gebhart/patrepeval huggingface dataset:
Spectroscopy of low-frequency noise and its temperature dependence in a superconducting qubit (2012)

We report a direct measurement of the low-frequency noise spectrum in a superconducting flux qubit. Our method uses the noise sensitivity of a free-induction Ramsey interference experiment, comprising free evolution in the presence of noise for a fixed period of time followed by single-shot qubit-state measurement. Repeating this procedure enables Fourier-transform noise spectroscopy with access to frequencies up to the achievable repetition rate, a regime relevant to dephasing in ensemble-averaged time-domain measurements such as Ramsey interferometry. Rotating the qubit's quantization axis allows us to measure two types of noise: effective flux noise and effective critical-current or charge noise. For both noise sources, we observe that the very same $1/f$-type power laws measured at considerably higher frequencies ($0.2\ensuremath{-}20$ MHz) are consistent with the noise in the $0.01\ensuremath{-}100$-Hz range measured here. We find no evidence of temperature dependence of the noises over $65\ensuremath{-}200$ mK, and also no evidence of time-domain correlations between the two noises. These methods and results are pertinent to the dephasing of all superconducting qubits.
Safety, pharmacokinetics, and liver-stage Plasmodium cynomolgi effect of high-dose ivermectin and chloroquine in Rhesus Macaques (2020)

Abstract Previously, ivermectin (1–10 mg/kg) was shown to inhibit liver-stage development of Plasmodium berghei in orally dosed mice. Here, ivermectin showed inhibition of the in vitro development of Plasmodium cynomolgi schizonts (IC 50 = 10.42 μM) and hypnozoites (IC 50 = 29.24 μM) in primary macaque hepatocytes when administered in high-dose prophylactically but not when administered in radical cure mode. The safety, pharmacokinetics, and efficacy of oral ivermectin (0.3, 0.6, and 1.2 mg/kg) with and without chloroquine (10 mg/kg) administered for seven consecutive days was evaluated for prophylaxis or radical cure of Plasmodium cynomolgi liver-stages in Rhesus macaques. No inhibition or delay to blood-stage P. cynomolgi parasitemia was observed at any ivermectin dose (0.3, 0.6, and 1.2 mg/kg). Ivermectin (0.6 and 1.2 mg/kg) and chloroquine (10 mg/kg) in combination were well-tolerated with no adverse events and no significant pharmacokinetic drug-drug interactions observed. Repeated daily ivermectin administration for seven days did not inhibit ivermectin bioavailability. It was recently demonstrated that both ivermectin and chloroquine inhibit replication of the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in vitro . Further ivermectin and chloroquine trials in humans are warranted to evaluate their role in Plasmodium vivax control and as adjunctive therapies against COVID-19 infections.
Multi-domain Network Virtualization (2018)

This document analyzes the problem of multi-provider multi-domain
orchestration, by first scoping the problem, then looking into
potential architectural approaches, and finally describing the
solutions being developed by the European 5GEx and 5G-TRANSFORMER
projects.
Video 1 from <i>In Vivo</i> Fluorescence Imaging of the Activity of CEA TCB, a Novel T-Cell Bispecific Antibody, Reveals Highly Specific Tumor Targeting and Fast Induction of T-Cell–Mediated Tumor Killing (2023)

&lt;p&gt;&lt;i&gt;In vitro&lt;/i&gt; live cell confocal imaging of LS174T RFP cells co-cultured with CFSE-labeled T-cells (E:T = 3:1) in the presence of CEA or a control TCB, respectively.&lt;/p&gt;
ZCOMP (2019)

Deep Neural Networks (DNNs) are becoming the prevalent approach in computer vision, machine learning, natural language processing, and speech recognition applications. Although DNNs are perceived as compute-intensive tasks, they also apply intense pressure on the capacity and bandwidth of the memory hierarchy, primarily due to the large intermediate data communicated across network layers. Prior work on hardware DNN accelerators leverages the cross-layer data sparsity via fully-customized datapaths. However, dynamically compressing/expanding such data is a challenging task for general-purpose multi-processors with virtual memory and hardware-managed coherent cache hierarchies.
All-Spectrum Cognitive Channelization around Narrowband and Wideband Primary Stations (2014)

