gebhart/patrepeval huggingface dataset:
Comparing quantum dynamical entropies (1998)

Last years, the search for a good theory of quantum dynamical entropy has been very much intensified. This is not only due to its usefulness in quantum probability but mainly because it is a very promising tool for the theory of quantum chaos. Nowadays, t
Human Airway Epithelial Cells SensePseudomonas aeruginosaInfection via Recognition of Flagellin by Toll-Like Receptor 5 (2005)

Pseudomonas aeruginosa, an opportunistic respiratory pathogen that infects the majority of patients with cystic fibrosis, initiates host inflammatory responses through interaction with airway epithelial cells. The Toll-like receptors (TLRs) are a family of pathogen pattern recognition receptors that play key roles in host innate immunity. In this study we aimed to determine whether TLRs mediate the interaction between P. aeruginosa and airway epithelial cells. Individual murine TLRs (TLR1 to TLR9) and dual combinations of these TLRs that activate an NF-kappaB-driven luciferase reporter in response to PAO1 were screened in HEK 293 cells. TLR5, TLR2, a combination of TLR1 and TLR2, or a combination of TLR2 and TLR6 responded to PAO1. Another P. aeruginosa strain, strain PAK, activated TLR5 similarly, while the isogenic flagellin-deficient strain PAK/fliC and the flagellum-free bacterium Haemophilus influenzae failed to activate TLR5. Reverse transcription-PCR was used to probe the presence of multiple TLRs (including TLR5) in primary human airway epithelial cells (HAECs). Immunostaining with TLR5 antibodies showed that TLR5 was expressed in HAECs and on the apical surface of the human trachea epithelium. In HAECs, PAO1, PAK, and Burkholderia cepacia, but not flagellin-deficient strain PAK/fliC or a B. cepacia fliC mutant, activated the NF-kappaB reporter. Dominant negative TLR5 specifically blocked the response to P. aeruginosa but not to the response to lipoteichoic acid, a specific ligand of TLR2. We also determined that MyD88, IRAK, TRAF6, and Toll-interacting protein (Tollip), but not TIRAP, were involved in the TLR-mediated response to P. aeruginosa in HAECs. These findings demonstrate that the airway epithelial receptor TLR5 senses P. aeruginosa through its flagellin protein, which may have an important role in the initiation of the host inflammatory reaction to clear the invading pathogen.
Clinical evaluation of inline motion correction for cardiac perfusion MRI (2011)

The purpose of this study is to evaluate the impact of non-rigid registration of cardiac perfusion images on image quality and diagnostic accuracy.
mmpdb: An Open-Source Matched Molecular Pair Platform for Large Multiproperty Data Sets (2018)

Matched molecular pair analysis (MMPA) enables the automated and systematic compilation of medicinal chemistry rules from compound/property data sets. Here we present mmpdb, an open-source matched molecular pair (MMP) platform to create, compile, store, retrieve, and use MMP rules. mmpdb is suitable for the large data sets typically found in pharmaceutical and agrochemical companies and provides new algorithms for fragment canonicalization and stereochemistry handling. The platform is written in Python and based on the RDKit toolkit. It is freely available from https://github.com/rdkit/mmpdb .
Finding the infectious dose for COVID-19 by applying an airborne-transmission model to superspreader events (2022)

We probed the transmission of COVID-19 by applying an airborne transmission model to five well-documented case studies-a Washington state church choir, a Korean call center, a Korean exercise class, and two different Chinese bus trips. For all events the likely index patients were pre-symptomatic or mildly symptomatic, which is when infective patients are most likely to interact with large groups of people. Applying the model to those events yields results that suggest the following: (1) transmission was airborne; (2) superspreading events do not require an index patient with an unusually high viral load; (3) the viral loads for all of the index patients were of the same order of magnitude and consistent with experimentally measured values for patients at the onset of symptoms, even though viral loads across the population vary by a factor of >108. In particular we used a Wells-Riley exposure model to calculate q, the total average number of infectious quanta inhaled by a person at the event. Given the q value for each event, the simple airborne transmission model was used to determined Sq, the rate at which the index patient exhaled infectious quanta and N0, the characteristic number of COVID-19 virions needed to induce infection. Despite the uncertainties in the values of some parameters of the superspreading events, all five events yielded (N0∼300-2,000 virions), which is similar to published values for influenza. Finally, this work describes the conditions under which similar methods can provide actionable information on the transmission of other viruses.
Progressive Muscle Cell Delivery as a Solution for Volumetric Muscle Defect Repair (2016)

