gebhart/patrepeval huggingface dataset:
Efficiency of chimeraplast gene targeting by direct nuclear injection using a GFP recovery assay (2003)

Traditional RNA-DNA chimeric oligonucleotides (chimeraplasts), composed of a continuous stretch of RNA and DNA residues in a duplex conformation, have been shown to correct single-base mutations in episomal and genomic DNA both in vitro and in vivo. In the current study, we have compared the efficiency of single-base pair correction between a traditionally designed chimeraplast (covalently linked duplex) and hybrid chimeraplasts (noncovalent duplexes formed from stretches of RNA and DNA nucleotides synthesized individually and hybridized in vitro). Six hybrid chimeraplasts of identical length were constructed with various lengths of target homology and strand location of the desired nucleotide change. These constructs were evaluated for their ability to correct a point mutation in the gene encoding recombinant enhanced green fluorescent protein (eGFP) that rendered the protein nonfluorescent. A plasmid encoding this mutant eGFP gene and a chimeraplast were co-introduced directly into the nuclei of primary fibroblasts by microinjection. As shown by the recovery of eGFP fluorescence, three of the six hybrid chimeraplasts demonstrated the ability to mediate gene correction (0.4-2.4%). Covalent joining of RNA and DNA strands in chimeraplasts was not necessary for correction of DNA mutations. However, the strand placement of the desired nucleotide change and the length of nonhomologous sequences flanking target nucleotides played a crucial role in the efficiency of chimeraplast-mediated gene correction. Despite the ability of certain chimeraplast designs to correct point mutations in episomal plasmids, targeted correction of integrated copies of the mutant eGFP transgene was unsuccessful in primary fibroblasts. These results demonstrate that, although chimeraplasts are fairly effective at targeting episomal DNA in primary cells, further optimization is required to increase the efficiency for targeting integrated genes.
Analysis of the formation of antigen-specific memory CD4+ T cell populations derived from single naïve precursors (LYM3P.731) (2014)

Abstract Following infection, a naive antigen-specific CD4+ T cell population proliferates and differentiates into to effector cell progeny that are either Th1 cells, which activate the microbicidal functions of macrophages, or T follicular helper cells, which help B cells make antibodies. After the resolution of infection, most antigen-specific cells die, while a small number of cells survive to form long-lived memory cells. The origins of these memory cells remain unclear. In this study, we tracked the differentiation clonal populations of CD4+ T cells, from single naïve cells into effector cells, and subsequently memory cells. We find that not all naïve CD4+ T cells that produce effector cell populations give rise to memory populations. However, when memory populations are formed, they are phenotypically similar to the effector populations in terms of Th1 and T follicular helper cell differentiation, suggesting that effector cell phenotype is maintained into memory, and that memory cells are derived from effector cells. Ongoing work is focused on determining the contributions of TCR signal strength and effector population burst size has in memory cell differentiation.
Modeling of optical alignment and metrology schemes used in integrated circuit manufacturing (1990)

The aim ofour work was to develop rigorous models to study various optical alignment and metrology schemes implemented in commercial tools. These schemes indude wafer alignment schemes in steppers and linewidth measurement schemes in optical microscopes. A simulator called METRO based on the models developed has been implemented to facilitate this task. Theoretical and experimental verification efforts have been performed to examine the validity of the simulation results and good agreement has been obtained. By utilizing METRO process engineers can gain more insight into the equipment under operation so as to obtain more accurate alignment and measurement results. Also the equation formulation in METRO is general enough so that optics designers can easily adopt or modify the code to help in devising innovative alignment and metrology schemes. 1.
[Clinical value of intracavitary electrograms stored by implantable automatic defibrillator in patients resuscitated after cardiac arrest]. (1995)

