gebhart/patrepeval huggingface dataset:
Fullerenols Revisited as Stable Radical Anions (2004)

The first exhaustive purification and characterization of the much-studied "fullerenols", prepared by reaction of C(60) in toluene with an oxygenated, aqueous NaOH solution using tetrabutylammonium hydroxide as a phase transfer catalyst, has been performed. The resulting fullerenol is not simply polyhydroxylated C(60) but rather is a structurally and electronically complex C(60) radical anion with a molecular formula of Na(+)(n)[C(60)O(x)(OH)(y)](n)(-) (where n = 2-3, x = 7-9, and y = 12-15) for three different, but identical, preparations. Surprisingly, Na(+)-fullerenol is paramagnetic, exhibiting mu(B) values in aqueous solution of 1.9-2.1 B.M. at 0.5 T and 300 K and R(1) proton relaxivities of 0.55-0.77 mM(-1)s(-1) at 20 MHz and 40 degrees C, values both slightly higher than those expected for a pure S = 1/2 spin system. ESR studies (ESE-FS and 2D nutation) of frozen aqueous solutions at 1.5 and 5.0 K establish that Na(+)-fullerenol is mainly S = 1/2 with a minor, but significant, component of S = 1. Thus, this is the first report to characterize these widely studied, water-soluble fullerenols as stable radical anions. The stability of the S = 1/2 Na(+)-fullerenol radical is likely due to a highly derivatized C(60) surface that protects a cyclopentadienyl radical center on the fullerene.
Rabi-oscillations-induced multiharmonic emission in a Maxwell-Schr�dinger study of a dense sample of molecules (2001)

A solution of the combined Maxwell–Schrödinger equations for the propagation of an ultraviolet (UV) pulse in a sample of model H2+-like molecules (with only two electronic states), shows a significant increase of the emission at 5–10 harmonics for a thick-density (line integrated density of 50 a.u.−2) vs. a thin-density case. The increase is more than two orders of magnitude larger than the expected factor (the ratio of the squared densities) and is due to a “sharpening” effect whereby Rabi oscillations induce a spatially rapidly varying electric field that has very sharp peaks. Equally important, the molecular degree of freedom is shown to exert a strong influence on the emitted radiation so that multiharmonic emission can be controlled by preparing molecules in specific initial wavepackets. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 260–267, 2001
Non-monotonic spatial structure of inter-neuronal correlations in prefrontal microcircuits (2017)

Abstract Correlated fluctuations of single neuron discharges, on a mesoscopic scale, decrease as a function of lateral distance in early sensory cortices, reflecting a rapid spatial decay of lateral connection probability and excitation. However, spatial periodicities in horizontal connectivity and associational input as well as an enhanced probability of lateral excitatory connections in the association cortex could theoretically result in non-monotonic correlation structures. Here we show such a spatially non-monotonic correlation structure, characterized by significantly positive long-range correlations, in the inferior convexity of the macaque prefrontal cortex. This functional connectivity kernel was more pronounced during wakefulness than anesthesia and could be largely attributed to the spatial pattern of correlated variability between functionally similar neurons during structured visual stimulation. These results suggest that the spatial decay of lateral functional connectivity is not a common organizational principle of neocortical microcircuits. A non-monotonic correlation structure could reflect a critical topological feature of prefrontal microcircuits, facilitating their role in integrative processes. Significance statement The spatial structure of correlated activity of neurons in lower-order visual areas has been shown to linearly decrease as a measure of distance. The shape of correlated variability is a defining feature of cortical microcircuits as it constrains the computational power and diversity of a region. We show here for the first time a non-monotonic spatial structure of functional connectivity in the pre-frontal cortex where distal interactions are just as strong as proximal interactions during visual engagement of functionally similar PFC neurons. Such a nonmonotonic structure of functional connectivity could have far-reaching consequences in rethinking the nature and the role of prefrontal microcircuits in various cognitive states.
Experiments In Layered Electro-Photographic Printing 267 (2000)

Electro-photographic printing processes employed by products such as laser printers and photocopiers are commonly used to deposit and fuse thin layers of thermoplastic powder onto paper. This report describes preliminary experiments aimed at adapting the electro-photographic printing process for use as a layered manufacturing technique. 3-D electro-photographic printing holds considerable potential as an inexpensive freeform fabrication technique that is suitable for office environments. The possibilities for selective coloring are also discussed.
A microfabricated electronic microplate platform for low-cost repeatable biosensing applications (2015)