Reconstructing functional volumetric tissue in vivo following implantation remains a critical challenge facing cell-based approaches. Several pre-vascularization approaches have been developed to increase cell viability following implantation. Structural and functional restoration was achieved in a preclinical rodent tissue defect; however, the approach used in this model fails to repair larger (>mm) defects as observed in a clinical setting. We propose an effective cell delivery system utilizing appropriate vascularization at the site of cell implantation that results in volumetric and functional tissue reconstruction. Our method of multiple cell injections in a progressive manner yielded improved cell survival and formed volumetric muscle tissues in an ectopic muscle site. In addition, this strategy supported the reconstruction of functional skeletal muscle tissue in a rodent volumetric muscle loss injury model. Results from our study suggest that our method may be used to repair volumetric tissue defects by overcoming diffusion limitations and facilitating adequate vascularization.
A dual-conversion zero-IF design for DVB-H RF tuner applications (2009)

This paper presents the RFIC design that uses TSMC 0.18 ¿m CMOS process to implement a DVB-H RF tuner. The design is based on a dual-conversion zero-IF architecture. Compared to the conventional up-down architecture, this adopted architecture has the advantages of no IF SAW filter but still can easily reject the image signal. To pass the protection-ratio specification, the most challenging one in DVB-H tuner specifications, this RFIC design is featured with a broadband LNA with a variable gain, a highly linear up-converting mixer with a double-balanced resistive FET architecture, and a high-linearity quadrature demodulator with the transconductance linearization technique. The important CW measured results is summarized as follows: The DC power consumption is 70.2 mW. From 50 to 860 MHz, the maximum gain varies from 19.7 to 29.2 dB with an adjustable attenuation more than 50 dB. Under the maximum-gain condition, the noise figure varies from 4.6 to 12 dB, and the OIP3 varies from 0.1 to 2.2 dBm. The CW test results agree quite well with the link-budget analysis results.
A Symbiotic Approach to Generating Stress Tolerant Crops (2022)

Studies were undertaken to determine if fungal endophytes from plants in stressful habitats could be commercialized to generate climate resilient crop plants. Fungal endophytes were isolated from weedy rice plants and grasses from South Korea and the USA, respectively. Endophytes (Curvularia brachyspora and www.videleaf.com Fusarium asiaticum) from weedy rice plants from high salt or drought stressed habitats in South Korea conferred salt and drought stress tolerance to weedy rice and commercial varieties reflective of the habitats from which they were isolated. Fungal endophytes isolated from grasses in arid habitats of the USA were identified as Trichoderma harzianum and conferred drought and heat stress tolerance to monocots and eudicots. Two T. harzianum isolates were exposed to UV mutagenesis to derive strains resistant to fungicides in seed treatment plant protection packages. Three strains that collectively had resistance to commonly used fungicides were used for field testing. The threestrain mixture (ThSM3a) increased crop yields proportionally to the level of stress plants experienced with average yields up to 52% under high and 3-5% in low stress conditions. This study demonstrates fungal endophytes can be developed as viable commercial tools for rapidly generating climate resilient crops to enhance agricultural sustainability.
Classification of Structured Descriptions (2006)

Many speech and language processing problems have been successfully cast as classification problems - associating a token with a label from a prespecified label set. However, in all these applications, the set of labels is regarded as a flat list of symbols with no inherent internal structure and no co-constraints among the labels. We present a classification task using structured word labels, called supertags, and discuss methods that exploit the structure of these labels in the context of natural language generation. Supertags encode predicate-argument information along with syntactic ordering constraints that can be exploited for realizing a sentence. We report the accuracy of supertagging models for a node using features derived from its local tree context and attributes of the supertags.
Generalized total variation denoising via augmented Lagrangian cycle spinning with Haar wavelets (2012)

