gebhart/patrepeval huggingface dataset:
Deep Sequencing Analyses of DsiRNAs Reveal the Influence of 3′ Terminal Overhangs on Dicing Polarity, Strand Selectivity, and RNA Editing of siRNAs (2012)

25/27 Base duplex RNAs that are substrates for Dicer have been demonstrated to enhance RNA interference (RNAi) potency and efficacy. Since the target sites are not always equally susceptible to suppression by small interfering RNA (siRNA), not all 27-mer duplexes that are processed into the corresponding conventional siRNAs show increased potency. Thus random designing of Dicer-substrate siRNAs (DsiRNAs) may generate siRNAs with poor RNAi due to unpredictable Dicer processing. Previous studies have demonstrated that the 3'-overhang affects dicing cleavage site and the orientation of Dicer entry. Moreover, an asymmetric 27-mer duplex having a 3' two-nucleotide overhang and 3'-DNA residues on the blunt end has been rationally designed to obtain greater efficacy. This asymmetric structure directs dicing to predictably yield a single primary cleavage product. In the present study, we analyzed the in vitro and intracellular dicing patterns of chemically synthesized duplex RNAs with different 3'-overhangs. Consistent with previous studies, we observed that Dicer preferentially processes these RNAs at a site 21-22 nucleotide (nt) from the two-base 3'-overhangs. We also observed that the direction and ability of human Dicer to generate siRNAs can be partially or completely blocked by DNA residues at the 3'-termimi. To examine the effects of various 3'-end modifications on Dicer processing in cells, we employed Illumina Deep sequencing analyses to unravel the fates of the asymmetric 27-mer duplexes. To validate the strand selection process and knockdown capabilities we also conducted dual-luciferase psiCHECK reporter assays to monitor the RNAi potencies of both the "sense" (S) and "antisense" (AS) strands derived from these DsiRNAs. Consistent with our in vitro Dicer assays, the asymmetric duplexes were predictably processed into desired primary cleavage products of 21-22-mers in cells. We also observed the trimming of the 3' end, especially when DNA residues were incorporated into the overhangs and this trimming ultimately influenced the Dicer-cleavage site and RNAi potency. Moreover, the observation that the most efficacious strand was the most abundant revealed that the relative frequencies of each "S" or "AS" strand are highly correlated with the silencing activity and strand selectivity. Collectively, our data demonstrate that even though the only differences between a family of DsiRNAs was the 3' two-nuclotide overhang, dicing polarity and strand selectivity are distinct depending upon the sequence and chemical nature of this overhang. Thus, it is possible to predictably control dicing polarity and strand selectivity via simply changing the 3'-end overhangs without altering the original duplex sequence. These optimal design features of 3'-overhangs might provide a facile approach for rationally designing highly potent 25/27-mer DsiRNAs.
Revertant muscle fibers expressing dystrophin do not tolerize the immune system in Duchenne muscular dystrophy: lessons learned from a Phase I clinical trial (96.9) (2010)

Abstract Duchenne muscular dystrophy (DMD) is characterized by progressive muscle weakness due to mutation of the dystrophin gene. Muscle inflammation is an unexplained feature of DMD. T lymphocytes dominate the inflammatory infiltrate but antigen(s) they target have not been identified. Here we evaluated T cell immunity to dystrophin in 6 humans with DMD before and after delivery of a gene therapy vector to skeletal muscle. The vector transgene encoded a miniaturized version of human dystrophin that restores muscle function in animal models of DMD. Sustained transgene expression was not observed in any of the subjects. Non-self epitopes encoded by the vector transgene, but deleted from the defective dystrophin gene, provoked CD4+ and CD8+ T cell responses in a subset of the subjects. Dystrophin-specific T cell immunity was unexpectedly detected in two subjects before gene therapy. Epitopes were mapped to revertant dystrophin protein spontaneously expressed in rare muscle fibers when alternative splicing restores the correct open reading frame. Delivery of the minidystrophin gene to skeletal muscle of one subject provoked a very rapid increase in the frequency of these self-reactive T cells. T cell priming by idiosyncratic expression of revertant dystrophin could explain muscle inflammation and contribute to the pathogenesis of DMD. Recall of auto-reactive T cells also has important clinical significance in the design and monitoring of experimental therapies for this disease.
Analysis of RF plasma using electrical equivalent circuit (2002)

