gebhart/patrepeval huggingface dataset:
BNT162b2-elicited neutralization of Delta plus, Lambda, Mu, B.1.1.519, and Theta SARS-CoV-2 variants (2022)

BNT162b2-elicited human sera neutralize the currently dominant Delta SARS-CoV-2 variant. Here, we report the ability of 20 human sera, drawn 2 or 4 weeks after two doses of BNT162b2, to neutralize USA-WA1/2020 SARS-CoV-2 bearing variant spikes from Delta plus (Delta-AY.1, Delta-AY.2), Delta-∆144 (Delta with the Y144 deletion of the Alpha variant), Lambda, B.1.1.519, Theta, and Mu lineage viruses. Geometric mean plaque reduction neutralization titers against Delta-AY.1, Delta-AY.2, and Mu viruses are slightly lower than against USA-WA1/2020, but all sera neutralize the variant viruses to titers of ≥80, and neutralization titers against the Delta-∆144, Lambda, B.1.1.519 and Theta variants not significantly reduced relative to those against USA-WA1/2020. The susceptibility of Delta plus, Lambda, B.1.1.519, Theta, Mu, and other variants to neutralization by the sera indicates that antigenic change has not led to virus escape from vaccine-elicited neutralizing antibodies and supports ongoing mass immunization with BNT162b2 to control the variants and to minimize the emergence of new variants.
Mind the Gap! Tailoring Sol-gel Ceramic Mesoporous Coatings on Labile Metal-organic Frameworks through Kinetic Control. (2021)

Surface engineering of metal-organic frameworks (MOFs) with a mesoporous silica coating can improve MOF mechanical properties and provide an easy way to decorate MOF nanoparticles with organic or biological molecules though silane chemistry or electrostatic interactions, while retaining open access to MOF porosity. Silica coating would be highly beneficial for employing MOFs in a wide range of applications such as catalysis or drug delivery. However, obtaining a stable, controlled core-shell structure using MOF nanoparticles as seed is challenging because of their intrinsic chemically labile nature. Here we analyze the factors that destabilize the core of the Zeolitic Imidazolate Framework-8 (ZIF-8) MOFs during the sol-gel deposition of a mesoporous silica shell causing a partial or total etching of the MOF material. Silicates in solution are found to scavenge Zn2+ ions removing them from the ZIF structure and causing a partial or complete dissolution of the ZIF seed. By carefully tuning the silicate concentration in solution simultaneous control can be obtained over both the ZIF-8 dissolution and the silica condensation kinetics, resulting in the growth of a uniform mesoporous silica shell while preserving the integrity of ZIF-8. The core-shell nanoparticles obtained show a compact core shell structure with no gap between the MOF core and the silica shell, even after calcination, while the crystalline ZIF-8 structure is retained. Overall, a general synthetic approach is presented for producing nanocomposite core-shell materials which can be applied to other MOF labile seed to design new hierarchical materials.
ChemInform Abstract: PHENYLATION OF CARBANIONS BY PI‐(CHLOROBENZENE)CHROMIUM TRICARBONYL (1975)

Abstract Die Titelreaktion wird an Beispielen demonstriert.
Highly reproducible Bragg grating acousto-ultrasonic contact transducers (2014)

Fiber optic acousto-ultrasonic transducers offer numerous applications as embedded sensors for impact and damage detection in industrial and aerospace applications as well as non-destructive evaluation. Superficial contact transducers with a sheet of fiber optic Bragg gratings has been demonstrated for guided wave ultrasound based measurements. It is reported here that this method of measurement provides highly reproducible guided ultrasound data of the test composite component, despite the optical fiber transducers not being permanently embedded in it.
Nonradiative energy transfer in a layered metal-dielectric nanostructure mediated by surface plasmons (2015)

