gebhart/patrepeval huggingface dataset:
29 TREATMENT OF DONOR CELLS WITH XENOPUS OOCYTE EXTRACT ENHANCED SOMATIC CELL NUCLEAR TRANSFER EMBRYO DEVELOPMENT (2011)

Somatic cell nuclear transfer (SCNT) efficiency in pigs and other species is still very low. This low efficiency and the occurrence of developmental abnormalities in offspring has been attributed to incomplete or incorrect reprogramming. Cytoplasmic extracts from both mammalian and amphibian oocytes can alter the epigenetic state of mammalian somatic nuclei as well as gene expression to more resemble that of pluripotent cells. Rathbone et al. (2010) has showed that pretreating somatic donor cells with frog oocyte extract (FOE) increased live birth in ovine. Liu et al. (2011) also reported that treating donor cells with FOE enhanced handmade clone embryo development in pigs. The aim of this study was to evaluate the early development of cloned embryos produced with porcine GFP fibroblasts pre-treated with a permeabilizing agent, digitonin and matured frog oocyte extract. Frog egg cytoplasmic extract was prepared from one frog's oocytes after being matured in vitro to MII stage. The experiment included 2 groups. In the FOE-treated group, GFP-tagged fetal fibroblasts were permeabilized by digitonin (15 ng mL–1) and incubated in FOE containing an ATP-regenerating system (2.5 mM ATP, 125 µM GTP, 62.5 µg mL–1 of creatine kinase, 25 mM phosphocreatine and 1 mM NTP) at room temperature (24°C) for 2 h; cell membranes were re-sealed by culturing in 10% FBS in DMEM media for 2.5 h at 38.5°C before used as donor cells. In the control group, the same donor cells were treated with digitonin, but without frog oocyte extract incubation. The SCNT embryos were produced by using the 2 groups of donor cells as described above. In total, 305 control and 492 FOE oocytes were enucleated from 8 biological replicates. Two hundred fifty control and 370 FOE couplets were fused and cultured in porcine zygote medium 3. Percent cleavage was recorded on Day 2 and the percent blastocyst formation was determined on Day 7 (SCNT day = 0). In addition, the number of nuclei in the blastocysts was recorded on Day 7. Percent fusion, cleavage, blastocyst formation and number of nuclei in blastocysts were analysed by using SAS software (v9.2), with day and treatment class as main effects. There was no difference in percent fusion (FOE, 76.2 ± 2.5% vs control, 80.8 ± 2.8%) or in cleavage (FOE: 74.8 ± 2.5% vs control: 74.6 ± 2.9%). Only green blastocysts with 16 or more nuclei were considered to be a true SCNT blastocyst. The percent blastocyst was higher in the FOE group than that in the control (13.9 ± 0.8% vs 9.5 ± 0.9%, P &amp;lt; 0.05), whereas the number of nuclei in the blastocysts was not different between the 2 groups (39.7 ± 2.4, 35.9 ± 3.8 for FOE and control, respectively). In conclusion, our study demonstrated that pre-treatment of donor cells with digitonin and Xenopus MII oocyte extract increased porcine SCNT embryo development to blastocyst and cloning efficiency. Funded by the National Natural Science Foundation of China (NO. 31071311), Natural Science Foundation of Fujian Province of China (No. 2009J06017) and NIH U42 RR18877.
New Concept in Stroke Diagnosis (2019)

Stroke is a life-threatening event that is expected to more than double over the next 40 years. Approximately 85% of strokes are ischemic in nature and result from thromboembolic occlusion of a major cerebral artery or its branches. One of the diagnostic methods for detection of the cerebral ischemia is the gadolinium-enhanced MRI imaging. It is mainly used in patients to detect brain tissue damaged by an ischemic stroke and brain hemorrhage. These techniques are expensive, require sophisticated machines and are time consuming. A recent study in acute stroke patients showed gadolinium leakage into ocular structures (GLOS) during MRI imaging with gadolinium administration. The results indicate that at 2 hours after administration of the contrast agent, GLOS was more common in the aqueous chamber alone, compared to the vitreous chamber with increasing amount in 24 hours after the administration of the contrast agent. This could be due to disruption of blood-ocular barrier similar to the disruption of blood-brain barrier in acute stroke. A new approach to diagnosis of acute stroke and transient ischemic attack (TIA) is through the detection of sodium fluorescein contrast agent in the eye by i.v. injection. The agent is safe and is used routinely in eye fluorescein angiography. Fluorescein fluorescence occurs at the visible wavelengths and can be detected by fluorescein angiography camera. The fluorescein angiography camera prices are affordable for any medical clinic. The innovation of this method is to leverage the eye as the window to the brain. The method can potentially detect acute stroke and TIA without MRI. This can have a far-reaching impact on the healthcare system. The eventual feature of the device will be portability and simplicity of operation that can be used by a medical technician in medical office, emergency outfits and even in ambulances given the portability.
Transport Of Surface‐Modified Nanoparticles Through Cell Monolayers (2005)