We consider the denoising of signals and images using regularized least-squares method. In particular, we propose a simple minimization algorithm for regularizers that are functions of the discrete gradient. By exploiting the connection of the discrete gradient with the Haar-wavelet transform, the n-dimensional vector minimization can be decoupled into n scalar minimizations. The proposed method can efficiently solve total-variation (TV) denoising by iteratively shrinking shifted Haar-wavelet transforms. Furthermore, the decoupling naturally lends itself to extensions beyond ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> regularizers.
Cross-Layer Congestion Control and Scheduling in Multi-Hop OFDMA Wireless Networks (2009)

In this paper, we consider joint end-to-end congestion control and multiuser scheduling in multi-hop wireless networks, where orthogonal frequency-division multiple access (OFDMA) is the air interface. Compared to its single-channel counterpart, this problem is significantly more challenging because subchannel assignment and power allocation for all nodes and network traffic need to be jointly optimized. To avoid cochannel inference, we first consider an OFDMA subchannel separation problem in multi-hop communication scenarios. Then, we address this cross-layer optimization problem by decomposing it into two subproblems: a TCP layer congestion control for traffic allocation and a weighted scheduling for OFDMA subchannel assignment and power control. Observing that the scheduling for multiuser OFDMA in multi-hop wireless networks is inherently NP-hard, we propose a low-complexity algorithm that ensures a solution converging to the optimum. The performance of the algorithm is demonstrated through simulations.
Prevalence and Risk Factors of Chronic Otitis Media: The Korean National Health and Nutrition Examination Survey 2010–2012 (2015)

Our population-based study showed that COM is not rare in Korea, and its development may be associated with various host and environmental factors. Further research on its relationships and the pathogenesis are needed.
In Vitro Selection of RNA Aptamers that Bind to Colicin E3 and Structurally Resemble the Decoding Site of 16S Ribosomal RNA (2004)

Colicin E3 is a ribonuclease that specifically cleaves at the site after A1493 of 16S rRNA in Escherichia coli ribosomes, thus inactivating translation. To analyze the interaction between colicin E3 and 16S rRNA, we used in vitro selection to isolate RNA ligands (aptamers) that bind to the C-terminal ribonuclease domain of colicin E3, from a degenerate RNA pool. Although the aptamers were not digested by colicin E3, they specifically bound to the protein (K(d) = 2-14 nM) and prevented the 16S rRNA cleavage by the C-terminal ribonuclease domain. Among these aptamers, aptamer F2-1 has a sequence similar to that of the region around the cleavage site from residue 1484 to 1506, including the decoding site, of E. coli 16S rRNA. The secondary structure of aptamer F2-1 was determined by the base pair covariation among the variants obtained by a second in vitro selection, using a doped RNA pool based on the aptamer F2-1 sequence. The sequence and structural similarities between the aptamers and 16S rRNA provide insights into the recognition of colicin E3 by this specific 16S rRNA region.
Genome wide DNA‐profiling of HIV‐related B‐cell lymphomas (2009)

Non-Hodgkin lymphomas (NHL) represent a frequent complication of human immunodeficiency virus (HIV) infection. To elucidate HIV-NHL pathogenesis, we performed a genome-wide DNA profiling based on a single nucleotide polymorphism-based microarray comparative genomic hybridization in 57 HIV-lymphomas and, for comparison, in 105 immunocompetent diffuse large B-cell lymphomas (IC-DLBCL). Genomic complexity varied across HIV-NHL subtypes. HIV-Burkitt lymphoma showed a significantly lower number of lesions than HIV-DLBCL (P = 0.032), whereas the median number of copy number changes was significantly higher in Epstein-Barr virus negative (EBV-) HIV-DLBCL (42.5, range 8-153) compared to EBV+ cases (22; range 3-41; P = 0.029). Compared to IC-DLBCL, HIV-DLBCL displayed a distinct genomic profile with no gains of 18q and specific genetic lesions. Fragile sites-associated genes, including FHIT (FRA3B), WWOX (FRA16D), DCC (FRA18B) and PARK2 (FRA6E) were frequently inactivated in HIV-NHL by interstitial deletions, and a significantly higher prevalence of FHIT alterations was observed in HIV-DLBCL compared to IC-DLBCL. The same genes involved by fragile site deletions were also frequently affected by aberrant methylation of regulative regions.
Analysis of two-dimensional photonic crystal with anisotropic gain (2011)