In this paper we design, implement, and experimentally evaluate a wireless software-defined radio platform for cognitive channelization in the presence of narrowband or wideband primary stations. Cognitive channelization is achieved by jointly optimizing the transmission power and the waveform channel of the secondary users. The process of joint resource allocation requires no a-priori knowledge of the transmission characteristics of the primary user and maximizes the signal-to- interference-plus-noise ratio (SINR) at the output of the secondary receiver. This is achieved by designing waveforms that span the whole continuum of available/device-accessible spectrum, while satisfying a peak power constraint for the secondary users and an interference temperature (IT) constraint for the primary users. We build a four-node software-defined radio testbed and experimentally demonstrate in an indoor laboratory environment the theoretical concepts of all-spectrum cognitive channelization in terms of pre-detection SINR and bit-error-rate (BER) at both primary and secondary receivers.
Supplementary Figure 3 from Combining a PI3K Inhibitor with a PARP Inhibitor Provides an Effective Therapy for BRCA1-Related Breast Cancer (2023)

&lt;p&gt;PDF file - 137K, Effects of the combination of NVP-BKM120 and Olaparib (left pair, treated with NVP-BKM120 at 30 mg/kg/day and Olaparib at 50 mg/kg/day) and of Olaparib alone (right pair, 50 mg/kg/day). Mice were imaged before and after 3 daily treatments, the repeat scan was obtained within 3 hours after the third treatment. The mouse on the right had multiple synchronous primary tumors, labeled in the before and after images with blue, orange and yellow arrows. Percent FDG-uptake was 65% (tumor with orange arrow), 55% (tumor with blue arrow) and 64% (tumor with yellow arrow). The mouse in the image pair on the right that was treated with Olaparib carried only one macroscopically detectable tumor (red arrow). Olaparib treatments increased FDG-uptake by 75% in this tumor. Note that in the after-Olaparib-treatment image (far right) several hotspots in the upper thorax are visible which upon necroscopy were found to be tumors of less than 2 mm in diameter&lt;/p&gt;
Soluble α-synuclein–antibody complexes activate the NLRP3 inflammasome in hiPSC-derived microglia (2021)

Parkinson's disease is characterized by accumulation of α-synuclein (αSyn). Release of oligomeric/fibrillar αSyn from damaged neurons may potentiate neuronal death in part via microglial activation. Heretofore, it remained unknown if oligomeric/fibrillar αSyn could activate the nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) family pyrin domain-containing 3 (NLRP3) inflammasome in human microglia and whether anti-αSyn antibodies could prevent this effect. Here, we show that αSyn activates the NLRP3 inflammasome in human induced pluripotent stem cell (hiPSC)-derived microglia (hiMG) via dual stimulation involving Toll-like receptor 2 (TLR2) engagement and mitochondrial damage. In vitro, hiMG can be activated by mutant (A53T) αSyn secreted from hiPSC-derived A9-dopaminergic neurons. Surprisingly, αSyn-antibody complexes enhanced rather than suppressed inflammasome-mediated interleukin-1β (IL-1β) secretion, indicating these complexes are neuroinflammatory in a human context. A further increase in inflammation was observed with addition of oligomerized amyloid-β peptide (Aβ) and its cognate antibody. In vivo, engraftment of hiMG with αSyn in humanized mouse brain resulted in caspase-1 activation and neurotoxicity, which was exacerbated by αSyn antibody. These findings may have important implications for antibody therapies aimed at depleting misfolded/aggregated proteins from the human brain, as they may paradoxically trigger inflammation in human microglia.
The efficacy of selective calculus ablation at 400 nm: comparison to conventional calculus removal methods (2013)

A desired outcome of scaling and root planing is the complete removal of calculus and infected root tissue and preservation of healthy cementum for rapid healing of periodontal tissues. Conventional periodontal treatments for calculus removal, such as hand instrument scaling and ultrasonic scaling, often deeply scrape the surface of the underlying hard tissue and may leave behind a smear layer. Pulsed lasers emitting at violet wavelengths (specifically, 380 to 400 nm) are a potential alternative treatment since they can selectively ablate dental calculus without ablating pristine hard tissue (i.e., enamel, cementum, and dentin). In this study, light and scanning electron microscopy are used to compare and contrast the efficacy of <i>in vitro</i> calculus removal for several conventional periodontal treatments (hand instruments, ultrasonic scaler, and Er:YAG laser) to calculus removal with a frequency-doubled Ti:sapphire (&lambda; = 400 nm). After calculus removal, enamel and cementum surfaces are investigated for calculus debris and damage to the underlying hard tissue surface. Compared to the smear layer, grooves, and unintentional hard tissue removal typically found using these conventional treatments, calculus removal using the 400-nm laser is complete and selective without any removal of pristine dental hard tissue. Based on these results, selective ablation from the 400-nm laser appears to produce a root surface that would be more suitable for successful healing of periodontal tissues.
Discovery of imidazole-based inhibitors of P. falciparum cGMP-dependent protein kinase (2021)