The electrical equivalent circuits of RF plasmas have been obtained by use of the accurate probe measurements and HSPICE simulation. Using the obtained equivalent circuits, the electrical characteristics of SF/sub 6/ and Ar plasmas have been compared. The SF/sub 6/ plasma displays sinusoidal waveforms of the plasma potential for the capacitive sheath characteristics. On the other hand, in Ar plasma the displacement current through the grounded electrode sheath is comparable to the conduction current. The plasma potential in Ar plasma has significantly higher harmonics for the nonlinear characteristics of the grounded electrode sheath. This analysis method serves as an essential tool for modelling RF plasmas.
AEP-LDPC ECC with Error Dispersion Coding for Burst Error Reduction of 2D and 3D NAND Flash Memories (2017)

To improve the reliability of Triple-Level Cell (TLC) NAND flash memory, Advanced Error Prediction (AEP) low-density parity-check (LDPC) ECC with Error Dispersion Coding is proposed. In the conventional LDPC, error-correction capability is degraded due to burst errors [1]. To reduce burst errors and improve the error-correction capabilities of LDPC, this paper proposes Error Dispersion Coding (EDC) which reduces burst errors, decreases the worst bit-error rate (BER) of Upper/Middle/Lower pages, and finally extends the data-retention time of TLC NAND flash memory. By applying proposed EDC, in 3D-TLC NAND flash memory, the burst errors and the worst BER are decreased by 87% and 40%, respectively. As a result, the acceptable data-retention time is extended by 1.8 and 2.6 times in 2D and 3D-TLC NAND flash memory, respectively.
Effect of Culture Age on Protective Potency of a Vaccine against Bovine Ringworm Prepared of Trichophyton verrucosum (2002)

Calves vaccinated with live vaccine against bovine ringworm prepared of a two-week-old culture of Trichophyton verrucosum showed satisfactory protection against experimental dermatophytic infection. Vaccines prepared of cultures of the same strain aged 37, 65, or 92 days were less effective.
PCEP Extension for Transporting TE Data (2015)

In order to compute and provide optimal paths, Path Computation
Elements (PCEs) require an accurate and timely Traffic Engineering
Database (TED). Traditionally this TED has been obtained from a link
state routing protocol supporting traffic engineering extensions.
This document extends the Path Computation Element Communication
Protocol (PCEP) with TED population capability.
ChemInform Abstract: Titanium‐Mediated Oxidative Arylation of Homoallylic Alcohols. (2011)

ChemInformVolume 42, Issue 24 Isocyclic Compounds ChemInform Abstract: Titanium-Mediated Oxidative Arylation of Homoallylic Alcohols. Kathleen S. Lee, Kathleen S. Lee Dep. Biochem., Univ. Tex. Southwest. Med. Cent., Dallas, TX 75390, USASearch for more papers by this authorJoseph M. Ready, Joseph M. Ready Dep. Biochem., Univ. Tex. Southwest. Med. Cent., Dallas, TX 75390, USASearch for more papers by this author Kathleen S. Lee, Kathleen S. Lee Dep. Biochem., Univ. Tex. Southwest. Med. Cent., Dallas, TX 75390, USASearch for more papers by this authorJoseph M. Ready, Joseph M. Ready Dep. Biochem., Univ. Tex. Southwest. Med. Cent., Dallas, TX 75390, USASearch for more papers by this author First published: 19 May 2011 https://doi.org/10.1002/chin.201124090Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume42, Issue24June 14, 2011 RelatedInformation
?Chronic electrical stimulation during the absolute refractory period of the myocardium improves severe heart failure (2004)

These preliminary data indicate that CCM by delivery of intermittent nonexcitatory electrical stimuli is a promising technique for improving ventricular systolic function and symptoms in patients with drug-refractory NYHA class III heart failure.
Biological Age Prediction From Wearable Device Movement Data Identifies Nutritional and Pharmacological Interventions for Healthy Aging (2021)