Photonic modes in a two-dimensional square-lattice photonic crystal (PC) with anisotropic gain are analyzed for the first time. A plane-wave expansion method is improved to include the gain, which depends on not only the position but also the propagation direction of each plane wave. The anisotropic gain varies the photonic band structure, the near-field distributions, and the gain dispersion curves through variation in PC symmetry. Low-threshold operation of a PC laser with anisotropic-gain material such as nonpolar InGaN requires that the direction of higher gain in the material aligns along the ΓX direction of the PC.
Personal broadband satellite systems and services (2002)

The Internet boom of the latter half of the last decade fuelled a proliferation of projects for satellite-based broadband Internet delivery systems. Some of these projects were based on existing satellite infrastructure, primarily offered by already established DBS operators; many more of these projects were new ventures seeking to finance sophisticated, bespoke satellite systems with the seemingly endless supply of venture capital that was available for investment in any new project associated with the Internet. The continued growth of the Internet is seen to provide a basis for investment in wideband Internet delivery and it is quite clear that terrestrial delivery systems such as cable and DSL will only be able to partially meet the demand for personal, broadband Internet access. (4 pages)
Label-Free Electrochemical Sensor for Ochratoxin A Using a Microfabricated Electrode with Immobilized Aptamer (2018)

Ochratoxin A (OTA) is one of the most abundant food-contaminating mycotoxins that is also a potential carcinogen and responsible for many diseases affecting humans. Consequently, a sensitive, portable device for the detection of OTA is highly desirable. In this study, a miniaturized electrochemical aptamer-based sensor was developed for the label-free, sensitive detection of OTA. For the construction of the sensor, a gold thin-film three-electrode system was fabricated using standard microfabrication techniques on a polystyrene substrate (25 mm × 25 mm). Subsequently, the thiol-modified linker, 6-mercaptohexanol, DNA aptamer, and methylene blue (MB) were sequentially applied to the working electrode to construct a sensing layer. MB served as a redox indicator that interacted with the aptamer via the guanine bases and phosphate backbone to form complexes. The addition of OTA to the sensor induced the folding of the aptamer, which was accompanied by the release of the aptamer–MB–OTA complex from the sensor. Thus, the amount of MB decreased with increasing concentration of OTA. Differential pulse voltammetry was used for monitoring the highly sensitive detection. The standard curve for OTA exhibited a wide linearity ranging from 0.1 to 300 ng mL–1 with a detection limit of 78.3 pg mL–1 (S/N = 3). The selectivity test confirmed that the aptamer had high affinity only for the target. The OTA recoveries with the proposed sensor in commercial samples of coffee and beer were 86.4–107%.
Microwave detection based on magnetoresistance effect in spintronic devices (2016)

We demonstrate a radio-frequency electromagnetic signal detection in spintronic devices utilizing various magnetoresistance effects. Different device layout is proposed such as tunneling magnetoresistance nano-pillar or giant magnetoresistance stripe, which enable DC voltage generation when a device is supplied with radio-frequency current. Depending on the detection method, sensitivity of up to 80 V/W was achieved in a frequency range between 1 - 10 GHz, depending on the magnetic field.
All-colloidal parity–time-symmetric microfiber lasers balanced between the gain of colloidal quantum wells and the loss of colloidal metal nanoparticles (2022)

