gebhart/patrepeval huggingface dataset:
Chronic infection due to Mycobacterium intracellulare in mice: association with macrophage release of prostaglandin E2 and reversal by injection of indomethacin, muramyl dipeptide, or interferon-gamma. (1986)

As a model for the study of human atypical mycobacterial disease, we explored the basis for the prolonged mycobacteriosis in mice infected with Mycobacterium intracellulare. Two weeks after i.v. injection of mycobacteria, peritoneal macrophages were found to be activated, as indicated by their capacity to produce large amounts of superoxide anion (O2-) in response to phorbol myristate acetate (PMA) or viable M. intracellulare. However, 4 wk after infection, despite the continued presence of large numbers of mycobacteria in the spleen, macrophages from infected animals produced low amounts of O2-. Unfractionated spleen cells from mice infected 4 wk earlier produced increased amounts of interleukin 2 and interferon (IFN) when stimulated with the mitogen concanavalin A, but less of these lymphokines than unstimulated cells when exposed to antigens derived from M. intracellulare, suggesting production of an inhibitory factor. Spleen cells from infected mice were not stimulated to incorporate [3H]thymidine by exposure to mycobacterial antigens; but this unresponsiveness could be reversed by addition of indomethacin to the cultures. Additional investigation showed that macrophages from infected animals produced large amounts of prostaglandin E2 (PGE2) when stimulated by mycobacterial antigens. In vitro, such concentrations of PGE2 inhibited uptake of [3H]thymidine by stimulated spleen lymphocytes from infected animals. Thus, it seemed likely that in infected animals, macrophage-derived PG suppressed production of IFN-gamma by lymphocytes, which in turn prevented activation of the macrophages to full microbicidal activity. To test this hypothesis, we administered either indomethacin, IFN-gamma, or muramyl dipeptide to infected mice. Mice treated with each of these agents showed decreased spleen and lung weights, and decreased numbers of viable mycobacteria in these organs. These results support the concept that interaction between the host and M. intracellulare is modulated profoundly by PG and suggest that administration of agents that directly promote macrophage activation can enhance resistance to infection by this organism.
Supp Figures from Global Phosphoproteomics Reveal CDK Suppression as a Vulnerability to KRas Addiction in Pancreatic Cancer (2023)

&lt;p&gt;Supplementary Figures&lt;/p&gt;
Molybdenum-Mediated Carbonylation of Aryl Halides with Nucleophiles Using Microwave Irradiation (2010)

A new, efficient, and practical molybdenum-mediated carbonylation of aryl and heteroaryl halides with a variety of nucleophiles is described using microwave irradiation. A range of reactions illustrating the wide scope of this chemistry were carried out and proceeded in good to excellent yields.
Forming Limits Prediction of FCC Sheet Metal Adopting Crystal Plasticity (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Complexity-Reduced Algorithm for Adaptive PAPR Reduction Method Using Null Space in MIMO Channel for MIMO-OFDM Signals (2019)

We propose a computational complexity-reduced algorithm for an adaptive peak-to-average power ratio (PAPR) reduction method previously developed by members of our research group that uses the null space in a multiple-input multiple-output (MIMO) channel for MIMO-orthogonal frequency division multiplexing (OFDM) signals. The proposed algorithm is an extension of the peak cancellation (PC) signal-based method that has been mainly investigated for per-antenna PAPR reduction approaches. This method adds the PC signal, which is designed so that the out-of-band radiation is removed/reduced, directly to the time-domain transmission signal at each antenna. By introducing a constraint so that the PC signal is transmitted only to the null space in the MIMO channel, the proposed method achieves approximately the same throughput-vs.-PAPR performance as the original method while dramatically reducing the required computational cost.
Digital Coherent Receiver Technology for 100-Gb/s Optical Transport Systems (2010)

Digital coherent receivers are expected to be the most important building block of 100-Gb/s optical transport systems. As a platform for evaluating their real-time operational stability and thus helping to realize product-level reliability, Fujitsu Laboratories and Fujitsu have fabricated a test circuit to implement basic algorithms such as carrier phase recovery and optical frequency offset compensation. The experimental results showed an excellent bit error ratio performance that is only 1 dB away from the theoretical limit.
Interactive refinement of supervised and semi-supervised sound source separation estimates (2013)