We synthesized three peptides, a D-polyarginyl peptide (r8(FITC)), a Tat peptide (Tat(FITC)), and a control peptide (Cp(FITC)) and attached each to amino-CLIO, a nanoparticle 30 nm in diameter. We then examined the effective permeability, Peff, of all six materials through CaCo-2 monolayers. The transport of peptide-nanoparticles was characterized by a lag phase (0-8 h) and a steady-state phase (9-27 h). The steady-state Peff values for peptides were in the order r8(FITC)>Tat(FITC)=Cp(FITC). When r8(FITC) and Tat(FITC) peptides were attached to the nanoparticle, they conferred their propensity to traverse cell monolayers onto the nanoparticle, whereas Cp(FITC) did not. Thus, when the r8(FITC) peptide was attached to the amino-CLIO nanoparticle, the resulting peptide-nanoparticle had a Peff similar to that of this poly-D-arginyl peptide alone. The Peff of r8(FITC)-CLIO (MW approximately 1000 kDa) was similar to that of mannitol (MW=182 Da), a poorly transported reference substance, with a far lower molecular weight. These results are the first to indicate that the modification of nanoparticles by attachment of membrane-translocating sequence-based peptides can alter nanoparticle transport through monolayers. This suggests that the surface modification of nanoparticles might be a general strategy for enhancing the permeability of drugs and that high-permeability nanoparticle-based therapeutics can be useful in selected pharmaceutical applications.
Supplementary Table 1 from Extracorporeal Photochemotherapy Drives Monocyte-to-Dendritic Cell Maturation to Induce Anticancer Immunity (2023)

&lt;p&gt;Supplementary Table 1 showing additional FACS analysis results for Figure 7A of the manuscript, for review and publication&lt;/p&gt;
Transport Cost for Carbon Removal Projects With Biomass and CO2 Storage (2021)

Strategies to remove carbon from the atmosphere are needed to meet global climate goals. Promising strategies include the conversion of waste biomass to hydrogen, methane, liquid fuels, or electricity coupled with CO 2 capture and storage (CCS). A key challenge for these projects is the need to connect geographically dispersed biomass supplies with geologic storage sites by either transporting biomass or CO 2 . We assess the cost of transport for biomass conversion projects with CCS using publicly available cost data for trucking, rail, and CO 2 pipelines in the United States. We find that for large projects (order of 1 Mt/yr CO 2 or greater), CO 2 by pipeline is the lowest cost option. However, for projects that send most of the biomass carbon to storage, such as gasification to hydrogen or electricity production, biomass by rail is a competitive option. For smaller projects and lower fractions of carbon sent to storage, such as for pyrolysis to liquid fuels, CO 2 by rail is the lowest cost option. Assessing three plausible example projects in the United States, we estimate that total transport costs range from $24/t-CO 2 stored for a gasification to hydrogen project traversing 670 km to $36/t for a gasification to renewable natural gas project traversing 530 km. In general, if developers have flexibility in choosing transport mode and project type, biomass sources and storage sites can be connected across hundreds of kilometers for transport costs in the range of $20-40/t-CO 2 stored. Truck and rail are often viable modes when pipelines cannot be constructed. Distances of 1,000 km or more can be connected in the same cost range when shared CO 2 pipelines are employed.
Suction and Pulsed Blowing Applied to Local Separation Downstream of Slat Cutout (2022)