Nonradiative energy transfer (NRET) has been applied in various applications of Nanosensors, Raman scattering, color tuning, light harvesting and organic light emitting structures. Due to the small range of donor-acceptor separation distance that NRET is effective, the improvement in energy transfer (ET) efficiency for thicker structures seems necessary. The plasmons resonance energy transfer (PRET) has been successfully employed to improve the NRET efficiency. The conventional plasmonic configuration consists of donor-metal nanostructure-acceptor shows remarkable improvement of PRET efficiency from the excited donor dipole to the acceptor molecule in longer separation distance. We report the first successful cascaded plasmons coupling in planar structure of donor/acceptor thin film that significantly gives rise to enhancement of ET efficiency. Moreover, the theoretical analysis shows an enhancement in induced electric field due to stratified metal-dielectric configuration compared to simple metal thin film. We observed ET efficiency increases more than 100% by applying dielectric layer between two metal films in plasmonic structure.
Introduction to Optimization in Electromagnetics (2006)

This chapter contains sections titled: Optimizing a Function of One Variable Optimizing a Function of Multiple Variables Comparing Local Numerical Optimization Algorithms Simulated Annealing Genetic Algorithm
An artificial photosynthesis anode electrode composed of a nanoparticulate photocatalyst film in a visible light responsive GaN-ZnO solid solution system (2016)

The artificial photosynthesis technology known as the Honda-Fujishima effect, which produces oxygen and hydrogen or organic energy from sunlight, water, and carbon dioxide, is an effective energy and environmental technology. The key component for the higher efficiency of this reaction system is the anode electrode, generally composed of a photocatalyst formed on a glass substrate from electrically conductive fluorine-doped tin oxide (FTO). To obtain a highly efficient electrode, a dense film composed of a nanoparticulate visible light responsive photocatalyst that usually has a complicated multi-element composition needs to be deposited and adhered onto the FTO. In this study, we discovered a method for controlling the electronic structure of a film by controlling the aerosol-type nanoparticle deposition (NPD) condition and thereby forming films of materials with a band gap smaller than that of the prepared raw material powder, and we succeeded in extracting a higher current from the anode electrode. As a result, we confirmed that a current approximately 100 times larger than those produced by conventional processes could be obtained using the same material. This effect can be expected not only from the materials discussed (GaN-ZnO) in this paper but also from any photocatalyst, particularly materials of solid solution compositions.
Process-Dependent Charges and Traps in Dielectrics on SiC (2006)

Dielectric charges and charge stability were compared in different dielectrics formed on SiC by different processing techniques. The concentration and transient behavior of the interface and trapped charges were investigated. Strong hysteresis and flat-band voltage drift under applied bias were observed in some of the samples. They are attributed to the trapping of the charge injected in the dielectrics. Differences in charge injection, charge trapping, and capture/emission of carriers by interface traps were pronounced for the investigated SiO2 and Si3N4 dielectrics.
Abstract 102: Pan-cancer analysis of sex differences in somatic mutation profiles (2016)

Abstract Sex influences the clinical and pathological characteristics of a number of cancers including those of the lung, colon and kidney. Men and women differ in incidence rate, response to treatment and survival - even after controlling for confounding factors such as smoking status, age and weight. Some gene-specific sex differences have been identified in these cancers, but there has not been a rigorous, genome-wide analysis of the mutational differences in tumors between men and women. We fill this gap, providing a comprehensive assessment of sex-associated differences in cancer genomics. We leverage resources from the International Cancer Genome Consortium-The Cancer Genome Atlas pan-cancer project, which includes genomic, transcriptomic and epigenomic profiles of 25,000 tumours and whole genome sequences of 5,000 tumours. Using this data, we analyzed mutational differences between the sexes in 15 tumor types. We use both univariate (t-test, proportions test) and multivariate (multinomial logistic regression) statistical techniques, along with bioinformatics and pathway analyses. We found distinct sex-associated genomic differences in the copy number aberration (CNA) profiles of six tumor types and in pan-cancer analysis. We observe higher genome instability in male-derived tumors and sex-biased mutations in specific genes and across genomic intervals. Using multivariate modeling to control for confounding variables reinforces the significance of sex in these genomic regions and also reveals additional sex-biased CNAs. Ongoing work with mRNA abundance data suggests an association between sex-differences in CNAs and mRNA abundance both in cis and in trans. Further investigation into affected genes and pathways may reveal fundamental differences in how tumors develop in men and women and provide explanations for reported clinical and pathological sex differences. Citation Format: Constance H. Li, Syed Haider, Paul C. Boutros. Pan-cancer analysis of sex differences in somatic mutation profiles. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 102.
The cortical evoked potential corresponds with deep brain stimulation efficacy in rats (2022)