We propose an interactive refinement method for supervised and semi-supervised single-channel source separation. The refinement method allows end-users to provide feedback to the separation process by painting on spectrogram displays of intermediate output results. The time-frequency annotations are then used to update the separation estimates and iteratively refine the results. The initial separation is performed using probabilistic latent component analysis and is then extended to incorporate the painting annotations using linear grouping expectation constraints via the framework of posterior regularization. Using a prototype user-interface, we show that the method is able to perform high-quality separation with minimal user-interaction.
Figure S2 from PET Imaging of TIGIT Expression on Tumor-Infiltrating Lymphocytes (2023)

&lt;p&gt;Supplementary Figure 2. HeLa cells stably expressing the mouse TIGIT receptor and eGFP.&lt;/p&gt;
Evolving physical design paradigms in the transition from 20/14 to 10nm process technology nodes (2014)

Advanced IC process technology nodes (28,20,14nm and below) have relied on the synergy of process-aware physical design and physical verification methodologies with design-aware yield engineering (on the manufacturing side), in order to fulfill ITRS scaling and performance requirements. These capabilities include not only additional design rules, or additional modeling capabilities, or incremental verification tools, but rather a qualitatively new set of DFM/DEM (Design For Manufacturing - Design Enabled Manufacturing) methodologies aimed at variability management, i.e. at characterization and remapping of systematic variability effects caused by design/process interaction. A typical example is a “correct by construction” router flow, augmented with yield detractor and yield enhancer patterns, implemented for 20nm high performance processor designs. In such a flow, timing (on the design side) and yield (on the manufacturing side) are co-optimized, in order to guarantee high yield and specified parametric performance in the first silicon run. In spite of current successes the incremental path down to 14nm will be disrupted, because of the hard physical limits simultaneously occurring in geometric scaling and electrical scaling, and the transition to 10 and 7 nm nodes will require a (re)volutionary DFM (Design For Manufacturing) paradigm. Building on the state-of-the-art in design/technology co-optimization this work will review the three most likely design/process scenarios for 10 and 7nm design enablement, which could potentially allow the synthesis of the “design gap” and “patterning gap” altogether.
Photonic crystal resonators for inverse-designed multi-dimensional optical interconnects (2022)

We experimentally demonstrate a 400 Gbit/s optical communication link utilizing wavelength-division multiplexing and mode-division multiplexing for a total of 40 channels. This link utilizes a novel, to the best of our knowledge, 400 GHz frequency comb source based on a chip-scale photonic crystal resonator. Silicon-on-insulator photonic inverse-designed 4 × 4 mode-division multiplexer structures enable a fourfold increase in data capacity. We show less than -10 dBm of optical receiver power for error-free data transmission in 34 out of a total of 40 channels using a PRBS31 pattern.
Identification of multiprotein complexes containing DNA replication factors by native immunoblotting of HeLa cell protein preparations with T-antigen-dependent SV40 DNA replication activity (1996)

Increasing evidence has supported the concept that many of the enzymes and factors involved in the replication of mammalian DNA function together as a multiprotein complex. We have previously reported on the partial purification of a multiprotein form of DNA polymerase from human HeLa cells shown to be fully competent to support origin-specific large T-antigen-dependent simian virus 40 (SV40) DNA replication in vitro. In an attempt to more definitively identify the complex or complexes responsible for DNA replication in vitro, partially purified human HeLa cell protein preparations competent to replicate DNA in vitro were subjected to native polyacrylamide gel electrophoresis and electrophoretically transferred to nitrocellulose. The Native Western blots were probed with a panel of antibodies directed against proteins believed to be required for DNA replication in vitro. Apparent complexes of 620 kDa and 500 kDa were identified by monoclonal antibodies directed against DNA polymerase alpha and DNA polymerase delta, respectively. To detect epitopes possibly unexposed within the native multiprotein complexes, blots were also analyzed following denaturation in situ following treatment with detergent and reducing agent. The epitope or access to the epitope recognized by the monoclonal antibody against DNA polymerase alpha was destroyed by exposure of the blots to denaturing conditions. In contrast, an epitope present on a very large complex of approximately 1000 kDa was recognized by a monoclonal antibody against proliferating cell nuclear antigen only following treatment of the native immunoblots with denaturing agents. Identification of these complexes will allow their further purification, characterization, and elucidation of their role in the replication of DNA.
Combinations of Monoclonal Antibodies to Anthrax Toxin Manifest New Properties in Neutralization Assays (2013)

