gebhart/patrepeval huggingface dataset:
Characterization of a K<sup>+</sup>-Induced Conformational Switch in a Human Telomeric DNA Oligonucleotide Using 2-Aminopurine Fluorescence (2009)

Human telomeric DNA consists of tandem repeats of the DNA sequence d(GGGTTA). Oligodeoxynucleotide telomere models such as d[A(GGGTTA)(3)GGG] (Tel22) fold in a cation-dependent manner into quadruplex structures consisting of stacked G-quartets linked by d(TTA) loops. NMR has shown that in Na(+) solutions Tel22 forms a "basket" topology of four antiparallel strands; in contrast, Tel22 in K(+) solutions consists of a mixture of unknown topologies. Our previous studies on the mechanism of folding of Tel22 and similar telomere analogues utilized changes in UV absorption between 270 and 325 nm that report primarily on G-quartet formation and stacking showed that quadruplex formation occurs within milliseconds upon mixing with an appropriate cation. In this study, we assess the dynamics and equilibria of folding of specific loops by using Tel22 derivatives in which the dA residues were serially substituted with the fluorescent reporter base, 2-aminopurine (2-AP). Tel22 folding induced by Na(+) or K(+) assessed by changes in 2-AP fluorescence consists of at least three kinetic steps with time constants spanning a range from milliseconds to several hundred seconds. Na(+)-dependent equilibrium titrations of Tel22 folding could be approximated as a cooperative two-state process. In contrast, K(+)-dependent folding curves were biphasic, revealing that different conformational ensembles are present in 1 and 30 mM K(+). This conclusion was confirmed by (1)H NMR. Molecular dynamics simulations revealed a K(+) binding pocket in Tel22 located near dA1 that is specific for the so-called hybrid-1 conformation in which strand 1 is in a parallel arrangement. The possible presence of this topologically specific binding site suggests that K(+) may play an allosteric role in regulating telomere conformation and function by modulating quadruplex tertiary structure.
Randomized, Controlled Dose-Ranging Study of the Selective Adenosine A <sub>2A</sub> Receptor Agonist Binodenoson for Pharmacological Stress as an Adjunct to Myocardial Perfusion Imaging (2004)

The selective adenosine A2A receptor agonist binodenoson results in an extent and severity of reversible perfusion defects on SPECT imaging similar to nonselective adenosine receptor stimulation, accompanied by a dose-related reduction in the incidence and severity of side effects.
Small Deletion Variants Have Stable Breakpoints Commonly Associated with Alu Elements (2008)

Copy number variants (CNVs) contribute significantly to human genomic variation, with over 5000 loci reported, covering more than 18% of the euchromatic human genome. Little is known, however, about the origin and stability of variants of different size and complexity. We investigated the breakpoints of 20 small, common deletions, representing a subset of those originally identified by array CGH, using Agilent microarrays, in 50 healthy French Caucasian subjects. By sequencing PCR products amplified using primers designed to span the deleted regions, we determined the exact size and genomic position of the deletions in all affected samples. For each deletion studied, all individuals carrying the deletion share identical upstream and downstream breakpoints at the sequence level, suggesting that the deletion event occurred just once and later became common in the population. This is supported by linkage disequilibrium (LD) analysis, which has revealed that most of the deletions studied are in moderate to strong LD with surrounding SNPs, and have conserved long-range haplotypes. Analysis of the sequences flanking the deletion breakpoints revealed an enrichment of microhomology at the breakpoint junctions. More significantly, we found an enrichment of Alu repeat elements, the overwhelming majority of which intersected deletion breakpoints at their poly-A tails. We found no enrichment of LINE elements or segmental duplications, in contrast to other reports. Sequence analysis revealed enrichment of a conserved motif in the sequences surrounding the deletion breakpoints, although whether this motif has any mechanistic role in the formation of some deletions has yet to be determined. Considered together with existing information on more complex inherited variant regions, and reports of de novo variants associated with autism, these data support the presence of different subgroups of CNV in the genome which may have originated through different mechanisms.
Equalization for Electrical Links: Current Design Techniques and Future Directions (2015)