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) antidromically activates the motor cortex (M1), and this cortical activation appears to play a role in the treatment of hypokinetic motor behaviors (Gradinaru V, Mogri M, Thompson KR, Henderson JM, Deisseroth K. <i>Science</i> 324: 354-359, 2009; Yu C, Cassar IR, Sambangi J, Grill WM. <i>J Neurosci</i> 40: 4323-4334, 2020). The synchronous antidromic activation takes the form of a short-latency cortical evoked potential (cEP) in electrocorticography (ECoG) recordings of M1. We assessed the utility of the cEP as a biomarker for STN DBS in unilateral 6-hydroxydopamine-lesioned female Sprague Dawley rats, with stimulating electrodes implanted in the STN and the ECoG recorded above M1. We quantified the correlations of the cEP magnitude and latency with changes in motor behavior from DBS and compared them to the correlation between motor behaviors and several commonly used spectral-based biomarkers. The cEP features correlated strongly with motor behaviors and were highly consistent across animals, whereas the spectral biomarkers correlated weakly with motor behaviors and were highly variable across animals. The cEP may thus be a useful biomarker for assessing the therapeutic efficacy of DBS parameters, as its features strongly correlate with motor behavior, it is consistent across time and subjects, it can be recorded under anesthesia, and it is simple to quantify with a large signal-to-noise ratio, enabling rapid, real-time evaluation. Additionally, our work provides further evidence that antidromic cortical activation mediates changes in motor behavior from STN DBS and that the dependence of DBS efficacy on stimulation frequency may be related to antidromic spike failure.<b>NEW & NOTEWORTHY</b> We characterize a new potential biomarker for deep brain stimulation (DBS), the cortical evoked potential (cEP), and demonstrate that it exhibits a robust correlation with motor behaviors as a function of stimulation frequency. The cEP may thus be a useful clinical biomarker for changes in motor behavior. This work also provides insight into the cortical mechanisms of DBS, suggesting that motor behaviors are strongly affected by the rate of antidromic spike failure during DBS.
Propagation of Mouse and Human T Cells with Defined Antigen Specificity and Function (2007)

Difficulties maintaining fully functional CD4+ T cells in culture have historically limited the study of their role in tumour rejection as well as other clinical applications. As the therapeutic value of current antitumour CD8+ T cell adoptive therapy becomes better defined, a strong impetus exists to determine optimal conditions for culturing antitumour CD4+ T cells. Our goal is to promote broadly polyclonal, antigen-specific CD4+ T cell responses of either Th1 or Th2 character for use in antitumour therapy or allograft facilitation, respectively. Similar obstacles exist in murine and human cultures: (1) during even brief periods of culture CD4+ T cells develop high 'background' reactivity to class II-positive antigen-presenting cells; (2) maintenance of antigen specificity as evidenced by cytokine secretion and short-term proliferation assays is insufficient to ensure bulk numerical expansion; (3) Th1-type CD4+ T cells often lose their potential for antigen-specific secretion of interleukin 2 on re-stimulation (though remain inducible by 12-O-tetradecanoylphorbol 13-acetate/ionomycin); (4) during prolonged culture selection pressure favours CD4+ subpopulations that recognize artifactual antigens such as culture medium proteins; (5) even with optimal culture conditions, cultured CD4+ T cells may function differently in vivo to uncultured CD4+ T cells. We have devised various strategies to surmount these obstacles by use of selected cytokines, antigen-presenting cells and timely culture manoeuvres.
Next generation focal plane array for infrared astronomy. (1998)