Monoclonal antibodies (MAbs) are potential therapeutic agents against Bacillus anthracis toxins, since there is no current treatment to counteract the detrimental effects of toxemia. In hopes of isolating new protective MAbs to the toxin component lethal factor (LF), we used a strain of mice (C57BL/6) that had not been used in previous studies, generating MAbs to LF. Six LF-binding MAbs were obtained, representing 3 IgG isotypes and one IgM. One MAb (20C1) provided protection from lethal toxin (LeTx) in an in vitro mouse macrophage system but did not provide significant protection in vivo. However, the combination of two MAbs to LF (17F1 and 20C1) provided synergistic increases in protection both in vitro and in vivo. In addition, when these MAbs were mixed with MAbs to protective antigen (PA) previously generated in our laboratory, these MAb combinations produced synergistic toxin neutralization in vitro. But when 17F1 was combined with another MAb to LF, 19C9, the combination resulted in enhanced lethal toxicity. While no single MAb to LF provided significant toxin neutralization, LF-immunized mice were completely protected from infection with B. anthracis strain Sterne, which suggested that a polyclonal response is required for effective toxin neutralization. In total, these studies show that while a single MAb against LeTx may not be effective, combinations of multiple MAbs may provide the most effective form of passive immunotherapy, with the caveat that these may demonstrate emergent properties with regard to protective efficacy.
Myelin-Associated Glycoprotein, a Cell Adhesion Molecule of Oligodendrocytes, is Phosphorylated in Brain (1988)

Myelin-associated glycoprotein (MAG) has been implicated in the mediation of interactions between oligodendrocytes and neurons during the development of the myelin sheath. Here we show that MAG is phosphorylated in intact myelinating mouse brain primarily at serine residues and to a lesser extent at threonine and tyrosine residues. In vivo, only the larger of the two developmentally regulated MAG isoforms is phosphorylated. MAG can be phosphorylated at tyrosine by the v-fps and v-src protein-tyrosine kinases in vitro and by a kinase endogenous to myelin membrane preparations. MAG phosphorylated in myelin membranes in vitro also contains phosphoserine and phosphothreonine. These observations suggest that phosphorylation of MAG is physiologically significant in regulating oligodendrocyte-neuron interactions.
Nanoparticles (NPs) of WO3-x Compounds by Polyol Route with Enhanced Photochromic Properties (2019)

Tungsten trioxide (WO3) is well-known as one of the most promising chromogenic compounds. It has a drastic change of coloration induced from different external stimuli and so its applications are developed as gas sensors, electrochromic panels or photochromic sensors. This paper focuses on the photochromic properties of nanoWO3, with tunable composition (with tunable oxygen sub-stoichiometry). Three reference samples with yellow, blue and black colors were prepared from polyol synthesis followed by post annealing under air, none post-annealing treatment, or a post-annealing under argon atmosphere. These three samples differ in terms of crystallographic structure (cubic system versus monoclinic system), oxygen vacancy concentration, electronic band diagram with occurrence of free or trapped electrons and their photochromic behavior. Constituting one main finding, it is shown that the photochromic behavior is highly dependent on the compound’s composition/color. Rapid and important change of coloration under UV (ultraviolet) irradiation was evidenced especially on the blue compound, i.e., the photochromic coloring efficiency of this compound in terms of contrast between bleached and colored phase, as the kinetic aspect is high. The photochromism is reversible in a few hours. This hence opens a new window for the use of tungsten oxide as smart photochromic compounds.
Examining the Complexity of Human RNA Polymerase Complexes using HaloTag Technology Coupled to Label Free Quantitative Proteomics (2011)