An experimental study on the application of active flow control (AFC) to a .4 scale model of a swept wing in a landing configuration was conducted. The wing is fitted with an ultrahigh bypass ratio (UHBR) engine nacelle. The highly efficient UHBR engines are characterized by a large diameter that interferes with the flow around the wing, especially with slats deflected, degrading its performance. An innovative AFC device, creating steady suction and pulsed blowing (PB), was installed in the leading-edge region of the wing, above the nacelle, and its performance was experimentally evaluated. The effects of the suction and PB mechanisms were examined individually and simultaneously using relevant normalized parameters to pave the way to a full-scale wind-tunnel test. It was shown that the AFC actuators increased lift by up to 3%, redirected the flow to the desired downstream direction, and reduced the size of the separation zone created due to the implementation of the UHBR nacelle. The next step is validating the small-scale results of this study in a full-scale wind-tunnel tests that would be the last step before the technology is flight test ready.
Solvent Effects on Hole-Edge Structure for Single-Wall Carbon Nanotubes and Single-Wall Carbon Nanohorns (2004)

To extend the application fields of single-wall carbon nanotubes (SWNTs) and single-wall carbon nanohorns (SWNHs), their chemical modification is essential. Since their graphene-sheet-based structures are chemically robust, only the edges of the graphene sheets, more specifically the oxygen-containing functional groups at hole edges, are useful sites for chemical modification. However, not much is known about the hole-edges, so the phenomenon reported here, that the hole edges easily react with conventional reagents, was previously unknown. We observed a lowering of the combustion temperature of SWNTs and SWNHs immersed in water; this lowering was induced as a result of the hydrolysis of oxygen-containing functional groups (anhydrides and/or lactones) at the hole edges. We also found that the reactivity of hole edges can be easily controlled through an appropriate choice of solvents. We believe that this study is helpful to our understanding of hole-edge chemistry and will help to enable the production of well-designed carbonaceous materials with high functionality.
Cascaded Optical Nonlinearities in Dielectric Metasurfaces (2022)

Since the discovery of the laser, optical nonlinearities have been at the core of efficient light conversion sources. Typically, thick transparent crystals or quasi-phase matched waveguides are utilized in conjunction with phase-matching techniques to select a single parametric process. In recent years, due to the rapid developments in artificially structured materials, optical frequency mixing has been achieved at the nanoscale in subwavelength resonators arrayed as metasurfaces. Phase matching becomes relaxed for these wavelength-scale structures, and all allowed nonlinear processes can, in principle, occur on an equal footing. This could promote harmonic generation via a cascaded (consisting of several frequency mixing steps) process. However, so far, all reported work on dielectric metasurfaces have assumed frequency mixing from a direct (single step) nonlinear process. In this work, we prove the existence of cascaded second-order optical nonlinearities by analyzing the second- and third-wave mixing from a highly nonlinear metasurface in conjunction with polarization selection rules and crystal symmetries. We find that the third-wave mixing signal from a cascaded process can be of comparable strength to that from conventional third-harmonic generation and that surface nonlinearities are the dominant mechanism that contributes to cascaded second-order nonlinearities in our metasurface.
Random-Forest-Inspired Neural Networks (2018)

Neural networks have become very popular in recent years, because of the astonishing success of deep learning in various domains such as image and speech recognition. In many of these domains, specific architectures of neural networks, such as convolutional networks, seem to fit the particular structure of the problem domain very well and can therefore perform in an astonishingly effective way. However, the success of neural networks is not universal across all domains. Indeed, for learning problems without any special structure, or in cases where the data are somewhat limited, neural networks are known not to perform well with respect to traditional machine-learning methods such as random forests. In this article, we show that a carefully designed neural network with random forest structure can have better generalization ability. In fact, this architecture is more powerful than random forests, because the back-propagation algorithm reduces to a more powerful and generalized way of constructing a decision tree. Furthermore, the approach is efficient to train and requires a small constant factor of the number of training examples. This efficiency allows the training of multiple neural networks to improve the generalization accuracy. Experimental results on real-world benchmark datasets demonstrate the effectiveness of the proposed enhancements for classification and regression.
Phenothiazine‐Based D–A–π–A Dyes for Highly Efficient Dye‐Sensitized Solar Cells: Effect of Internal Acceptor and Non‐Conjugated π‐Spacer on Device Performance (2016)