Intervening in aging processes is hypothesized to extend healthy years of life and treat age-related disease, thereby providing great benefit to society. However, the ability to measure the biological aging process in individuals, which is necessary to test for efficacy of these interventions, remains largely inaccessible to the general public. Here we used NHANES physical activity accelerometer data from a wearable device and machine-learning algorithms to derive biological age predictions for individuals based on their movement patterns. We found that accelerated biological aging from our "MoveAge" predictor is associated with higher all-cause mortality. We further searched for nutritional or pharmacological compounds that associate with decelerated aging according to our model. A number of nutritional components peak in their association to decelerated aging later in life, including fiber, magnesium, and vitamin E. We additionally identified one FDA-approved drug associated with decelerated biological aging: the alpha-blocker doxazosin. We show that doxazosin extends healthspan and lifespan in <i>C. elegans</i>. Our work demonstrates how a biological aging score based on relative mobility can be accessible to the wider public and can potentially be used to identify and determine efficacy of geroprotective interventions.
Anisotropic Nd/sub 2/Fe/sub 14/B based magnet powders with high remanences produced by modified HDDR process (1999)

It is well established that the hydrogenation-decomposition-desorption-recombination (HDDR) process can produce anisotropic Nd2Fe14B-based magnet powders having high coercivities [l].
ChemInform Abstract: ELECTROCHEMISTRY AND PHOTOELECTROCHEMISTRY OF IRON(III) OXIDE (1983)

Abstract Mit Hinweis auf die evtl. Anwendung als n‐Typ‐Halbleiter in Solar‐Photoelektrolyse‐Zellen wurden Oberflächen‐ und Bulk‐Eigenschaften von poly‐ und einkristallinem Fe 2 O 3 untersucht.
Toll-like Interleukin 1 Receptor Regulator Is an Important Modulator of Inflammation Responsive Genes (2019)

TILRR (Toll-like interleukin-1 receptor regulator), a transcript variant of FREM1, is a novel regulatory component, which stimulates innate immune responses through binding to IL-1R1 (Interleukin-1 receptor, type 1) and TLR (Toll-like receptor) complex. However, it is not known whether TILRR expression influences other genes in the NFκB signal transduction and pro-inflammatory responses. Our previous study identified FREM1 as a novel candidate gene in HIV-1 resistance/susceptibility in the Pumwani Sex worker cohort. In this study, we investigated the effect of TILRR overexpression on expression of genes in the NFκB signaling pathway <i>in vitro</i>. The effect of TILRR on mRNA expression of 84 genes related to NFκB signal transduction pathway was investigated by qRT-PCR. Overexpression of TILRR on pro-inflammatory cytokine/chemokine(s) secretion in cell culture supernatants was analyzed using Bioplex multiplex bead assay. We found that TILRR overexpression significantly influenced expression of many genes in HeLa and VK2/E6E7 cells. Several cytokine/chemokine(s), including IL-6, IL-8 (CXCL8), IP-10, MCP-1, MIP-1β, and RANTES (CCL5) were significantly increased in the cell culture supernatants following TILRR overexpression. Although how TILRR influences the expression of these genes needs to be further studied, we are the first to show the influence of TILRR on many genes in the NFκB inflammatory pathways. The NFκB inflammatory response pathways are extremely important in microbial infection and pathogenesis, including HIV-1 transmission. Further study of the role of TILRR may identify the novel intervention targets and strategies against HIV infection.
Numerical analysis of the lattice Boltzmann method for simulation of linear acoustic waves (2017)

We analyze a linear lattice Boltzmann (LB) formulation for simulation of linear acoustic wave propagation in heterogeneous media. We employ the single-relaxation-time Bhatnagar-Gross-Krook as well as the general multirelaxation-time collision operators. By calculating the dispersion relation for various 2D lattices, we show that the D2Q5 lattice is the most suitable model for the linear acoustic problem. We also implement a grid-refinement algorithm for the LB scheme to simulate waves propagating in a heterogeneous medium with velocity contrasts. Our results show that the LB scheme performance is comparable to the classical second-order finite-difference schemes. Given its efficiency for parallel computation, the LB method can be a cost effective tool for the simulation of linear acoustic waves in complex geometries and multiphase media.
Integration of Backscatter Communication with Multi-cell NOMA: A Spectral Efficiency Optimization under Imperfect SIC (2022)