Efficient determination of protein interactions and cellular localization remains a challenge in higher order eukaryotes and creates a need for robust technologies for functional proteomics studies. To address this, the HaloTag technology was developed for highly efficient and rapid isolation of intracellular complexes and correlative in vivo cellular imaging. Here we demonstrate the strength of this technology by simultaneous capture of human eukaryotic RNA polymerases (RNAP) I, II, and III using a shared subunit, POLR2H, fused to the HaloTag. Affinity purifications showed successful isolation, as determined using quantitative proteomics, of all RNAP core subunits, even at expression levels near endogenous. Transient known RNAP II interacting partners were identified as well as three previously uncharacterized interactors. These interactions were validated and further functionally characterized using cellular imaging. The multiple capabilities of the HaloTag technology demonstrate the ability to efficiently isolate highly challenging multiprotein complexes, discover new interactions, and characterize cellular localization.
Direct Reductive Amination of Aldehydes and Ketones Using Phenylsilane:  Catalysis by Dibutyltin Dichloride (2001)

A procedure for direct reductive amination of aldehydes and ketones was developed which uses phenylsilane as a stoichiometric reductant and dibutyltin dichloride as a catalyst. Suitable amines included anilines and dialkylamines but not monoalkylamines.
Sensing of transmission opportunities at the Medium Access Control layer for cognitive radio networks (2009)

Detection of transmission opportunities is the critical part of establishing a cognitive radio network. Traditionally, it is achieved via spectrum sensing carried out at the physical layer to detect unused frequency bands. In this paper, we propose a novel approach to detect transmission opportunities at the Medium Access Control (MAC) layer based on the concept of interference temperature. In this approach, secondary transmissions are overlayed on top of primary transmissions as long as they do not affect the primary transmission. A Transmit Margin is defined and used to quantify the spare capacity in the primary network. We setup a system to estimate and track the Packet Error Rates (PER) and use it as a metric for transmit opportunity detection. A distributed estimation procedure to increase the robustness of the estimate is also proposed for cognitive radio networks. The scope of this hitherto unexplored area of cognitive radios is demonstrated and applied to IEEE 802.11 wireless networks through simulation studies.
Irregular turbocodes (2002)

We construct irregular turbocodes with systematic bits that participate in varying numbers of trellis sections. By making the original rate 1/2 turbocode of Berrou et al. slightly irregular, we obtain a coding gain of 0.15 dB at BER=10/sup -4/.
0761 Adaptability of the Treating Obstructive Sleep Apnea Using Targeted Hypoglossal Nerve Stimulation (OSPREY) Trial (2022)

Abstract Introduction With few exceptions, clinical trials of hypoglossal nerve stimulation (HGNS) for obstructive sleep apnea (OSA) are single-arm, open-label studies sometimes followed by short-term, unblinded, randomized withdrawal. By contrast, the THN3 study was a parallel-arm, randomized, controlled trial (RCT) of targeted HGNS (THN) in moderate to severe OSA, and provided higher-level evidence of HGNS safety and efficacy.Despite generating strong evidence, conventional RCTs are risky due to their inherent inflexible designs. We therefore launched a confirmatory THN RCT (OSPREY) with an adaptive, Bayesian “Goldilocks” design that optimize its sample size dynamically, yet achieve high-confidence results. Methods Four scenarios were simulated within the OSPREY design framework (randomized 2:1 Treatment:Control) for the primary endpoint of apnea-hypopnea index (AHI) response rate (RR): nominal with results equal to those of THN3 (Treatment AHI RR 52%/Control AHI RR 20%), improved Treatment RR (63%/20%), worsened Treatment RR (41%/20%) and null [Treatment RR=Control RR] (20%/20%). Each scenario was simulated 10 times with 10,000 simulations of each interim analysis. Subject outcomes were determined by randomly drawing from a binomial distribution with the relevant AHI RR.Interim analyses in OSPREY begin at 50 randomized subjects and repeat every 20 additional subjects to the maximum sample size of 150, with opportunities for early success and futility at each milestone to generate high-confidence results from an optimal sample size. OSPREY assesses secondary endpoints including quality of life inventories (Epworth Sleepiness Scale; Functional Outcomes of Sleep Questionnaire; EQ-5D, SF-6D and PROMIS sleep questionnaires) and oximetry metrics (Oxygen Desaturation Index, %sleep time below 90% oxygen saturation). Previous results suggest secondary endpoints will be adequately powered at the final sample size determined by AHI RR. Results Simulations produced the following outcomes formatted as [scenario: randomized sample size, overall success rate, probability of early success, mean success probability]: null: 150, 0%, 0%, 2.47%; nominal: 130-150, 100%, 80%, 95.3%; improved: 90-130, 100%, 100%, 98.9%; worsened: 150, 100%, 0%, 68.6%. Conclusion OSPREY is uniquely able to adapt to various Treatment/Control response scenarios and should provide high-confidence confirmation of the safety and efficacy of THN therapy in moderate to severe OSA. Support (If Any) LivaNova
Cloning, sequencing, and functional analysis of a Marek's disease virus origin of DNA replication (1991)