ABSTRACT The discovery of new targets for treatment of malaria and in particular those aimed at the pre-erythrocytic stage in the life cycle, advanced with the demonstration that orally administered inhibitors of Plasmodium falciparum cGMP-dependent protein kinase (PfPKG) could clear infection in a murine model. This enthusiasm was tempered by unsatisfactory safety and/or pharmacokinetic issues found with these chemotypes. To address the urgent need for new scaffolds, this manuscript presents initial structure-activity relationships in an imidazole scaffold at four positions, representative in vitro ADME, hERG characterization and cell-based anti-parasitic activity. This series of PfPKG inhibitors has good in vitro PfPKG potency, low hERG activity and cell-based anti-parasitic activity against multiple Plasmodium species that appears to correlate with in vitro potency.
Experimental Investigation of 2:1 and 3:1 Internal Resonances in Nonlinear MEMS Arch Resonators (2016)

We demonstrate experimentally internal resonances in MEMS resonators. The investigation is conducted on in-plane MEMS arch resonators fabricated with a highly doped silicon. The resonators are actuated electrostatically and their stiffness are tuned by electrothermal loading by passing an electrical current though the microstructures. We show that through this tuning, the ratio of the various resonance frequencies can be varied and set at certain ratios. Particularly, we adjust the resonance frequencies of two different vibrational modes to 2:1 and 3:1. Finally, we validate the internal resonances at these ratios through frequency-response curves and FFTs.
Droplet-based mRNA sequencing of fixed and permeabilized cells by CLInt-seq allows for antigen-specific TCR cloning (2021)

T cell receptors (TCRs) are generated by somatic recombination of V/D/J segments to produce up to 10<sup>15</sup> unique sequences. Highly sensitive and specific techniques are required to isolate and identify the rare TCR sequences that respond to antigens of interest. Here, we describe the use of mRNA sequencing via cross-linker regulated intracellular phenotype (CLInt-Seq) for efficient recovery of antigen-specific TCRs in cells stained for combinations of intracellular proteins such as cytokines or transcription factors. This method enables high-throughput identification and isolation of low-frequency TCRs specific for any antigen. As a proof of principle, intracellular staining for TNFα and IFNγ identified cytomegalovirus (CMV)- and Epstein-Barr virus (EBV)-reactive TCRs with efficiencies similar to state-of-the-art peptide-MHC multimer methodology. In a separate experiment, regulatory T cells were profiled based on intracellular FOXP3 staining, demonstrating the ability to examine phenotypes based on transcription factors. We further optimized the intracellular staining conditions to use a chemically cleavable primary amine cross-linker compatible with current single-cell sequencing technology. CLInt-Seq for TNFα and IFNγ performed similarly to isolation with multimer staining for EBV-reactive TCRs. We anticipate CLInt-Seq will enable droplet-based single-cell mRNA analysis from any tissue where minor populations need to be isolated by intracellular markers.
Non-invasive determination of mitral valve acoustic properties: a proposed method to determine tissue alterations due to disease (2003)

The purpose of this study was to determine the time-frequency content of the heart sounds, in both animal and computer models. In normal, unoperated sheep (N=8), the first heart sounds (S1) were recorded with an acoustic sensor. Data analysis consisted of cross-correlation of successive heartbeats to determine beat-to-beat regularity, as well as a Wigner time-frequency distribution analysis, to generate time-frequency "signatures" of each S1. In addition, a dynamic, fluid-structure coupled finite element model (FEM) of the mitral valve was constructed, and an identical time-frequency analysis of the normal velocity vector of the valve elements was performed. The average cross-correlation coefficient for the eight consecutive beats of all eight sheep was 0.90. The time-frequency signatures were generally the shape of a descending crescent centered on 65 Hz. Time frequency analysis of the normal velocity vector of the FEM valve elements was a descending crescent centered on 48 Hz. We conclude that time-frequency analysis can be used to obtain a "signature" of the radiated vibrations of the mitral valve, which correlates with numerical models.
Surfactant and Plasticizer Segregation in Thin Poly(vinyl alcohol) Films (2015)