Another article in this issue, the introductory article by Tony Chan Carusone, discussed how the limited bandwidth of an electrical channel causes distortion (e.g., broadening) of the pulses traveling from transmitter to receiver. Without compensating for such distortion, the maximum data rate of a typical electrical link would be limited to only a few gigabits per second to avoid excessive intersymbol interference (ISI). The key to achieving dramatically higher data rates (up to 56 Gb/s in the latest proposed standards) is to employ channel equalization. This article describes the most common types of equalizers used in electrical links today.
Direct Cytoplasmic Delivery and Nuclear Targeting Delivery of HPMA-MT Conjugates in a Microtubules Dependent Fashion (2016)

As the hearts of tumor cells, the nucleus is the ultimate target of many chemotherapeutic agents and genes. However, nuclear drug delivery is always hampered by multiple intracellular obstacles, such as low efficiency of lysosome escape and insufficient nuclear trafficking. Herein, an N-(2-hydroxypropyl) methacrylamide (HPMA) polymer-based drug delivery system was designed, which could achieve direct cytoplasmic delivery by a nonendocytic pathway and transport into the nucleus in a microtubules dependent fashion. A special targeting peptide (MT), derived from an endogenic parathyroid hormone-related protein, was conjugated to the polymer backbone, which could accumulate into the nucleus a by microtubule-mediated pathway. The in vitro studies found that low temperature and NaN3 could not influence the cell internalization of the conjugates. Besides, no obvious overlay of the conjugates with lysosome demonstrated that the polymer conjugates could enter the tumor cell cytoplasm by a nonendocytic pathway, thus avoiding the drug degradation in the lysosome. Furthermore, after suppression of the microtubule dynamics with microtubule stabilizing docetaxel (DTX) and destabilizing nocodazole (Noc), the nuclear accumulation of polymeric conjugates was significantly inhibited. Living cells fluorescence recovery after photobleaching study found that the nuclear import rate of conjugates was 2-fold faster compared with the DTX and Noc treated groups. These results demonstrated that the conjugates transported into the nucleus in a microtubules dependent way. Therefore, in addition to direct cytoplasmic delivery, our peptide conjugated polymeric platform could simultaneously mediate nuclear drug accumulation, which may open a new path for further intracellular genes/peptides delivery.
Strong optical coupling between mutually orthogonal plasmon oscillations in a silver nanosphere–nanowire joined system (2012)

A top-to-bottom joined system consisting of a silver nanowire and nanospheres was fabricated by embedding silver nanospheres on a glass or silicon substrate on which 3-aminothiophenol as an analyte molecule was adsorbed, and then placing silver nanowires on the substrate to make gap sites between a nanowire and nanospheres. In the far-field Raman measurements, the sphere under the wire exhibited more than 60 times higher Raman enhancement than isolated spheres. The surface enhanced Raman scattering (SERS) spectra obtained by the 647.1 nm excitation showed highly polarized feature, exhibiting ca. 4 times higher SERS intensity for the electric field parallel to the wire axis than that perpendicular to the wire axis while those by the 514.5 nm excitation showed non-polarized feature against the incident electric field direction. The polarized feature by the 647.1 nm excitation is explained in terms of optical coupling in a vertical direction to the substrate plane, between the silver nanosphere and the longitudinal surface plasmon mode of the nanowire. The longitudinal plasmon of the nanowire functions as an antenna of the incident radiation field in this type of coupled plasmon mode, to yield the confined field. Near-field two-photon excitation imaging measurements as well as numerical calculations of the localized electric field around the system support this idea and indicate that the coupling between the surface plasmon of silver nanospheres and the longitudinal mode of silver nanowires is site-selective.
Estimation of Potential and Convertible Arable Land in China (2001)

