission blankets are described in detail. An analysis of symbiosis based on the Th-U fuel cycle is summarized. The conditions required for high-level waste transmutation are presented; Augean systems seem best suited to actinide waste burning. It is concluded that basic physics of various fission-fusion systems has been surveyed but the engineering and economic aspects of combined systems have been largely ignored. It remains to be shown whether fission-fusion systems will prove superior to alternative methods of accomplishing the same ends.
Effects of tocopherols and their mixtures on the oxidative stability of olive oil and linseed oil under heating (2000)

The tested tocopherols (γ,δ,α) showed antioxidative activity at all levels of addition to the monounsaturated olive oil, the effects increased as a function of concentrations (maximum: +287% with 800 mg γ-tocopherol/100 g oil compared to the control oil). In the highly unsaturated linseed oil, which contains 58 mg/100 g initial concentration of γ-tocopherol, γ-tocopherol showed antioxidative behavior up to the addition of 100 mg/ 100 g oil. Additions of more than the 100 mg/100 g affected the oil, resulting in a faster oxidation. Mixtures of γ/δ-tocopherols in olive oil were found to protect more efficiently than both vitamins when added separately α-tocopherol reduced effects of other tocopherols in both plant oils. The stabilizing effect of added tocopherols and their mixtures (100 mg/100 g oil each) in olive oil are γ/δ-T>γ-T>δ-T>γ/α-T>δ/α-T>α-T and in linseed oil γ-T>γ/δ-T>δ-T>γ/α-T>α-T>α/δ-T.
Role of Metals in the Reaction Catalyzed by Protein Farnesyltransferase (2000)

Protein farnesyltransferase catalyzes the posttranslational farnesylation of several proteins involved in signal transduction, including Ras, and is a target enzyme for antitumor therapies. Efficient product formation catalyzed by protein farnesyltransferase requires an enzyme-bound zinc cation and high concentrations of magnesium ions. In this work, we have measured the pH dependence of the chemical step of product formation, determined under single-turnover conditions, and have demonstrated that the prenylation rate constant is enhanced by two deprotonations. Substitution of the active site zinc by cadmium demonstrated that one of the ionizations reflects deprotonation of the metal-coordinated thiol of the peptide "CaaX" motif, pK(a1) = 6.0. These data provide additional evidence for the direct involvement of a metal-coordinated sulfur nucleophile in catalysis. The second ionization was assigned to a hydroxyl on the pyrophosphate moiety of farnesyl pyrophosphate, pK(a2) = 7.4. Deprotonation of this group is important for binding of magnesium. This second ionization is not observed for catalysis in the absence of magnesium or when the substrate is farnesyl monophosphate. These data indicate that the maximal rate constant for prenylation requires formation of a zinc-coordinated thiolate nucleophile and enhancement of the electrophilic character at C1 of the farnesyl chain by magnesium ion coordination of the pyrophosphate leaving group.
Trapping Malicious Crawlers in Social Networks (2020)

In this paper, we study a problem of trapping malicious web crawlers in social networks to minimize the attacks from crawlers with malicious intents to steal personal/private information. The problem is to find where to place a given set of traps over a graph so as to minimize the expected number of users who possibly fall prey to a (possibly random) set of malicious crawlers, each of which traverses the graph in a random-walk fashion for a random finite time. We first show that this problem is NP-hard and also a monotone submodular maximization problem. We then present a greedy algorithm that achieves a ($1-1/e$)-approximation. We also develop an $(ε,δ)$-approximation Monte Carlo estimator to ease the computation of the greedy algorithm and thus make the algorithm scalable for large graphs. We finally present extensive simulation results to show that our algorithm significantly outperforms other baseline algorithms based on various centrality measures.
An Ultimate Stereocontrol in Supramolecular Photochirogenesis: Photocyclodimerization of 2-Anthracenecarboxylate Mediated by Sulfur-Linked β-Cyclodextrin Dimers (2019)

Stereoisomeric β-cyclodextrin (CD) dimers linked with a sulfur atom or an arene spacer were designed to create a tethered dual CD capsule for precisely manipulating the regio- and enantioselectivities of the photocyclodimerization of 2-anthracenecarboxylate (AC) to four stereoisomeric classical 9,10:9',10'-cyclodimers and two nonclassical 5,8:9',10'-cyclodimers. Among the dimeric CD hosts prepared, exo-3-thia-β-CD dimer formed 1:1 and 1:2 host-guest complexes with AC in aqueous solutions, the former of which hindered but the latter facilitated the AC photocyclodimerization with regio- and enantioselectivities much higher than those obtained with native β-CD or the rest of the β-CD dimers. The stereochemical outcomes turned out to be highly sensitive to and hence critically manipulable by the linking position and configuration of the connected saccharide units and the linker length, as well as the external variants, such as temperature, pH, and added salt. Eventually, the photocyclodimerization of AC mediated by the dimeric β-CD host gave enantiopure syn-head-to-tail-9,10:9',10'-cyclodimer in 97-98% yield in a pH 5.1 buffer solution at 0.5 °C and also in an aqueous CsCl solution at -20 °C.
Overexpression of Carnitine Palmitoyltransferase-1 in Skeletal Muscle Is Sufficient to Enhance Fatty Acid Oxidation and Improve High-Fat Diet–Induced Insulin Resistance (2008)