A major limitation of implantable defibrillators in the past has been the inability to document the arrhythmia precipitating discharge of the device. Although symptoms can be of some help in identifying the arrhythmia, symptomatic supraventricular arrhythmias and asymptomatic ventricular tachycardia (VT) have been documented in some cases before device discharge. The aim of this study was to systematically assess the value of stored intracardiac electrograms by implantable cardioverter-defibrillator in survivors of cardiac arrest during an antiarrhythmic drug free-period, in order to better define the arrhythmic profile determining device activation. The stored intracardiac electrograms of a fourth-generation cardioverter-defibrillator, implanted in 18 survivors of cardiac arrest were retrieved. The number of device activations, and the characteristics of any stored arrhythmic events were analyzed. A total number of 249 arrhythmic events were detected and stored over a mean follow-up of 378 +/- 107 days. These resulted in 78 delivered shocks, 84% of which were appropriate. Most of the detected events were episodes of unsustained VTs (33%), and atrial fibrillation or flutter (31%), which led to inappropriate shocks in 16% of the cases. The remaining recorded events were: sustained VT or fibrillation (66 episodes, 26%), sinus rhythm (11 events, 4%), not classified episode (6%). Of the 171 (69%) arrhythmic episodes not resulting in shocks, 73 events aborted before shock delivery by the device's reconfirmation algorithm, and the remaining 98 (39%) were detected but unsustained in duration, thus terminating before charging. In some cases, sustained and unsustained episodes of both supraventricular and ventricular arrhythmias gave symptoms.(ABSTRACT TRUNCATED AT 250 WORDS)
Implementation of New Cable Condition–Monitoring Technology at Oyster Creek Nuclear Generating Station (2017)

This paper reports the results of in situ cable testing performed at the Oyster Creek Nuclear Generating Station in September 2016 to assess the aging condition of a number of cables as installed in the plant. Despite having been in service for over 40 years, our results found that these cables still met their qualification criteria, were in good working condition, and could continue to serve the plant for the foreseeable future. Some degradation in the cable insulation was noted but not as much as one would expect after more than 40 years of service in a nuclear power plant. Specifically, test results revealed that 10% of cables exhibited a noticeable degree of degradation, 30% were only slightly degraded, and the remaining 60% were essentially unaffected by aging. In the case of jacketed cables, which were assessed using walkdowns performed by the plant’s personnel, almost all aging and degradation were limited to the jacket material while the underlying cable insulation was largely unaffected. This is consistent with laboratory test results, which have shown that jacket material, especially Neoprene and Hypalon, degrade much faster than cross-linked polyethylene (XLPE) and other materials that are used for primary cable insulation.
AGE-Induced Interference of Glucose Uptake and Transport as a Possible Cause of Insulin Resistance in Adipocytes (2011)

The purpose of this study was to investigate the distinct roles of advanced glycation end products (AGEs) on insulin-mediated glucose disposal in 3T3-L1 adipocytes and C2C12 skeletal muscle cells. AGE-modified proteins, namely, GO-AGEs, were prepared by incubating bovine serum albumin (BSA) with glyoxal (GO) for 7 days. Glucose utilization rates and the expression of insulin signaling-associated proteins, including Akt, insulin receptor substrate-1, and glucose transporter 4, were determined. GO-AGEs caused insulin resistance (IR) by suppressing insulin-stimulated glucose uptake both in 3T3-L1 adipocytes and C2C12 muscle cells. Interestingly, an unexpected finding was that insulin-stimulated glucose transport in adipocytes was affected by GO-AGEs in a biphasic manner, with an initial steep increase (168%) during the first 8 h of incubation followed by a significantly impaired uptake after extended culture times (24-48 h, p < 0.05). Treatment with GO-AGEs for 24 h markedly accelerated lipid droplet formation compared to the BSA control; however, it was blocked by incubation with an anti-RAGE antibody. Our study suggests that GO-AGEs induce an early dramatic elevation of glucose transport in adipocytes that may be related to the activation of insulin signaling; however, subsequent IR may result from increased oxidative stress and proinflammatory TNF-α production.
Shear-induced migration in flowing polymer solutions: Simulation of long-chain DNA in microchannels (2004)