It is an urgent subject to know the geographical distribution of potential arable land in order to estimate the potential land productivity in China. In this study we have developed a 2km-grid digital map of potential arable land of China in consideration of only natural conditions, such as topographical factors, climatic factors, and soil and water factors. Furthermore, we have developed a map of convertible arable land by overlaying with the map of potential arable land and that of actual arable land in 1997. The results showed that:(1) A large amount ofconvertible arable land is distributed in the north of China, such as Inner Mongolia, Heilongjiang and Liaoning Provinces, while a small amount of convertible land in the south and Qingzang Plateau;(2) Some areas in Shanxi, Shaanxi provinces in the Loess Plateau and Sichuan Province, which are considered not to be suitable for cultivation, have been cultivated. In such areas, cultivation should be stopped and cultivated land should be returned to grassland or forestland.
Global diversity in the human salivary microbiome (2009)

The human salivary microbiome may play a role in diseases of the oral cavity and interact with microbiomes from other parts of the human body (in particular, the intestinal tract), but little is known about normal variation in the salivary microbiome. We analyzed 14,115 partial ( approximately 500 bp) 16S ribosomal RNA (rRNA) sequences from saliva samples from 120 healthy individuals (10 individuals from each of 12 worldwide locations). These sequences could be assigned to 101 known bacterial genera, of which 39 were not previously reported from the human oral cavity; phylogenetic analysis suggests that an additional 64 unknown genera are present. There is high diversity in the salivary microbiome within and between individuals, but little geographic structure. Overall, approximately 13.5% of the total variance in the composition of genera is due to differences among individuals, which is remarkably similar to the fraction of the total variance in neutral genetic markers that can be attributed to differences among human populations. Investigation of some environmental variables revealed a significant association between the genetic distances among locations and the distance of each location from the equator. Further characterization of the enormous diversity revealed here in the human salivary microbiome will aid in elucidating the role it plays in human health and disease, and in the identification of potentially informative species for studies of human population history.
An IR local positioning system for smart items and devices (2004)

This paper describes IRIS-LPS (InfraRed Indoor Scout), an optical infrared local positioning system. The tracked objects carry active tags that emit infrared signals which are received by a stationary mounted stereo-camera. The system is based on cheap off-the-shelf components, is easy to deploy, and features a large range of coverage. It is capable of tracking a large number of tags without significant performance impact, since the sampling rate remains constant with an increasing number of tags. A test installation of the system has been evaluated in a lecture hall. The positioning system is utilized by our audio-centric user terminal called Talking Assistant. This and other application scenarios are described at the end.
Dissociation mechanisms of neutral methyl stearate and its hydrogen atom adduct formed from the respective positive ions by electron transfer (2006)

The mechanism of dissociation of neutral methyl stearate and its hydrogen atom adduct was investigated by charge inversion mass spectrometry using an alkali metal target. Migrations of functional groups in fatty acid ester ions are often observed during the dissociation of the cations in collisionally activated dissociation (CAD). In the charge inversion spectrum, the main dissociation channels of methyl stearate molecule are the loss of a CH3 radical or a H atom. To identify the source of the CH3 radical and the H atom, the charge inversion spectra of partially deuterated methyl stearate (C17H35COOCD3) were measured. The loss of CH3 occurred through elimination from the methoxy methyl group and that of H occurred through elimination from the hydrocarbon chain of the fatty acid group. In the protonated ester, a simultaneous loss of CH3 (from the methoxy methyl group) and a H atom or a H2 molecule was observed. The charge inversion process gave the dissociation fragments with almost no migration of atoms. Only a few peaks that were structure sensitive were observed in the higher mass region in the charge inversion spectra; these peaks were associated with dissociations of energy-selected neutral species, unlike the case of CAD spectra in which they result from dissociation of ions. Charge inversion mass spectrometry with alkali metal targets provided direct information on the dissociation mechanism of methyl stearate and its hydrogen atom adduct without any migration of functional groups.
Mining trust and distrust relationships in social Web applications (2010)