Future wireless networks are expected to connect large-scale low-powered communication devices using the available spectrum resources. Backscatter communications (BC) is an emerging technology towards battery-free transmission in future wireless networks by leveraging ambient radio frequency (RF) waves that enable communications among wireless devices. Non-orthogonal multiple access (NOMA) has recently drawn significant attention due to its high spectral efficiency. The combination of these two technologies can play an important role in the development of future networks. This paper proposes a new optimization approach to enhance the spectral efficiency of nonorthogonal multiple access (NOMA)-BC network. Our framework simultaneously optimizes the power allocation of base station and reflection coefficient (RC) of the backscatter device in each cell under the assumption of imperfect signal decoding. The problem of spectral efficiency maximization is coupled on power and RC which is challenging to solve. To make this problem tractable, we first decouple it into two subproblems and then apply the decomposition method and Karush-Kuhn-Tucker conditions to obtain the efficient solution. Numerical results show the performance of the proposed NOMA-BC network over the pure NOMA network without BC.
Carbon-Nanotube Field-Effect Transistors with Very High Intrinsic Transconductance (2003)

We investigated intrinsic transconductance of carbon-nanotube field-effect transistors (CNTFETs) with carbon nanotubes (CNTs) grown by chemical vapor deposition. The measured transconductance at a drain voltage of -1 V was 8.7 µS for a CNT with a diameter of 1.5 nm. Very high intrinsic transconductance of 20 µS was estimated by considering the contribution of parasitic resistance. Apparent and intrinsic transconductance per unit channel width were 5800 µS/µm and 13000 µS/µm, respectively. These are considerably larger than those for the state-of-the-art Si metal oxide semiconductor field effect transistors (MOSFETs). Parasitic resistance is dominated by the resistance of the CNT portions between the gate and contacts. We expect the performance of CNTFETs will advance further by improving CNT quality and by optimizing device structures.
Direct electrochemical conversion of carbon: systems for efficient conversion of fossil fuels to electricity (2000)

The direct electrochemical conversion of carbon involves discharge of suspensions of reactive carbon particles in a molten salt electrolyte against an oxygen (air) cathode. (Figure 1). The free energy and the enthalpy of the oxidation reaction are nearly identical. This allows theoretical efficiencies ({Delta}G(T)/{Delta}H) to approach 100% at temperatures from 500 to 800 C. Entropy heat losses are therefore negligible. The activities of the elemental carbon and of the carbon dioxide product are uniform throughout the fuel cell and constant over discharge time. This stabilizes cell EMF and allows full utilization of the carbon fuel in a single pass. Finally, the energy cost for pyrolysis of hydrocarbons is generally very low compared with that of steam reforming or water gas reactions. Direct electrochemical conversion of carbon might be compared with molten carbonate fuel cell using carbon rather than hydrogen. However, there are important differences. There is no hydrogen involved (except from trace water contamination). The mixture of molten carbonate and carbon is not highly flammable. The carbon is introduced in as a particulate, rather than as a high volume flow of hydrogen. At the relatively low rates of discharge (about 1 kA/m{sup 2}), the stoichiometric requirements for carbon dioxide by the cathodic reaction may be met by diffusion across the thin electrolyte gap. We report recent experimental work at LLNL using melt slurries of reactive carbons produced by the thermal decomposition of hydrocarbons. We have found that anodic reactivity of carbon in mixed carbonate melts depends strongly on form, structure and nano-scale disorder of the materials, which are fixed by the hydrocarbon starting material and the conditions of pyrolysis. Thus otherwise chemically pure carbons made by hydrocarbon pyrolysis show rates at fixed potentials that span an order of magnitude, while this range lies 1-2 orders of magnitude higher than the current density of graphite plate electrodes. One carbon materials was identified which delivered anode current densities of 1 kA/m{sup 2} at 0.8 V (i.e., 80% efficiency, based on the standard enthalpy of carbon/oxygen reaction, and assuming full conversion), which we believe to be sufficiently great to allow practical application in fuel cell arrays. Since the hydrocarbon starting materials are ''ash free,'' entrainment of ash into the melt is not limiting. Finally, the use of fine carbon particulates in slurries avoids cost and logistics of carbon electrode manufacture and distribution.
Clinical Design Functions: Round Table Discussions on the Bioengineering of Liquid Ventilators (2009)