The vertical depth distributions of individual additive components [cetyltrimethylammonium bromide (CTAB), deuterated pentaethylene glycol monododecyl ether (d25-C12E5), and deuterated glycerol (d-glycerol)] in PVA films have been isolated and explored by ion beam analysis techniques and neutron reflectometry. The additives display an unexpectedly rich variety of surface and interfacial behaviors in spin-cast films. In separate binary films with PVA, both d-glycerol and CTAB were evenly distributed, whereas d25-C12E5 showed clear evidence for surface and interfacial segregation. The behavior of each surfactant in PVA was reversed when the plasticizer (glycerol) was also incorporated into the films. With increasing plasticizer content, the surface activity of d25-C12E5 systematically decreased, but remarkably, when glycerol and CTAB were present in PVA, the surface and interfacial activities of CTAB increased dramatically in the presence of glycerol. Quantification of the surface excess by ion beam analysis revealed that, in many cases, the adsorbed quantity far exceeded what could reasonably be explained by a single layer, thus indicating a wetting transition of the small molecules at the surface or interface of the film. It appears that the surface and interfacial behaviors are partly driven by the relative surface energies of the components, but are also significantly augmented by the incompatibility of the components.
Layered TiO2 Nanosheet‐Supported NiCo2O4 Nanoparticles as Bifunctional Electrocatalyst for Overall Water Splitting (2018)

Abstract Exploring the generation of efficient and long‐lasting bifunctional electrocatalysts obtained from low‐cost transition metal oxides is crucial to the optimal production of hydrogen and oxygen by electrocatalytic water splitting. This study aims to demonstrate the applicability of layered TiO 2 nanosheets as support for designing electrocatalysts. We have demonstrated the performance by decorating the TiO 2 support with NiCo 2 O 4 nanoparticles (NiCo 2 O 4 /TiO 2 ) as catalysts for electrocatalytic overall water splitting. Moreover, the corrosion effect of usually used carbon‐based supporting materials can decrease the working efficiency and, thus, the overall performance of the catalysts. In this aspect, TiO 2 can be a better alternative to carbon‐based systems. Layered TiO 2 was synthesized at room temperature, and a simple heat treatment protocol was employed for the large‐scale synthesis of NiCo 2 O 4 /TiO 2 . TiO 2 facilitated the formation of smaller NiCo 2 O 4 nanoparticles, also improving the dispersion. This bifunctional electrocatalyst exhibits high OER and HER performance with a low overpotential of 309 mV and 185 mV respectively, at a current density of 10 mA cm −2 . TiO 2 supported catalyst also exhibits other advantages like remarkable durability in the alkaline medium along with high turnover frequency (TOF) values. This inexpensive catalyst can deliver a current density of 10 mA cm −2 at only 1.64 V with a steady performance for more than 12 h for overall water splitting. Thus, this homemade system provides a proficient and low‐cost alternative to the more expensive systems such as RuO 2 , IrO 2 or Pt for the electrochemical water splitting applications.
REARRANGEMENT MECHANISMS OF SOME CYCLIC SULFOXIDES (1991)

Abstract Under neutral conditions cis sulfoxides 5 underwent a sigmatropic rearrangement with 2-methylene hydrogens to give sulfenic acids 18, followed by Cyclization to dihydro-1,4-dithiins 2. The trans sulfoxides 6 rearranged involving 2-methyl hydrogens to form isomeric dihydrodithiins 3 via sulfenic acids 19. In the reactions of both the sulfoxides, sulfides 4 and disulfides 11 were also formed as minor side products. In the presence of acid catalyst cis sulfoxides 5 produced 2 in quantitative yields while the trans sulfoxides 6 gave a mixture of 2 and 3. The mechanism of formation of 2,3,4 and 11 are discribed.
ChemInform Abstract: First Evidence for the Formation of a Geminal Dizinc Carbenoid: A Highly Stereoselective Synthesis of 1,2,3‐Substituted Cyclopropanes. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
THE THICKNESS DEPENDENT STRUCTURE OF COPPER PHTHALOCYANINE FILMS (2002)

We deposited copper phthalocyanine (CuPc) films on (100) silicon wafers by means of a vacuum evaporation method and investigated the dependence of X-ray diffraction pattern on film thickness. We concluded that the planar molecule of CuPc is stacked normal to the substrate within 700 nm from an interface. Above 700 nm, four types of nearly parallel stacking were also observed. These results show the spontaneous formation of the two-layer structure in CuPc films thicker than 700 nm.
Abstract 354: Mucinous phenotype is associated with response to neoadjuvant chemotherapy in microsatellite instable resectable gastric cancer (2021)