We simulate dilute solution dynamics of long flexible polymer molecules in pressure driven flow in channels with widths of roughly 0.1-10 times the polymer bulk radius of gyration. This is done using a self-consistent coarse-grained Langevin description of the polymer dynamics and a numerical simulation of the flow in the confined geometry that is generated by the motions of polymer segments. Results are presented for a model of DNA molecules of approximately 10-100 microm contour length in micron-scale channels. During flow, the chains migrate toward the channel centerline, in agreement with well-known experimental observations. The thickness of the resulting hydrodynamic depletion layer increases with molecular weight at constant flow strength; higher molecular weight chains therefore move with a higher average axial velocity than lower molecular weight chains. In contrast, if the hydrodynamic effects of the confining geometry are neglected, depletion of concentration is observed in the center of the channel rather than at the walls, contradicting experimental observations. The mechanisms for migration are illustrated using a simple kinetic theory dumbbell model of a confined flexible polymer. The simple theory correctly predicts the trends observed in the detailed simulations. We also examine the steady-state stretch of DNA chains as a function of channel width and flow strength. The flow strength needed to stretch a highly confined chain away from its equilibrium length is shown to increase with decreasing channel width, independent of molecular weight; this is fairly well explained using a simple blob picture.
Abstract WP119: Transcriptome Analysis of Motor Cortex Network Responses in Spontaneously Recovered Stroke Mice (2017)

Introduction: Spontaneous recovery after stroke occurs in both human and animals. However, the underlying molecular mechanisms driving spontaneous recovery are still unclear. This study investigates the molecular mechanisms driving spontaneous recovery after unilateral experimental stroke using RNA sequencing (RNAseq). Methods: Ischemic stroke was induced in C57BL/6J adult male mice by transient MCAO. Neurological score, vertical pole, and rotating horizontal beam test were performed at baseline and post stroke days (PD) 4, 8, and 14. All mice were sacrificed at PD15 and processed for immunohistochemistry or Hi-seq. Infarcts were visualized by T2WI at PD2 using 7T MR scanner or histology at PD15. All stroke mice included in the study have comparable cortico-striatal infarcts and exhibit similar prestroke baseline performance and PD4 deficits. These mice were further categorized into spontaneously recovered and non-recovered groups based on their rotating beam performance during recovery. Results: Out of 35 stroke mice with abovementioned similar conditions, 9 (26%) were categorized into spontaneously recovered group and 26 (74%) were categorized into non-recovered group. Hierarchical clustering analysis supported this categorization. At PD14, the spontaneously recovered group exhibited significant improvement in beam performance in distance traveled and speed (p&lt;0.001). Using Ingenuity Pathway Analysis, the comparison of RNAseq transcriptome between ipsilesional and contralesional primary motor cortex (iM1 and cM1) in spontaneously recovered and non-recovered stroke mice revealed significant differential molecular pathways, including glutamate, calcium, and neurotrophin signaling pathways. Conclusions: Our study demonstrates that stroke mice with similar cortico-striatal infarct size can exhibit significant differences in their behavioral recovery outcome. The transcriptome profile in iM1-cM1 network at 2 weeks post-stroke highlighted several molecular pathways that were significantly different between spontaneously recovered and non-recovered mice. Validation of key molecular candidates from the RNAseq data would provide insights into the molecular mechanisms mediating spontaneous recovery after stroke.
Mode structure in an optically pumped D/sub 2/O far-infrared ring laser (1990)

The mode structures in an optically pumped D/sub 2/O far-infrared ring laser and a corresponding linear resonator have been compared. While single-mode operation can be obtained over the whole useful pressure range in the ring structure, this is only possible at pressures greater than 8 torr in the linear resonator case. A numerical model predicts quite well the pulse shape, pressure dependence, and influence of the resonator quality in the ring cavity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Signatures of Response to the Proteasome Inhibitor Bortezomib in Diffuse Large B-Cell Lymphoma. (2005)