During the 6th International Symposium on Perfluorocarbon Application and Liquid Ventilation, a round table discussion on bioengineering was held in which different experts shared their opinions and experiences about the use of a total liquid ventilator design for clinical applications. To structure the discussion, all experts were invited to contribute their knowledge within the context of three matrixes related to the liquid ventilators: 1) function and technology, 2) ventilation modes, and 3) risk analyses. The outcome of this international conference recommends continued development of a total liquid ventilator toward clinical applications.
Biomimetic Kinetic Resolution: Highly Enantio- and Diastereoselective Transfer Hydrogenation of Aglain Ketones To Access Flavagline Natural Products (2014)

We have previously reported asymmetric syntheses and absolute configuration assignments of the aglains (+)-ponapensin and (+)-elliptifoline and proposed a biosynthetic kinetic resolution process to produce enantiomeric rocaglamides and aglains. Herein, we report a biomimetic approach for the synthesis of enantiomerically enriched aglains and rocaglamides via kinetic resolution of a bridged ketone utilizing enantioselective transfer hydrogenation. The methodology has been employed to synthesize and confirm the absolute stereochemistries of the pyrimidone rocaglamides (+)-aglaiastatin and (-)-aglaroxin C. Additionally, the enantiomers and racemate of each metabolite were assayed for inhibition of the heat-shock response, cytotoxicity, and translation inhibition.
Beam Deflection Measurements of Transient Nonlinear Refraction in Air in the Mid-IR (2019)

Using the Beam Deflection Technique, the bound-electronic and nuclear reorientation contributions to the nonlinear refraction of air are separately measured in the mid-infrared as a function of time below the ionization threshold.
Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21 (2007)

The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p), estimated to be 10% of 21p. This region contains extensive euchromatic-like sequence and includes on average one transcript every 100 kb. These transcripts show multiple inter- and intrachromosomal copies, and extensive copy number and sequence variability. The sequencing of the "heterochromatic" regions of the human genome is likely to reveal many additional functional elements and provide important evolutionary information.
The Role of the Chemical Shift Difference in a Two-Site Exchange Model Under an On-Resonance Spin-Lock RF Field (2018)

The manuscript investigates the role of the chemical shift difference between two exchanging pools under a spin-lock RF field. The results demonstrate that the width of the dispersion of R1rho is determined mainly by the chemical shift difference when the exchange is slow. This work may give a new insight into the spin dynamics under a spin-lock condition and the results may be relevant to the fields using the spin-lock technique, such as protein NMR and MRI contrast.&lt;br&gt;
Validation of the Positive Social Interdependence Readiness Scale for Cooperative Learning (2019)

Purpose: Many instructional strategies for cooperative learning have been used in medical education, such as team-based education, inter-professional education, and problem-based learning. However, useful assessment tools for investigating students' readiness for cooperative learning are lacking. Therefore, the present study developed the Positive Social Interdependence Readiness Scale (PSIRS) questionnaire based on the cooperative learning theory. This paper presents the development and validation of the PSIRS for use with undergraduate health care students in the context of cooperative learning. Methods: A version of the PSIRS questionnaire was administered to 207 health care undergraduates who participated in cooperative learning activities under three models at Taipei Medical University. Results: Three factors, measured by 39 survey statements, were identified from the statistical analysis of the survey data, namely cooperative learning appreciation, the psychological characteristics of Positive Social Interdependence, and students' confidence in teamwork effectiveness. The internal consistency measure was 0.983. Analysis of variance demonstrated some key differences in the three factors among courses. Conclusions: The validated PSIRS questionnaire was proven to be applicable and able to differentiate between student subgroups. More applications and factor influencing PSIRS inquiry are suggested in the future.