Our data provide clear evidence that a physiological increase in the capacity of long-chain fatty acyl CoA entry into mitochondria is sufficient to ameliorate lipid-induced insulin resistance in muscle.
The influence of Self-Organized Learning Environments (SOLEs) on EFL students in a college in Oman (2019)

This paper is part of a larger project where the researchers explored English as a Foreign Language (EFL) students' experiences in learning English using Self-Organized Learning Environments (SOLEs) within the context of their English foundation year in a college setting in Oman. The purpose that guided this current paper is to investigate whether SOLE pedagogy is able to positively influence Omani EFL college students' learning beliefs and behaviours.
Internet of Things Architecture Based on Integrated PLC and 3G Communication Networks (2011)

Internet of Things (IoT) applications are developed and implemented through enlightened communication networks. The phenomena is proving a fact that research in IoT architecture becomes important domain in realizing IoT framework. Therefore, in this paper a new IoT architecture is purposed combining two sophisticated communication networks: power line communication (PLC) and 3G networks. This combination is motivated by scalability advantages of (PLC) and 3G networks. Further, the 3G-PLC networks test bed is constructed and analyzed to show its feasibility in supporting IoT applications.
Integration organischer Laser in Lab-on-Chip Systeme (2011)

In dieser Arbeit wird eine Plattform für einwegtaugliche photonische Systeme auf Polymerbasis vorgestellt, in die sowohl organische Halbleiterlaser als auch optofluidische Laser integriert sind. Lab-on-Chip Systeme mit integrierten organischen Halbleiterlasern, Wellenleitern und Mikrofluidikkanälen werden realisiert und mit integrierten Lasern Fluoreszenz angeregt. Auf den Chips wird eine Funktionalisierung aufgebracht und es werden Wellenleitergitterkoppler aus Phospholipiden untersucht.
Non-Invasive Ventilation in Premature Infants: Based on Evidence or Habit (2013)

Despite surfactant and mechanical ventilation being the standard of care for preterm infants with respiratory failure, non-invasive respiratory support is increasingly being employed in neonatal units. The latter can be accomplished in a variety of ways but none of them have been proven so far to be superior to intubation and mechanical ventilation. Nonetheless, they appear to be safe and effective in experienced hands. This article relates to the use of non-invasive forms of respiratory support and evidence is reviewed from the clinical trials which have evaluated the use of these techniques.
Numerical simulations of heating patterns and tissue temperature response due to high-intensity focused ultrasound (2000)

The results of this paper show-for an existing high intensity, focused ultrasound (HIFU) transducer-the importance of nonlinear effects on the space/time properties of wave propagation and heat generation in perfused liver models when a blood vessel also might be present. These simulations are based on the nonlinear parabolic equation for sound propagation and the bio-heat equation for temperature generation. The use of high initial pressure in HIFU transducers in combination with the physical characteristics of biological tissue induces shock formation during the propagation of a therapeutic ultrasound wave. The induced shock directly affects the rate at which heat is absorbed by tissue at the focus without significant influence on the magnitude and spatial distribution of the energy being delivered. When shocks form close to the focus, nonlinear enhancement of heating is confined in a small region around the focus and generates a higher localized thermal impact on the tissue than that predicted by linear theory. The presence of a blood vessel changes the spatial distribution of both the heating rate and temperature.
Thermodynamic stability of the 5′ dangling‐ended DNA hairpins formed from sequences 5′‐(XY)<sub>2</sub>GGATAC(T)<sub>4</sub>GTATCC‐3′, where X, Y = A,T,G,C (1990)

Expressions for the partition function Q (T) of DNA hairpins are presented. Calculations of Q (T), in conjunction with our previously reported numerically exact algorithm [T. M. Paner, M. Amaratunga, M. J. Doktycz, and A. S. Benight (1990) Biopolymers, 29, 1715-1734], yield a numerical method to evaluate the temperature dependence of the transition enthalpy, entropy, and free energy of a DNA hairpin directly from its optical melting curve. No prior assumptions that the short hairpins melt in a two-state manner are required. This method is then applied in a systematic manner to investigate the stability of the six basepair duplex stem 5'-GGATAC-3' having four-base dangling single-strand ends with the sequences (XY)2, where X, Y = A, T, G, C, on the 5' end and a T4 loop on the 3' end. Results show that all dangling ends of the sample set stabilize the hairpin against melting. Increases in transition temperatures as great as 4.0 degrees C above the blunt-ended control hairpin were observed. The hierarchy of the hairpin transition temperatures is dictated by the identity of the first base of the dangling end adjoining the duplex in the order: purine greater than T greater than C. Calculated melting curves of every hairpin were fit to experimental curves by adjustment of a single parameter in the numerically exact theoretical algorithm. Exact fits were obtained in all cases. Experimental melting curves were also calculated assuming a two-state melting process. Equally accurate fits of all dangling-ended hairpin melting curves were obtained with the two-state model calculation. This was not the case for the melting curve of the blunt-ended hairpin, indicating the presence of a four-base dangling-end drives hairpin melting to a two-state process. Q (T) was calculated as a function of temperature for each hairpin using the theoretical parameters that provided calculated curves in exact agreement with the experimentally obtained optical melting curves. From Q (T), the temperature dependence of the transition enthalpy delta H, entropy delta S, and free energy delta G were calculated for every hairpin providing a quantitative assessment of the effects of dangling ends on hairpin thermodynamics. Comparisons of our results are made with those of the Breslauer group [M. Senior, R. A. Jones, and K. J. Breslauer (1988) Biochemistry 27, 3879-3885] on the T2 5' dangling-ended d(GC)3 duplexes.(ABSTRACT TRUNCATED AT 400 WORDS)
29.3: Barrier Rib Molding Process using Capillary Action (2003)