Abstract The proteasome inhibitor, bortezomib (VELCADE®, formerly PS341), has significant anti-tumor activity in several lymphoid malignancies. Reported targets of this broad-based inhibitor include the NF K B pathway (I K B A). Recently defined subtypes of large B-cell lymphoma (LBCL) exhibit constitutive activation of NF K B, prompting us to analyze the efficacy of bortezomib in a panel of 10 DLBCL cell lines. Six of the diffuse LBCL cell lines were sensitive to bortezomib treatment at doses below 10 nM (range IC50 = 2.9 to 6.9 nM) whereas 4 cell lines were resistant at 10 nM (IC50 = 14.8 to 70.2 nM). Baseline proteasomal function, as defined by cleavage of the 20S proteasome-specific fluorogenic peptide LLVY-AMC, was similar in sensitive and resistant DLBCLs; however, the IC50 for bortezomib proteasomal inhibition was somewhat lower in sensitive vs. resistant lines (sens. vs res., p = .04, one-sided t test). Baseline NF K B activity varied widely in the DLBCL cell lines and did not differ in cell lines that were sensitive vs. resistant to bortezomib. Ten nM bortezomib did not inhibit NF K B activity in resistant DLBCL cell lines whereas the same dose reduced NF K B activity in sensitive DLBCL cell lines (sens. vs. res., p &amp;lt; .005, rank test [Mann-Whitney]). However, 5 of 6 sensitive DLBCL cell lines had very low baseline NF K B levels (&amp;lt; 0.5 relative absorbance units) suggesting that NF K B inhibition was not a major factor in bortezomib response and prompting further analysis of additional bortezomib targets. Three sensitive and 1 resistant DLBCL cell line were selected for detailed analyses of transcriptional profiles following bortezomib treatment. We developed an algorithm for identifying genes that were significantly up- or down-regulated in the bortezomib-sensitive cell lines but unchanged in the resistant line. In addition, we utilized gene set enrichment analysis (GSEA) and gene ontogeny (GO) termed enrichment to interpret the molecular signatures of response. Genes down-regulated in response to bortezomib included critical B-cell transcription factors, components of the B-cell receptor signaling cascade and genes regulating mitosis and cell cycle control; up-regulated genes included heat shock proteins (HSP) and multiple proteasomal components. Consistent with the functional data, down-regulation of NF K B target genes was not a common feature in all bortezomib-sensitive cell lines. In contrast, target genes of the c-MYC transcription factor were significantly down-regulated and c-MYC activity was decreased in sensitive (but not resistant) DLBCL cell lines following bortezomib treatment (sens. vs. res., p &amp;lt; .005, rank test). Taken together, the results provide insights into likely mechanisms of action of bortezomib in DLBCL, highlighting c-MYC as a potentially important target and identifying HSP as a complementary target to overcome bortezomib resistance.
Finger gesture recognition with smart skin technology and deep learning (2023)

Abstract Finger gesture recognition (FGR) was extensively studied in recent years for a wide range of human-machine interface applications. Surface electromyography (sEMG), in particular, is an attractive, enabling technique in the realm of FGR, and both low and high-density sEMG were previously studied. Despite the clear potential, cumbersome electrode wiring and electronic instrumentation render contemporary sEMG-based finger gestures recognition to be performed under unnatural conditions. Recent developments in smart skin technology provide an opportunity to collect sEMG data in more natural conditions. Here we report on a novel approach based on soft 16 electrode array, a miniature and wireless data acquisition unit and neural network analysis, in order to achieve gesture recognition under natural conditions. FGR accuracy values, as high as 93.1%, were achieved for 8 gestures when the training and test data were from the same session. For the first time, high accuracy values are also reported for training and test data from different sessions for three different hand positions. These results demonstrate an important step towards sEMG based gesture recognition in non-laboratory settings, such as in gaming or Metaverse.
Développements méthodologiques de l'IRM à bas champ : Elastographie, Interaction IRM-Ultrasons et Polarisation Dynamique Nucléaire (2005)