Three new D-A-π-A metal-free organic dyes based on phenothiazine as a donor (D) and non-conjugated π-spacer were designed and synthesized. The incorporation of different 'internal acceptors' (electron traps) such as benzothiadiazole (BTD), benzotriazole (BTA), and pyridine were shown to allow systematic tuning of the energy levels and the photophysical properties. The AI-1 dye showed lower electronic disorder compared with the other two dyes. The efficiencies achieved with AI-1, AI-2, and AI-3 dyes were 8.5 % (J<sub>sc</sub> =15.42 mA cm<sup>-2</sup> , V<sub>oc</sub> =0.78 V, FF=68 %), 7 % (J<sub>sc</sub> =12.8 mA cm<sup>-2</sup> , V<sub>oc</sub> =0.78 V, FF=68 %) and 6.7 % (J<sub>sc</sub> =11.57 mA cm<sup>-2</sup> , V<sub>oc</sub> =0.82 V, FF=68.26 %), respectively. The incorporation of non-conjugated phenothiazine as a π-spacer in D-A-π-A dyes showed remarkable enhancement in the photovoltaic performance of dye-sensitized solar cell (DSSC) devices. The sealed DSSC devices with iodide/tri-iodide (I<sup>-</sup> /I<sub>3</sub> <sup>-</sup> )-based liquid electrolyte showed promising stability under ambient conditions.
Performance monitoring for plume remediation and containment action (1996)

This is the final report of a one year, Laboratory Directed Research and Development project at the Los Alamos National Laboratory. Bioremediation is a promising alternative to conventional cleanup technologies because of its relative speed, safety, and cost. However, current methods for measuring and evaluating the performance of bioremediation are inadequate. The development of the basic understanding and methods for assessing bioremediation research sites. This project sought to develop an improved understanding of the pathways and genes employed by bacteria in the catabolism of pollutants in actual field situations.
Pulse-amplitude equalization by negative impulse modulation for rational harmonic mode locking (2006)

We propose a novel technique based on negative impulse modulation for pulse repetition rate multiplication by rational harmonic mode locking with pulse-amplitude-equalized pulses directly from the laser cavity. We have generated a pulse train of 15 GHz with more than 16 dB suppression of unwanted amplitude modulation spurs by using a 1 GHz RF signal. This is the highest suppression ratio for a repetition rate multiplication factor of 15 to our knowledge.
Structure-based site-directed photo-crosslinking analyses of multimeric cell-adhesive interactions of voltage-gated sodium channel β subunits (2016)

The β1, β2, and β4 subunits of voltage-gated sodium channels reportedly function as cell adhesion molecules. The present crystallographic analysis of the β4 extracellular domain revealed an antiparallel arrangement of the β4 molecules in the crystal lattice. The interface between the two antiparallel β4 molecules is asymmetric, and results in a multimeric assembly. Structure-based mutagenesis and site-directed photo-crosslinking analyses of the β4-mediated cell-cell adhesion revealed that the interface between the antiparallel β4 molecules corresponds to that in the trans homophilic interaction for the multimeric assembly of β4 in cell-cell adhesion. This trans interaction mode is also employed in the β1-mediated cell-cell adhesion. Moreover, the β1 gene mutations associated with generalized epilepsy with febrile seizures plus (GEFS+) impaired the β1-mediated cell-cell adhesion, which should underlie the GEFS+ pathogenesis. Thus, the structural basis for the β-subunit-mediated cell-cell adhesion has been established.
Forward-Secure Linkable Ring Signatures from Bilinear Maps (2018)

We present the first linkable ring signature scheme with both unconditional anonymity and forward-secure key update: a powerful tool which has direct applications in elegantly addressing a number of simultaneous constraints in remote electronic voting. We propose a comprehensive security model, and construct a scheme based on the hardness of finding discrete logarithms, and (for forward security) inverting bilinear or multilinear maps of moderate degree to match the time granularity of forward security. We prove efficient security reductions—which, of independent interest, apply to, and are much tighter than, linkable ring signatures without forward security, thereby vastly improving the provable security of these legacy schemes. If efficient multilinear maps should ever admit a secure realisation, our contribution would elegantly address a number of problems heretofore unsolved in the important application of (multi-election) practical Internet voting. Even if multilinear maps are never obtained, our minimal two-epoch construction instantiated from bilinear maps can be combinatorially boosted to synthesise a polynomial time granularity, which would be sufficient for Internet voting and more.
An Experimental Study of the Turbulence Structue in a Premixed Jet Flame (1984)