Abstract Background: Epstein-Barr virus positivity (EBV+) and microsatellite instability (MSI-high) have been shown to be positive prognostic factors for long term survival in resectable gastric cancer (GC) in several studies. However, the benefit of perioperative treatment in patients with MSI-high tumors remains topic of discussion. Here, we present the clinicopathological outcome of patients with EBV+ and MSI-high GCs treated with surgery only in the Dutch D1/D2 trial, and treated with chemotherapy or chemoradiotherapy after preoperative chemotherapy and surgery in the CRITICS trial. Patients and methods: EBV was determined in tumor tissue using EBV-encoded RNA in situ hybridization (EBER-ISH). PCR and/or immunohistochemistry were performed to determine MSI status. Results were correlated to histopathological response, morphological tumor characteristics and survival. Results: In the Dutch D1/D2 trial 10.5% (47/447) of tumors were EBV+ and 10.5% (47/447) were MSI-high. In the CRITICS trial 5.5% (25/451) of tumors were EBV+ and 5.5% (25/451) were MSI-high tumors. In the Dutch D1/D2 trial, five-year overall survival probability was 51.1% for EBV+, 46.8% for MSI-high, and 42.5% for EBV-/MSS (P=0.19). In the CRITICS trial, five-year overall survival was 56.0% for EBV+, 47.3% for MSI-high, and 36.5% for EBV-/MSS (P=0.22). In the CRITICS trial, 3 (12.5%) MSI-high tumors showed moderate to complete histopathological response. Interestingly, all three showed a mucinous phenotype. Eight (36.4%) EBV+ and 114 (29.9%) EBV-/MSS tumors showed moderate to complete histopathological response. None of the EBV+ GCs showed mucinous differentiation. Conclusions: The favorable outcome of GC patients with resectable EBV+ or MSI-high tumors compared to EBV-/MSS tumors remains after perioperative chemotherapy. In MSI-high tumors significant histopathological response to neoadjuvant chemotherapy was found only in those with a mucinous phenotype. Citation Format: H.D. Biesma, A.T.T.D. Soeratram, K. Sikorska, I.A. Caspers, H.F. van Essen, J.M.P. Egthuijsen, A. Mookhoek, D.M. Hoek, W. Vos, H.W.M. van Laarhoven, M. Nordsmark, D.L. van der Peet, F.A.R.M. Warmerdam, M.M. Geenen, O.J.L. Loosveld, J.E.A. Portielje, M. Los, E. Meershoek - Klein Kranenbarg, H.H. Hartgrink, J. van Sandick, C.J.H. van de Velde, M. Verheij, A. Cats, B. Ylstra, N.C.T. van Grieken, On behalf of the CRITICS investigators. Mucinous phenotype is associated with response to neoadjuvant chemotherapy in microsatellite instable resectable gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 354.
Baseline multimodal information predicts future motor impairment in premanifest Huntington's disease (2018)

In Huntington's disease (HD), accurate estimates of expected future motor impairments are key for clinical trials. Individual prognosis is only partially explained by genetics. However, studies so far have focused on predicting the time to clinical diagnosis based on fixed impairment levels, as opposed to predicting impairment in time windows comparable to the duration of a clinical trial. Here we evaluate an approach to both detect atrophy patterns associated with early degeneration and provide a prognosis of motor impairment within 3 years, using data from the TRACK-HD study on 80 premanifest HD (pre-HD) individuals and 85 age- and sex-matched healthy controls. We integrate anatomical MRI information from gray matter concentrations (estimated via voxel-based morphometry) together with baseline data from demographic, genetic and motor domains to distinguish individuals at high risk of developing pronounced future motor impairment from those at low risk. We evaluate the ability of models to distinguish between these two groups solely using baseline imaging data, as well as in combination with longitudinal imaging or non-imaging data. Our models show improved performance for motor prognosis through the incorporation of imaging features to non-imaging data, reaching 88% cross-validated accuracy when using baseline non-longitudinal information, and detect informative correlates in the caudate nucleus and the thalamus both for motor prognosis and early atrophy detection. These results show the plausibility of using baseline imaging and basic demographic/genetic measures for early detection of individuals at high risk of severe future motor impairment in relatively short timeframes.