This thesis deals with two aspects of low field (0.2 T) Magnetic Resonance Imaging (MRI) : the research of new constrats due to the interaction between Nuclear Magnetic Resonance (NMR) and acoustics (elastography, spin-phonon interaction) and enhancement of the signal-to-noise ratio by Dynamic Nuclear Polarization (DNP). Magnetic Resonance Elastography (MRE) allows to assess some viscoelastic properties of tissues by visualization of the propagation of low frequency acoustic strain waves. A review on MRE is given, as well as a study on local measurement of the acoustic absorption coefficient. The next part is dedicated to MRI-ultrasound interaction. First, the ultrasonic transducer was calibrated for power and acoustic field using the comparison of two methods : the radiation force method (balance method) and laser interferometry. Then, we tried to modify the T1 contrast of tissues by spin-phonon interaction due to the application of ultrasound at the resonance frequency at 0.2 T, which is about 8.25 MHz. No modification of T1 contrast has been obtained, but the acoustic streaming phenomenon has been observed in liquids. MRI visualization of this streaming could make possible to calibrate transducers as well as to assess some mechanical properties of viscous fluids. The goal of the last part was to set up DNP experiments at 0.2 T in order to enhance the NMR signal. This double resonance method is based on the polarization transfer of unpaired electrons of free radicals to the surrounding protons of water. This transfer occurs by cross relaxation during the saturation of an electronic transition using Electronic Paramagnetic Resonance (EPR). Two EPR cavities operating at 5.43 GHz have been tested on oxo-TEMPO free radicals (nitroxide). An enhancement of the NMR signal by a factor 30 was obtained during these preliminary experiments.
ChemInform Abstract: ORGANO‐KUPFERCHEMIE, RK. VON ALPHA‐AETHYLEN‐SULFONEN MIT LITHIUMDIALKYLCUPRATEN (1973)

Abstract Aus den Oxoverbindungen (I) erhält man mit Sulfonomethylphosphonat‐ Anionen die ungesättigten Sulfone (II), die mit den Lithiumdialkylcupraten (III) die Addukte (IV) ergeben.
Nuclear receptors: emerging drug targets for parasitic diseases (2017)

Parasitic worms infect billions of people worldwide. Current treatments rely on a small group of drugs that have been used for decades. A shortcoming of these drugs is their inability to target the intractable infectious stage of the parasite. As well-known therapeutic targets in mammals, nuclear receptors have begun to be studied in parasitic worms, where they are widely distributed and play key roles in governing metabolic and developmental transcriptional networks. One such nuclear receptor is DAF-12, which is required for normal nematode development, including the all-important infectious stage. Here we review the emerging literature that implicates DAF-12 and potentially other nuclear receptors as novel anthelmintic targets.
On the throughput analysis of LTE and WiFi in unlicensed band (2014)

In this paper, the co-channel performance of large scale deployment of LTE in Unlicensed (LTE-U) band and WiFi is studied using stochastic geometry. Analytical expressions of LTE-U throughput in presence of WiFi are presented and are partly validated by the simulation results. The LTE-U Low Power Nodes (LPNs) are deployed as Poisson Point Process (PPP), and, the WiFi transmissions are modeled as hardcore Matérn point process. Using this analytical approach the impact of various parameters such as sensing threshold and transmission power on the co-existence of LTE-U and WiFi is studied.
ChemInform Abstract: TiO2 in Organic Photosynthesis: Sunlight‐Induced Functionalization of Heterocyclic Bases (2010)

Abstract Review: 79 refs.
Barely dressed single atoms in an optical resonator (1989)

Fundamental processes occur when a single atom interacts with a single mode of the radiation field. Shift, splitting, and broadening experiments are discussed.
Synthesis of bis(hydroxyethyl ether)s of aromatic dihydroxy compounds and poly(ether-carbonate)s with bisphenol A (1998)

A new class of copoly(ether-carbonate)s was synthesized using a melt polycondensation reaction of the bis(hydroxyethyl ether) of bisphenol A with bisphenols and diphenyl carbonate. Copolymers with a wide range of Tg values (62–140°C) were obtained. The copolymer structures were established by 1H NMR, 13C NMR and FTIR investigations. © 1998 Society of Chemical Industry
An Azomethine Ylide Approach to Complex Alkaloid-like Heterocycles (2007)

The nitrone above is readily available via the intramolecular aza Diels-Alder reaction of an amino acid derived triene in acetic acid. Subsequent treatment of the nitrone in refluxing toluene with substituted actetylenes produced the pictured pyrrole. At lower temperatures a 2,3-dihydroisoxazole, which is the product of a 3+2 dipolar cycloaddition, is produced. Upon heating in refluxing toluene the 2,3-dihydroisoxazole is converted to the pyrrole.