Abstract In this study, barrier ribs of plasma display panel were formed via capillary molding process. Various types of working molds were prepared by casting liquid polydimethylsiloxane on master molds that were produced from a photoresist film. A thermosetting paste was filled into the cavities of working molds by means of capillary action of paste and was cured prior to removing the molds. The effects of solid loading in the paste, prefiring temperature and type of barrier ribs on the sintering shrinkage were investigated. It was demonstrated that various types of barrier ribs could be produced successfully by sintering the ribs formed by the molding process.
Structure/Function Relationships Responsible for Coenzyme Specificity and the Isomerase Activity of Human Type 1 3β-Hydroxysteroid Dehydrogenase/Isomerase (2003)

Human type 1 3 beta-hydroxysteroid dehydrogenase/isomerase (3 beta-HSD/isomerase) catalyzes the two sequential enzyme reactions on a single protein that converts dehydroepiandrosterone or pregnenolone to androstenedione or progesterone, respectively, in placenta, mammary gland, breast tumors, prostate, prostate tumors, and other peripheral tissues. Our earlier studies show that the two enzyme reactions are linked by the coenzyme product, NADH, of the 3 beta-HSD activity. NADH activates the isomerase activity by inducing a time-dependent conformational change in the enzyme protein. The current study tested the hypothesis that the 3 beta-HSD and isomerase activities shared a common coenzyme domain, and it characterized key amino acids that participated in coenzyme binding and the isomerase reaction. Homology modeling with UDP-galactose-4-epimerase predicts that Asp36 is responsible for the NAD(H) specificity of human 3 beta-HSD/isomerase and identifies the Rossmann-fold coenzyme domain at the amino terminus. The D36A/K37R mutant in the potential coenzyme domain and the D241N, D257L, D258L, and D265N mutants in the potential isomerase domain (previously identified by affinity labeling) were created, expressed, and purified. The D36A/K37R mutant shifts the cofactor preference of both 3 beta-HSD and isomerase from NAD(H) to NADP(H), which shows that the two activities utilize a common coenzyme domain. The D257L and D258L mutations eliminate isomerase activity, whereas the D241N and D265N mutants have nearly full isomerase activity. Kinetic analyses and pH dependence studies showed that either Asp257 or Asp258 plays a catalytic role in the isomerization reaction. These observations further characterize the structure/function relationships of human 3 beta-HSD/isomerase and bring us closer to the goal of selectively inhibiting the type 1 enzyme in placenta (to control the timing of labor) or in hormone-sensitive breast tumors (to slow their growth).
Tissue Plasminogen Activator in the Treatment of Anterior Chamber Fibrin in Post-Vitrectomized Eyes (1995)

Nine cases of postvitrectomy fibrin in the anterior chamber unresponsive to systemic and topical steroid and anti-inflammatory agents were treated with intracameral injection of human recombinant tissue plasminogen activator. All patients either had gone through multiple operations, prolonged operations or had significant preoperative inflammations. Eight cases showed significant clear-up of the fibrin within several hours after injection of five to 25 ug tissue plasminogen activator. No complications were noticed in these cases. One case with rubeosis and long standing fibrin developed total hyphema after injection of 25 ug of tissue plasminogen activator. These initial experiences suggested usefulness of tissue plasminogen activator in the treatment of intractable postvitrectomy fibrin formation in the anterior chamber.
Experimental studies of strong dipolar interparticle interaction in monodisperse Fe3O4 nanoparticles (2007)

Interparticle interaction of monodisperse Fe3O4 nanoparticles has been experimentally investigated by dispersing the nanoparticles in solvents. With increasing the interparticle distances to larger than 100nm in a controlled manner, the authors found that the blocking temperature (TB) of the nanoparticles drops continuously and eventually gets saturated with a total drop in TB of 7–17K observed for 3, 5, and 7nm samples, compared with their respective nanopowder samples. By carefully studying the dependence of TB on the interparticle distance, the authors could demonstrate that the experimental dependence of TB follows the theoretical curve of the dipole-dipole interaction.