By the immense growth of social applications in web environment, the role of trust in connecting people is getting more important than ever. Although many researchers have already conducted comprehensive studies on the trust related applications, the understanding of distrust relations is still unclear to the researchers. In this paper, we have investigated some of mechanisms that determine the signs of links in trust networks which consist of both trust and distrust relationships. Achieving this, we develop a framework of trust sign prediction, taking a machine-learning approach. We report experiments conducted on Epinions which is a well-known and very large collection of data dealing with trust computation. Empirical results show that the sign of relations in the trust networks can be effectively predicted using pre-trained classifiers.
Polyphenol-enriched berry extracts naturally modulate reactive proteins in model foods (2017)

Healthy foods like polyphenol-rich berries and high quality edible proteins are in demand in today's functional food marketplace, but it can be difficult to formulate convenient food products with physiologically-relevant amounts of these ingredients and still maintain product quality. In part, this is because proteins can interact with other food ingredients and precipitate destabilizing events, which can disrupt food structure and diminish shelf life. Proteins in foods can also interact with human receptors to provoke adverse consequences such as allergies. When proteins and polyphenols were pre-aggregated into stable colloidal particles prior to use as ingredients, highly palatable food formulations (with reduced astringency of polyphenols) could be prepared, and the overall structural properties of food formulations were significantly improved. All of the nutritive and phytoactive benefits of the proteins and concentrated polyphenols remained highly bioavailable, but the protein molecules in the particle matrix did not self-aggregate into networks or react with other food ingredients. Both the drainage half-life (a marker of structural stability) and the yield stress (resistance to flow) of model foams made with the protein-polyphenol particles were increased in a dose-dependent manner. Of high significance in this complexation process, the reactive allergenic epitopes of certain proteins were effectively blunted by binding with polyphenols, attenuating the allergenicity of the food proteins. Porcine macrophages produced TNF-α proinflammatory cytokine when provoked with whey protein, but, this response was blocked completely when the cells were stimulated with particles that complexed whey protein with cinnamon-derived polyphenols. Cytokine and chemokine production characteristic of allergic reactions were blocked by the polyphenols, allowing for the potential creation of hypoallergenic protein-berry polyphenol enriched foods.
Prospects of Neutralizing Nanobodies Against SARS-CoV-2 (2021)

Since December 2019, the SARS-CoV-2 has erupted on a large scale worldwide and spread rapidly. Passive immunization of antibody-related molecules provides opportunities for prevention and treatment of high-risk patients and children. Nanobodies (Nbs) have many strong physical and chemical properties. They can be atomized, administered by inhalation, and can be directly applied to the infected site, with fast onset, high local drug concentration/high bioavailability, and high patient compliance (no needles). It has very attractive potential in the treatment of respiratory viruses. Rapid and low-cost development of Nbs targeting SARS-CoV-2 can quickly be achieved. Nbs against SARS-CoV-2 mutant strains also can be utilized quickly to prevent the virus from escaping. It provides important technical supports for the treatment of the SARS-CoV-2 and has the potential to become an essential medicine in the toolbox against the SARS-CoV-2.
Analyzing Document Intensive Business Processes using Ontology (2015)

Knowledge is manifested in an enterprise in various forms ranging from unstructured operational data, to structured information like programs, as well as relational data stored in databases to semi-structured information stored in XML files. This information embodies the core of an enterprise knowledge base and analyzing the knowledge base can result in intelligent decision making. In order to realize this goal we begin with representing and analyzing unstructured knowledge present in an enterprise. In particular, this paper presents a real life example of a document intensive business process (International Trade) and attempts to model and analyze the process in a formal way. Typically, the information contained in a document intensive business process is of operational nature and requires extensive manual verification, which is both time consuming and error prone. Therefore, this research aims to eliminate such exhaustive manual verification by constructing a knowledge base in the form of ontology and apply suitable rule based reasoners to automate the verification process.
Automatic test-generation for predicates [software testing] (1996)