This work presents a disposable `electronic microplate' (e-microplate) platform that enables the reusability of the corresponding CMOS biosensor thereby reducing cost and increasing throughput relative to non-disposable systems. The e-microplate utilizes mechanically-flexible interconnects (MFIs) and through-silicon-vias (TSVs) to electrically interconnect the electrodes on the CMOS biosensor to the electrodes on the e-microplate while maintaining a physical separation between the aforementioned substrate tiers. Measurements performed show that the incorporation of the e-microplate does not degrade the sensing amplifier's gain, 3dB bandwidth, or the input referred noise, and thus ensures the accurate sensing of weak signals from living cells under test. Impedance mapping for saline and Dulbecco's Phosphate Buffered Saline (DPBS) solutions performed through the e-microplate confirm functional accuracy of the assembled system.
Communicating Structure and Function in Synthetic Biology Diagrams (2019)

Biological engineers often find it useful to communicate using diagrams. These diagrams can include information both about the structure of the nucleic acid sequences they are engineering and about the functional relationships between features of these sequences and/or other molecular species. A number of conventions and practices have begun to emerge within synthetic biology for creating such diagrams, and the Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard to organize, systematize, and extend such conventions in order to produce a coherent visual language. Here, we describe SBOL Visual version 2, which expands previous diagram standards to include new functional interactions, categories of molecular species, support for families of glyph variants, and the ability to indicate modular structure and mappings between elements of a system. SBOL Visual 2 also clarifies a number of requirements and best practices, significantly expands the collection of glyphs available to describe genetic features, and can be readily applied using a wide variety of software tools, both general and bespoke.
Arbitrary-transport-length analysis of hologram formation in electro-optic crystals (1980)

Abstract Holographic grating formation by the photorefractive effect in electro-optic crystals is analyzed allowing for arbitrary transport lengths. The analysis, which allows for the feedback effect of the space-charge field and nonsinusoidal gratings, is applicable over the entire range of exposures.
Comparison of Certolizumab Pegol, Etanercept, Adalimumab and Infliximab (2006)

Purpose: Proinflammatory cytokines, such as interleukin-1ββ (IL-1ββ) are over-expressed by monocytes/macrophages in patients with Crohn's disease (CD). It has been suggested that anti-tumor necrosis factor αα (TNFαα) agents mediate an inhibitory effect on lipopolysaccharide (LPS)-induced cytokine production via membrane TNFαα signalling. This study compared LPS-stimulated production of IL-1ββ in the presence of certolizumab pegol (an antibody Fab' fragment conjugated with polyethylene glycol) and other anti-TNF agents. Methods: Monocytes were positively selected using CD14+ magnetic microbead-associated cell sorting (MACS) from peripheral blood mononuclear cells of normal human donors. Purified monocytes were pre-incubated for 1 hr with certolizumab pegol, etanercept, adalimumab, infliximab (100 μg/mL to 100 pg/mL) or a relevant control. After extensive washing, the monocytes were incubated — with or without LPS (100 ng/mL) — for 4 hours at 37°C. Supernatants were assessed for IL-1ββ (by enzyme-linked immunosorbent assay) and a range of chemokines, cytokines and other proteins (by Luminex). Results: LPS-stimulated production of IL-1ββ by monocytes appeared to be completely inhibited in a dose-dependent manner by certolizumab pegol, infliximab and adalimumab. In contrast, etanercept was much less efficient at mediating this activity, causing only partial inhibition of cytokine production. Certolizumab pegol was approximately 100-fold more potent than infliximab and adalimumab at inhibiting the release of IL-1ββ by monocytes. The effects of infliximab and adalimumab were similar. The Luminex analysis of a panel of cytokines and chemokines showed a range of effects with inhibition of IL-10 and IL-12 being the most profound. Again etanercept was not as potent as the other anti-TNFs agents at inhibiting these cytokines. Conclusions: Effective inhibition of IL-1ββ production was seen with certolizumab pegol; inhibition was more potent than with adalimumab or infliximab. Even at high concentrations of etanercept, inhibition of IL-1ββ production was only partial. These are in vitro data, however, the comparative trends in inhibition of cytokine production stimulated by bacterial products appear to reflect the clinical efficacy of these anti-TNF agents in CD. The potent inhibition by certolizumab pegol of cytokine production by monocytes may represent an important mechanism of action in CD.
Package Model for Efficient Simulation, Design, and Characterization of High Performance Electronic Systems (2006)