本論文は予混合噴流火炎の乱れ構造に関するものであり、特に火炎面での乱れ生成の機構と、外炎に存在する大きなスケールの渦の役割を論じている。乱れ構造は軸対称非旋回圧縮性流れの乱れエネルギ式中の対流項、生成項を実験的に見積ることによって検討した。その結果、火炎面における熱膨張、特に流線の曲りに基づく圧力変動による生成項((p'/r)∂(rv')/∂r)^^^-が火炎の乱れ生成に重要な役割をもつことが明らかとなった。
L’os sous chondral et l’angiogenèse : deux nouvelles cibles thérapeutiques de l’arthrose (2012)

peer reviewed
Virtual Massive MIMO Beamforming Gains for 5G User Terminals (2016)

For future 5G systems significant performance benefits are expected from massive MIMO, especially in combination with tight inter-cell cooperation including joint-transmission using cooperative multi-point transmission. Most massive MIMO evaluations concentrate on the base station side with the goal to achieve high spectral efficiency by MU-MIMO or large coverage by strong beamforming gains. Especially for the, here interesting, below 6 GHz RF-bands user equipment (UE) sided analysis is typically limited to four or mostly eight antenna elements per UE, which can be justified by the limited space to place more antenna elements as well as the related UE complexity. At the same time, there would be many benefits from UE-sided beamforming, ranging from improved channel estimation and prediction accuracy, effective interference suppression up to coverage and spectral efficiency gains on the system level. In our previous work, we have already proposed virtual beamforming for channel estimation and prediction, while here we extend the concept to user data transmission over virtually generated beams. Virtual beamforming directly applied to user data can be very inefficient, a challenge we overcome by parallel transmission over a set of coded virtual beams.
Towards the lasing spaser: controlling metamaterial optical response with semiconductor quantum dots (2009)

We report the first experimental demonstration of compensating Joule losses in metallic photonic metamaterial using optically pumped PbS semiconductor quantum dots.
Penetration of Triphenylphosphonium Derivatives through the Cell Envelope of Bacteria of Mycobacteriales Order (2023)

The penetration of substances through the bacterial cell envelope is a complex and underinvestigated process. Mitochondria-targeted antioxidant and antibiotic SkQ1 (10-(plastoquinonyl)decyltriphenylphosphonium) is an excellent model for studying the penetration of substances through the bacterial cell envelope. SkQ1 resistance in Gram-negative bacteria has been found to be dependent on the presence of the AcrAB-TolC pump, while Gram-positive bacteria do not have this pump but, instead, have a mycolic acid-containing cell wall that is a tough barrier against many antibiotics. Here, we report the bactericidal action of SkQ1 and dodecyl triphenylphospho-nium (C<sub>12</sub>TPP) against <i>Rhodococcus fascians</i> and <i>Mycobacterium tuberculosis</i>, pathogens of plants and humans. The mechanism of the bactericidal action is based on the penetration of SkQ1 and C<sub>12</sub>TPP through the cell envelope and the disruption of the bioenergetics of bacteria. One, but probably not the only such mechanism is a decrease in membrane potential, which is important for the implementation of many cellular processes. Thus, neither the presence of MDR pumps, nor the presence of porins, prevents the penetration of SkQ1 and C<sub>12</sub>TPP through the complex cell envelope of <i>R. fascians</i> and <i>M. tuberculosis</i>.
How do I implement an outpatient program for the administration of convalescent plasma for COVID‐19? (2022)

Convalescent plasma, collected from donors who have recovered from a pathogen of interest, has been used to treat infectious diseases, particularly in times of outbreak, when alternative therapies were unavailable. The COVID-19 pandemic revived interest in the use of convalescent plasma. Large observational studies and clinical trials that were executed during the pandemic provided insight into how to use convalescent plasma, whereby high levels of antibodies against the pathogen of interest and administration early within the time course of the disease are critical for optimal therapeutic effect. Several studies have shown outpatient administration of COVID-19 convalescent plasma (CCP) to be both safe and effective, preventing clinical progression in patients when administered within the first week of COVID-19. The United States Food and Drug Administration expanded its emergency use authorization (EUA) to allow for the administration of CCP in an outpatient setting in December 2021, at least for immunocompromised patients or those on immunosuppressive therapy. Outpatient transfusion of CCP and infusion of monoclonal antibody therapies for a highly transmissible infectious disease introduces nuanced challenges related to infection prevention. Drawing on our experiences with the clinical and research use of CCP, we describe the logistical considerations and workflow spanning procurement of qualified products, infrastructure, staffing, transfusion, and associated management of adverse events. The purpose of this description is to facilitate the efforts of others intent on establishing outpatient transfusion programs for CCP and other antibody-based therapies.