The authors propose a new technique for the automatic generation of test cases for predicates. Earlier, they proposed an efficient effective test generation strategy for Boolean expressions. They now extend this strategy to predicates. Their new strategy addresses several issues, including: analysis of dependencies between relational expressions in a predicate /spl Pscr/; generation of test constraints for /spl Pscr/ based on the detection of Boolean and relational operator faults in /spl Pscr/; and generation of actual tests according to the generated test constraints for /spl Pscr/. They propose: the use of constraint logic programming (CLP) to automate test-data generation for a predicate; and an incremental approach to apply CLP techniques to solve a constraint system. Since their technique is specification-based, it can facilitate generation of anticipated outputs for actual tests.
Microwave-Assisted Synthesis of a Series of Lanthanide Metal–Organic Frameworks and Gas Sorption Properties (2012)

A series of isostructural microporous lanthanide metal-organic frameworks (MOFs) formulated as [Ln(2)(TPO)(2)(HCOO)]·(Me(2)NH(2))·(DMF)(4)·(H(2)O)(6) {Ln = Y (1), Sm (2), Eu (3), Gd (4), Tb (5), Dy (6), Ho (7), Er (8), Tm (9), Yb (10), and Lu (11); H(3)TPO = tris-(4-carboxylphenyl)phosphineoxide; DMF = N,N-dimethylformamide} has been synthesized under microwave-assisted solvothermal reaction for 30 min. Alternatively, if a conventional solvothermal reaction is carried out under the same temperature, a much longer time (3 days) is needed for the same phase in similar yield. Structure analysis reveals that the framework is a 4,8-connected network with point symbol (4(10)·6(16)·8(2)) (4(5)·6)(2), which is the subnet of alb net. Thermal gravimetric analyses performed on as-synthesized MOFs reveal that the frameworks have high thermal stability. The luminescent properties of 2, 3, 5, and 6 were investigated and show characteristic emissions for Sm(III), Eu(III), Tb(III), and Dy(III) at room temperature, respectively. Gas sorption properties of 1 and 3 were studied by experimentally measuring nitrogen, argon, carbon dioxide, methane, and hydrogen sorption isotherms. The resulting materials show high and preferential CO(2) adsorption over N(2) gas at ambient temperature, indicating that the present materials can be applied in a CO(2) capture process.
Reflection and emission of Brillouin zone edge states for active photonic crystal waveguides (2005)

A one-dimensional photonic crystal is patterned into an active planar waveguide containing multiple InGaAs quantum wells. External coupling reflectivity is used to map out the photonic band structure, revealing a clear anti-crossing at ~1.37 eV in the 45° TM polarized spectrum. The band structure is compared to and confirmed by scattering-matrix calculations. Photoluminescence measurements are performed in the same geometry on the patterned and unpatterned regions of the sample. The latter shows conventional quantum-well emission and GaAs emission with increasing pump power. In contrast, the spectra from the patterned sample contain a sharp mode from the dielectric-like band of the anti-crossing, corresponding to the Brillouin zone edge. Power-dependent excitation shows this mode to be strongly super-linear, indicative of band edge lasing.
A Study on the Holding of LED Sapphire Substrate Using Alumina Electrostatic Chuck with Fine Electrode Pattern (2011)

In this work, handling of sapphire substrate for LED by using an electrostatic chuck was studied. The electrostatic chuck consisted of alumina dielectric, which was doped with 1.2 wt% <TEX>$TiO_2$</TEX>. As the volume resistivity of alumina dielectric was decreased, the electrostatic force was increased by Johnsen-Rahbek effect. The narrower width and gap size of electrode led to the stronger electrostatic force. When alumina dielectric with <TEX>$3.20{\times}10^{11}{\Omega}{\cdot}cm$</TEX> resistivity and 3 mm width/1.5 mm gap sized electrode was used, the strongest electrostatic force in this work was obtained, which value reached to ~14.46 gf/<TEX>$cm^2$</TEX> at 2.5 kV for 4-inch sapphire substrate. This results show that alumina electrostatic chuck with low resistivity and fine electrode pattern is suitable for handling of sapphire substrate for LED.