Previously, we isolated a replicon from a defective Marek's disease virus (MDV), analogous to defective herpes simplex viruses (amplicons). Defective viruses contain cis-acting elements required for DNA synthesis and virus propagation such as an origin of DNA replication and a packaging-cleavage signal site. In this report, the MDV replicon was utilized to locate an origin of MDV DNA replication. A comparison of MDV replicon sequences with other herpesvirus replication origin sequences revealed a 90-bp sequence containing 72% identity to the lytic origin (oris) of herpes simplex virus type 1. This 90-bp sequence displayed no similarity to betaherpesvirus or gammaherpesvirus replication origins. The 90-bp sequence is arranged as an imperfect palindrome centered around an A+T-rich region. This sequence also contains a 9-bp motif (5'CGTTCGCAC3') highly conserved in alphaherpesvirus replication origins. To test functionality of the 90-bp putative MDV replication origin, we conducted DpnI replication assays with subclones generated from the 4-kbp MDV replicon. A 700-bp MDV replicon subfragment containing the 90-bp putative MDV replication origin sequence is capable of replicating in chicken embryo fibroblast cells cotransfected with helper virus DNA. In conclusion, we identified a functional origin of DNA replication in MDV. Similarity of MDV origin sequences to those of alphaherpesviruses supports the current contention that MDV is more closely related to alphaherpesviruses than to gammaherpesviruses.
Development of a Functionalizable External β‐Turn Mimic Based on a cis‐Fused 1,7‐Naphthyridine Scaffold (2003)

Abstract An intramolecular Diels−Alder strategy using 2(1 H )‐pyrazinones was applied to generate a substituted perhydro‐1,7‐naphthyridine ring system that served as a scaffold to construct the type VI β‐turn mimic 2 , featuring a cis ‐amide linkage between the central i +1 and i +2 residues. The synthesis permits mimicking of the amino acid side chains of the central dipeptide, a unique feature for external‐turn mimics. Modeling studies indicated that the cis ‐fused bicyclic system adopts a conformation suitable for induction of a β‐turn when the angular position 8a bears a non‐H substituent. Extensive NMR analysis of an 8a‐methyl derivative 25 confirmed its β‐turn‐inducing properties in various solvents, including water. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)
Optimized use of selective harmonic elimination techniques for three-phase AC/DC converters for high power applications (2005)

The use of optimized firing patterns for selective harmonic elimination presents several advantages over other modulating techniques. Particularly, in terms of number of eliminated harmonics and commutation frequency. However, the high amplitude for the first group of characteristic harmonics is considered a disadvantage. This paper presents an improvement in the use of selective harmonic elimination techniques for high power rectifiers when two or more three-phase AC/DC cells are simultaneously operated. Indeed, the relative displacement and modulation indexes of the modulating techniques are optimized in order to minimize the amplitude of the first group of characteristic harmonics. Thus minimizing the THD of the AC line currents. The paper includes a systematic formulation of the equations and procedure for the displacement and modulation index computation. Preliminary simulated results confirm the validity of theoretical considerations.