Lasers based on semiconductor colloidal quantum wells (CQWs) have attracted wide attention, thanks to their facile solution-processability, low threshold and wide range spectral tunability. Colloidal microlasers based on whispering-gallery-mode (WGM) resonators have already been widely demonstrated. However, due to their microscale size typically supporting multiple modes, they suffer from multimode competition and higher threshold. The ability to control the multiplicity of modes oscillating within colloidal laser resonators and achieving single-mode lasers is of fundamental importance in many photonic applications. Here we show that as a unique, simple and versatile architecture of all-colloidal lasers intrinsically enabled by balanced gain/loss segments, the lasing threshold reduction and spectral purification can be readily achieved in a system of a WGM-supported microfiber cavity by harnessing the notions of parity-time symmetry (PT). In particular, we demonstrate a proof-of-concept PT-symmetric microfiber laser employing CQWs as the colloidal gain medium along with a carefully tuned nanocomposite of Ag nanoparticles (Ag NPs) incorporated into a PMMA matrix altogether and conveniently coated around a coreless microfiber as a rigorously tailored colloidal loss medium to balance the gain. The realization of gain/loss segments in our PT-symmetric all-colloidal arrangement is independent of selected pumping, reducing the complexity of the system and making compact device applications feasible, where control over the pumping is not possible. We observed a reduction in the number of modes, resulting in a reduced threshold and enhanced output power of the PT-symmetric laser. The PT-symmetric CQW-WGM microcavity architecture offers new opportunities towards simple implementation of high-performance optical resonators for colloidal lasers.
Antisense Therapeutics (2019)

This chapter assesses the status of the technology, discusses the technology in the pharmacological context in which it is best understood, and deals with some of the controversies with regard to the technology and the interpretation of experiments. Interest in developing antisense technology and in exploiting it for therapeutic purposes has been intense. Phosphorothioate oligonucleotides can be prepared consistently and with excellent purity. The structure of the Ribonucleic acid (RNA) has a profound influence on the affinity of the oligonucleotide and on the rate of binding of the oligonucleotide to its RNA target. Clearly, the ultimate biological effect of an oligonucleotide will be influenced by the local concentration of the oligonucleotide at the target RNA, the concentration of the RNA, the rates of synthesis and degradation of the RNA, the type of terminating mechanism, and the rates of the events that result in termination of the RNA’s activity.
NMDA receptor subunit‐dependent modulation by conantokin‐G and Ala(7)‐conantokin‐G (2005)

The modulation of recombinant NMDA receptors by conantokin-G (con-G) and Ala7-conantokin-G (Ala7-Con-G) was investigated in Xenopus oocytes injected with capped RNA coding for NR1 splice variants and NR2 subunits using the two-electrode voltage clamp technique. Glutamate exhibited a marginally higher apparent affinity for NR2A-containing receptors than NR2B-containing receptors, regardless of the NR1 subunit present. Conantokins were bath applied to give cumulative concentration responses in the presence of 3 and 30 mum glutamate. Both contantokins exhibited biphasic concentration-response relationships at NR2A-containing NMDA receptors, producing potentiation at low conantokin concentrations and inhibition at high concentrations. These effects were stronger with glutamate concentrations near its EC50, and less marked at saturating concentrations. In contrast, the conantokin concentration-response relation was monophasic and inhibitory at NR2B-containing receptors. We conclude that the combinations of subunits that comprise the NMDA receptor complex influence conantokin and glutamate affinities and the nature of the responses to conantokins.
Comparison between optical-resolution photoacoustic microscopy and confocal laser scanning microscopy for turbid sample imaging (2015)

Thickness estimation is a common task in optical coherence tomography (OCT). This study discusses and quantifies the intensity noise of three commonly used broadband sources, such as a supercontinuum source, a superluminescent diode (SLD), and a swept source. The performance of the three optical sources was evaluated for a thickness estimation task using both the fast Fourier transform (FFT) and maximum-likelihood (ML) estimators. We find that the source intensity noise has less impact on a thickness estimation task compared to the width of the axial point-spread function (PSF) and the trigger jittering noise of a swept source. Findings further show that the FFT estimator yields biased estimates, which can be as large as 10% of the thickness under test in the worst case. The ML estimator is by construction asymptotically unbiased and displays a 10× improvement in precision for both the supercontinuum and SLD sources. The ML estimator also shows the ability to estimate thickness that is at least 10× thinner compared to the FFT estimator. Finally, findings show that a supercontinuum source combined with the ML estimator enables unbiased nanometer-class thickness estimation with nanometer-scale precision.