A short wavelength 2048x2048 focal plane array (FPA) with 18 μm pixel pitch is being developed for infrared astronomy. The HAWAII-2 FPA will be a hybrid comprising a HgCdTe-based detector array flip-chip bonded to a CMOS silicon multiplexer through indium interconnects. The first FPAs will have cut-off wavelength of 2.5 μm, but the readout is being designed to service detector cutoff wavelengths beyond 5 μm. The 18 μm pixel pitch was selected to accommodate both reasonable telescope optics and fabrication of the large readout (≃ 40 x 40 mm 2 ) using world-class sub-micron photolithography to maximize yield of high quality devices. Defect-free multiplexer yield >5% is expected in the first lot which will be fabricated on Rockwell's commercial production line in 0.8 μm CMOS. The HgCdTe photovoltaic detector arrays will be fabricated on ≥3″ diameter sapphire or silicon wafers. We also report the latest 1024x1024 FPA results with 2.5 μm HgCdTe detectors on sapphire substrates.
Optimization of the In Vivo Potency of Pyrazolopyrimidine MALT1 Protease Inhibitors by Reducing Metabolism and Increasing Potency in Whole Blood (2020)

The paracaspase MALT1 has gained increasing interest as a target for the treatment of subsets of lymphomas as well as autoimmune diseases, and there is a need for suitable compounds to explore the therapeutic potential of this target. Here, we report the optimization of the <i>in vivo</i> potency of pyrazolopyrimidines, a class of highly selective allosteric MALT1 inhibitors. High doses of the initial lead compound led to tumor stasis in an activated B-cell-like (ABC) diffuse large B-cell lymphoma (DLBCL) xenograft model, but this compound suffered from a short <i>in vivo</i> half-life and suboptimal potency in whole blood. Guided by metabolism studies, we identified compounds with reduced metabolic clearance and increased <i>in vivo</i> half-life. In the second optimization step, masking one of the hydrogen-bond donors of the central urea moiety through an intramolecular interaction led to improved potency in whole blood. This was associated with improved <i>in vivo</i> potency in a mechanistic model of B cell activation. The optimized compound led to tumor regression in a CARD11 mutant ABC-DLBCL lymphoma xenograft model.
Characterization of CSF Hydrodynamics in the Presence and Absence of Tonsillar Ectopia by Means of Computational Flow Analysis (2009)

Circumferential velocities and pressure gradients in the spinal canal, which may be clinically relevant to Chiari I and other malformations, can be obtained by CFA in patient-specific geometries.
Scanning-fiber-based imaging method for tissue engineering (2012)

A scanning-fiber-based method developed for imaging bioengineered tissue constructs such as synthetic carotid arteries is reported. Our approach is based on directly embedding one or more hollow-core silica fibers within the tissue scaffold to function as micro-imaging channels (MIC). The imaging process is carried out by translating and rotating an angle-polished fiber micro-mirror within the MIC to scan excitation light across the tissue scaffold. The locally emitted fluorescent signals are captured using an electron multiplying CCD camera and then mapped into fluorophore distributions according to fiber micro-mirror positions. Using an optical phantom composed of fluorescent microspheres, tissue scaffolds, and porcine skin, we demonstrated single-cell-level imaging resolution (20 to 30 μm) at an imaging depth that exceeds the photon transport mean free path by one order of magnitude. This result suggests that the imaging depth is no longer constrained by photon scattering, but rather by the requirement that the fluorophore signal overcomes the background "noise" generated by processes such as scaffold autofluorescence. Finally, we demonstrated the compatibility of our imaging method with tissue engineering by visualizing endothelial cells labeled with green fluorescent protein through a ≈ 500 μm thick and highly scattering electrospun scaffold.
Wire and Cable Applications of Polyethylene (2017)

This chapter contains sections titled: Overview Communications Applications PE in Power Cable Applications Specialty Applications Additive Requirements Extrusion Processing Summary
Low-Frequency Carrier Kinetics in Perovskite Solar Cells (2019)