As bit rates are approaching 10 Gbps with ever-increasing requirement for package performance, multi-layer FC-BGA package are gradually becoming a de facto for high performance system. Since the signal frequency is now in the range of noise generated by power plane resonances, it presents a major challenge to model the complex interaction between signal traces and power/ground planes. Any attempt to segment the package into smaller pieces to simplify the computation may compromise the accuracy, diminishing the resonance effect. Conversely, full package model created from field solver is impractical and too expensive to generate. This paper presents a methodology to unify signal and power integrity into a single simulation model derived from conventional signal and power integrity models. The proposed method utilizes piece-wise modeling approach to dissect the package structures into component models and unify them into a single simulation circuit. The proposed approach can be extended to full system simulation, resulting in fast computation for design space exploration where massive simulations are necessary
Next-generation sequencing identifies novel microRNAs in peripheral blood of lung cancer patients (2011)

MicroRNAs (miRNAs) are increasingly envisaged as biomarkers for various tumor and non-tumor diseases. MiRNA biomarker identification is, as of now, mostly performed in a candidate approach, limiting discovery to annotated miRNAs and ignoring unknown ones with potential diagnostic value. Here, we applied high-throughput SOLiD transcriptome sequencing of miRNAs expressed in human peripheral blood of patients with lung cancer. We developed a bioinformatics pipeline to generate profiles of miRNA markers and to detect novel miRNAs with diagnostic information. Applying our approach, we detected 76 previously unknown miRNAs and 41 novel mature forms of known precursors. In addition, we identified 32 annotated and seven unknown miRNAs that were significantly altered in cancer patients. These results demonstrate that deep sequencing of small RNAs bears high potential to quantify miRNAs in peripheral blood and to identify previously unknown miRNAs serving as biomarker for lung cancer.
MR-based keyhole SPECT for small animal imaging (2011)

The rationale for multi-modality imaging is to integrate the strengths of different imaging technologies while reducing the shortcomings of an individual modality. The work presented here proposes a limited-field-of-view (LFOV) SPECT reconstruction technique that can be implemented on a multi-modality MR/SPECT system that can be used to obtain simultaneous MRI and SPECT images for small animal imaging. The reason for using a combined MR/SPECT system in this work is to eliminate any possible misregistration between the two sets of images when MR images are used as a priori information for SPECT. In nuclear imaging the target area is usually smaller than the entire object; thus, focusing the detector on the LFOV results in various advantages including the use of a smaller nuclear detector (less cost), smaller reconstruction region (faster reconstruction) and higher spatial resolution when used in conjunction with pinhole collimators with magnification. The MR/SPECT system can be used to choose a region of interest (ROI) for SPECT. A priori information obtained by the full field-of-view (FOV) MRI combined with the preliminary SPECT image can be used to reduce the dimensions of the SPECT reconstruction by limiting the computation to the smaller FOV while reducing artifacts resulting from the truncated data. Since the technique is based on SPECT imaging within the LFOV it will be called the keyhole SPECT (K-SPECT) method. At first MRI images of the entire object using a larger FOV are obtained to determine the location of the ROI covering the target organ. Once the ROI is determined, the animal is moved inside the radiofrequency (rf) coil to bring the target area inside the LFOV and then simultaneous MRI and SPECT are performed. The spatial resolution of the SPECT image is improved by employing a pinhole collimator with magnification >1 by having carefully calculated acceptance angles for each pinhole to avoid multiplexing. In our design all the pinholes are focused to the center of the LFOV. K-SPECT reconstruction is accomplished by generating an adaptive weighting matrix using a priori information obtained by simultaneously acquired MR images and the radioactivity distribution obtained from the ROI region of the SPECT image that is reconstructed without any a priori input. Preliminary results using simulations with numerical phantoms show that the image resolution of the SPECT image within the LFOV is improved while minimizing artifacts arising from parts of the object outside the LFOV due to the chosen magnification and the new reconstruction technique. The root-mean-square-error (RMSE) in the out-of-field artifacts was reduced by 60% for spherical phantoms using the K-SPECT reconstruction technique and by 48.5-52.6% for the heart in the case with the MOBY phantom. The K-SPECT reconstruction technique significantly improved the spatial resolution and quantification while reducing artifacts from the contributions outside the LFOV as well as reducing the dimension of the reconstruction matrix.
Wissen vermehren – Naturwissenschaftler vernetzen (2008)

Abstract Sören Hofmayer Weil kaum ein wissenschaftlicher Fortschritt ohne das Wissen anderer möglich ist, ist eine vernetzte Wissenschaftswelt nützlich. Die Internetplattform Researchgate verbindet Forscher weltweit.
Supplementary Figure 2 from Suppression of MicroRNA-9 by Mutant EGFR Signaling Upregulates FOXP1 to Enhance Glioblastoma Tumorigenicity (2023)

&lt;p&gt;PDF file - 99KB, Mesenchymal GBMs show an overall decrease in miR-9 expression.&lt;/p&gt;
Observation of the Decays Λ[superscript 0][subscript b] → χ[subscript c1]pK[superscript −] and Λ[subscript 0][subscript b] → χ[subscript c2]pK− (2017)

The first observation of the decays Λ[superscript 0][subscript b] →χ[subscript c1]pK[superscript -] and Λ[superscript 0][subscript b] →χ[subscript c2]pK[superscript -] is reported using a data sample corresponding to an integrated luminosity of 3.0 fb[superscript -1], collected by the LHCb experiment in pp collisions at center-of-mass energies of 7 and 8 TeV. The following ratios of branching fractions are measured: B(Λ[superscript 0][subscript b] →χ[subscript c1]pK[superscript -])/B(Λ[superscript 0][subscript b]→J/ψpK[superscript -]) = 0.242±0.014±0.013±0.009, B(Λ[superscript 0][subscript b] → χ[subscript c2]pK[superscript -])/B(Λ[subscript 0][subscript b] →J/ψpK[superscript -]) = 0.248±0.020±0.014±0.009, B(Λ[subscript 0][subscript b] →χ[subscript c2]pK[superscript -])/B(Λ[superscript 0][subscript b] → χ[subscript c1]pK[superscript -]) = 1.02±0.10±0.02±0.05, where the first uncertainty is statistical, the second systematic, and the third due to the uncertainty on the branching fractions of the χ[subscript c1] → J/ψγ and χ[subscript c2] → J/ψγ decays. Using both decay modes, the mass of the Λ[superscript 0][subscript b] baryon is also measured to be m[subscriprt Λ[superscript 0][subscript b0]] = 5619.44±0.28±0.26 MeV/c[superscript 2], where the first and second uncertainties are statistical and systematic, respectively.
Abstract 3663: An anti-CD4 depleting antibody reverses regulatory T-cell-induced suppression of dendritic cells while preventing nonspecific CD4+ T cell responses in tumor-bearing mice (2017)

Abstract Administration of an anti-CD4 depleting antibody induces tumor-specific CD8+ T cell responses in tumor-bearing mice, although the mechanisms underlying this phenomenon remain unclear. CD4+ Foxp3+ regulatory T cells (Treg) impair antigen presentation by DCs through CTLA4-mediated down-regulation of CD80/CD86. In the present study, we investigated the effects of an anti-CD4 depleting monoclonal antibody (mAb) on DC responses in the B16F10 and LLC subcutaneous tumor models, and compared these effects with those of Treg targeting therapy. Administration of anti-CD4 mAb up-regulated CD80/CD86 in tumor-infiltrating DCs, and in migrating-type but not resident-type DC subsets in the tumor-draining lymph node. The upregulation of CD80/CD86 on these DC populations was correlated with increased proliferation of tumor-specific CD8+ T cells in the tumor-draining lymph node. Anti-CD4 mAb-induced CD80/CD86 up-regulation and tumor-specific CD8+ T cell responses were remarkably higher than that induced by an anti-CD25 depleting mAb or an anti-CTLA4 blocking mAb, and were equivalent to that induced by diphtheria-toxin-induced selective depletion of Tregs in Foxp3-DTR mice. Importantly, the activation of CD4+ conventional T cells and B cells in the peripheral lymph nodes that was observed following Treg depletion was not observed following anti-CD4 mAb administration. In conclusion, anti-CD4 depleting antibody therapy is an effective way to evoke anti-tumor CD8+ T cell responses by reversing regulatory T cell-induced suppression of dendritic cells, and to reduce the risk of severe autoimmunity in cancer patients. Citation Format: Satoshi Ueha, Haru Ogiwara, Shoji Yokochi, Yoshiro Ishiwata, Francis Shand, Shohei Hori, Kazuhiro Kakimi, Satoru Ito, Kouji Matsushima. An anti-CD4 depleting antibody reverses regulatory T-cell-induced suppression of dendritic cells while preventing nonspecific CD4+ T cell responses in tumor-bearing mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3663. doi:10.1158/1538-7445.AM2017-3663
Understanding the electro-catalytic oxidation mechanism of urea on nickel electrodes in alkaline medium (2012)