Hybrid organic-inorganic halide perovskite solar cells have emerged as leading candidates for third-generation photovoltaic technology. Despite the rapid improvement in power conversion efficiency (PCE) for perovskite solar cells in recent years, the low-frequency carrier kinetics that underlie practical roadblocks such as hysteresis and degradation remain relatively poorly understood. In an effort to bridge this knowledge gap, we perform here correlated low-frequency noise (LFN) and impedance spectroscopy (IS) characterization that elucidates carrier kinetics in operating perovskite solar cells. Specifically, we focus on planar cell geometries with a SnO<sub>2</sub> electron transport layer and two different hole transport layers-namely, poly(triarylamine) (PTAA) and spiro-OMeTAD. PTAA and spiro-OMeTAD cells with moderate PCEs of 5-12% possess a Lorentzian feature at ∼200 Hz in LFN measurements that corresponds to a crossover from electrode to dielectric polarization. In comparison, spiro-OMeTAD cells with high PCEs (>15%) show 4 orders of magnitude lower LFN amplitude and are accompanied by a cyclostationary process. Through a systematic study of more than a dozen solar cells, we establish a correlation with noise amplitude, PCE, and fill factor. Overall, this work establishes correlated LFN and IS as an effective methodology for quantifying low-frequency carrier kinetics in perovskite solar cells, thereby providing new physical insights that can rationally guide ongoing efforts to improve device performance, reproducibility, and stability.
Abstract C067: Mechanistic study of the superior anti-cancer properties of a first-in-class small molecule targeting PCNA (2019)

Abstract Proliferating cell nuclear antigen (PCNA), through its interaction with various proteins involved in DNA synthesis, cell cycle regulation, and DNA repair, plays a central role in maintaining genome stability. We previously reported a novel cancer associated PCNA isoform (dubbed caPCNA), which was predominantly expressed in a broad range of cancer cells and tumor tissues, but not significantly in non-malignant cells. We found that the caPCNA-specific antigenic site lies between L126 and Y133, a region within the interdomain connector loop of PCNA that is known to be a major binding site for many of PCNA’s interacting proteins. A cell permeable peptide harboring the L126-Y133 sequence inhibited PCNA function in cancer cells and selectively kills cancer cells and xenograft tumors. Based on these observations, we sought small molecules targeting this peptide region of PCNA as potential broad-spectrum anti-cancer agents. Our effort led to a drug candidate, AOH1996, which selectively kills a broad range of cancer cells at high nanomolar concentrations, but is not associated with significant toxicity to non-malignant cells. It also works synergistically with DNA damaging chemotherapeutic drugs, such as cisplatin and irinotecan, to selectively kill cancer cells. This compound is orally available to animals and suppresses tumor growth in a dosage form compatible to clinical applications. Importantly, it doesn’t cause significant toxicity at 2.5 times its effective dose. Mechanistically, AOH1996 competes with T3, a known PCNA ligand, for binding to PCNA. However, the mechanism by which AOH1996 exerts its effect on cancer cells may not be identical to what have been reported for the T3 analogs. In particular, we found that AOH1996 interferes with the association of PCNA and its binding proteins, leading to DNA replication stress, blockade of homologous recombination-mediated DNA repair, and induction of apoptosis in cancer cells. These findings demonstrated the potential of this compound as a novel therapeutic agent warranting clinical investigation for cancer treatment. We have started planning a phase 1 clinical study for this compound. Citation Format: Long Gu, Min Li, Robert Lingeman, Robert J Hickey, Yilun Liu, Linda H Malkas. Mechanistic study of the superior anti-cancer properties of a first-in-class small molecule targeting PCNA [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C067. doi:10.1158/1535-7163.TARG-19-C067
<title>Light scattering in biological tissues: comparison between theory and experiments of spatial and temporal intensity profiles</title> (1995)

The propagation of light in biological tissues has been studied theoretically by Monte Carlo simulations and experimentally in vitro on bovine and porcine liver, human breast tissues and fat emulsions. The spatial intensity profile of a scattered collimated beam is measured at the output surface of the sample and compared to theoretical predictions. Measurements on fat emulsions and liver are in good agreement with theory. Absorption and reduced scattering coefficients can be obtained by finding a simulated profile matching our experiments. The precision of these values has been confirmed by the comparison between simulations and experiments on the temporal spread of light pulses. On the contrary the width of the spatial intensity profiles measured on breast tissues are systematically too large to be predicted by our simulations. The heterogeneity of the sample, not considered in simulations, could explain these differences.
Rapid switching solid state electrochromic devices based on complementary conducting polymer films (1996)

New electrochromic materials (ECMs) must exhibit rapid response times, long‐term stability, and a large difference in percentage transmittance between the bleached and colored states. The design, fabrication, and characterization of fast, solid‐state, dual conducting polymer EC devices that utilize PEDOT (see Figure) as the cathodically coloring material are described, following background information on ECMs. magnified image