Abstract In this paper, the electrocatalytic behavior of urea oxidation on a nickel electrode in alkaline medium was investigated using various electrochemical techniques: cyclic voltammetry (CV), linear sweep voltammetry (LSV), and rotating disc electrode voltammetry (RDE). Possible mechanisms have been proposed on the basis of the cyclic voltammetry data. The urea oxidation current shows a strong dependence on the concentration of urea and potassium hydroxide that enables the experimental determination, by Tafel studies, of the kinetic reaction orders for the oxidation of urea. The Tafel studies show reaction orders of 0.3 and 2, with respect to urea and OH − concentrations, respectively. The diffusion coefficient of urea was found to be 0.85 × 10 −5  cm 2  s −1 . The presence of a mixed-controlled process (diffusion and kinetics) was confirmed for the oxidation of urea.
Low temperature backside damascene processing on temporary carrier wafer targeting 7μm and 5μm pitch microbumps for N equal and greater than 2 die to wafer TCB stacking (2022)

In this paper, for first time, damascene process on thinned and bonded device wafer to a carrier using TBM layer is introduced. All the BS process steps including, dielectric depositions, etching, seed/barrier deposition, plating and CMP are performed at temperatures within the thermal budget of TBM layer. FIB images show no impact of BS processing on FS bumps. This process is done on a test vehicle with 20, 10, 7 and 5um pitch structures in F2F and B2F (or F2B) forms, where good electrical data, good solder joint formation and good reliability performance is obtained.
Electron Microscopy Study of the Deactivation of Nickel Based Catalysts for Bio Oil Hydrodeoxygenation (2014)

Hydrodeoxygenation (HDO) is proposed as an efficient way to remove oxygen in bio-oil, improving its quality as a more sustainable alternative to conventional fuels in terms of CO2 neutrality and relative short production cycle [1]. Ni and Ni-MoS2 nanoparticles supported on ZrO2 show potential as high-pressure (100 bar) catalysts for purification of bio-oil by HDO. However, the catalysts deactivate in presence of sulfur, chlorine and potassium species, which are all naturally occurring in real bio-oil. The deactivation mechanisms of the Ni/ZrO2 have been investigated through scanning transmission electron microscopy (STEM), energy dispersive X-ray spectroscopy (EDX), scanning electron microscopy (SEM) and X-ray diffraction (XRD). Catalytic testing has been performed using guaiacol in 1-octanol acting as a model compound for bio-oil. Addition of sulphur (0.3 vol% octanethiol) in the feed resulted in permanent deactivation of the catalyst by formation of a catalytically inactive Ni-S phase, as suggested by the very similar spatial distribution of nickel and sulphur signals in STEM-EDX elemental maps (Figure 1) and confirmed by XRD and X-ray absorption spectroscopy (XAS) techniques. Deactivation by chlorine (0.3 vol% chlorooctane) co-feeding was found to be reversible, as the catalyst could regain close to its initial deoxygenation activity upon restoration of a clean feed. SEM-EDX investigations excluded the presence of chlorine species; however, XRD analysis revealed sintering of nickel nanoparticles (Figure 2). Impregnating KCl and KNO3 on two different batches of catalysts decreased permanently their deoxygenation activity, suggesting the adsorption of potassium at low coordinated nickel sites [2]. The high mobility of potassium under the electron beam [3] prevented the spatial distribution study of this element through STEM-EDX. Moreover, nickel sintering was observed in the KCl poisoned sample and was ascribed once again to the formation of mobile Ni-Cl species upon reaction of HCl with surface oxides [4]. Furthermore, environmental transmission electron microscopy (ETEM) has been used in order to investigate the oxidation of Ni-MoS2/ZrO2 catalyst active phase as a function of different HDO reaction conditions and using methanol as a model molecule for bio-oil.