gebhart/patrepeval huggingface dataset:
Table S1 from Inhibition of BET Bromodomain Proteins with GS-5829 and GS-626510 in Uterine Serous Carcinoma, a Biologically Aggressive Variant of Endometrial Cancer (2023)

&lt;p&gt;Cell lines characteristics and tissue source.&lt;/p&gt;
Quantitative PCR-Based Measurement of Nuclear and Mitochondrial DNA Damage and Repair in Mammalian Cells (2008)

In this chapter, we describe a gene-specific quantitative polymerase chain reaction (QPCR)-based assay for the measurement of DNA damage, using amplification of long DNA targets. This assay has been extensively used to measure the integrity of both nuclear and mitochondrial genomes exposed to different genotoxins, and has proved particularly valuable in identifying reactive oxygen species-mediated mitochondrial DNA (mtDNA) damage. QPCR can be used to quantify the formation of DNA damage, as well as the kinetics of damage removal. One of the main strengths of the assay is that it permits monitoring the integrity of mtDNA directly from total cellular DNA without the need for isolating mitochondria, or a separate step of mtDNA purification. Here we discuss advantages and limitations of using QPCR to assay DNA damage in mammalian cells. In addition, we give a detailed protocol for the QPCR assay that helps facilitate its successful deployment in any molecular biology laboratory.
Herman N. Eisen: Mentor to many (2015)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Demystifying speckle field quantitative phase microscopy (2021)

Quantitative phase microscopy (QPM) has found significant applications in the field of biomedical imaging which works on the principle of interferometry. The theory behind achieving interference in QPM with conventional light sources such as white light and lasers is very well developed. Recently, the use of dynamic speckle illumination (DSI) in QPM has attracted attention due to its advantages over conventional light sources such as high spatial phase sensitivity, single shot, scalable field of view (FOV) and resolution. However, the understanding behind obtaining interference fringes in QPM with DSI has not been convincingly covered previously. This imposes a constraint on obtaining interference fringes in QPM using DSI and limits its widespread penetration in the field of biomedical imaging. The present article provides the basic understanding of DSI through both simulation and experiments that is essential to build interference optical microscopy systems such as QPM, digital holographic microscopy and optical coherence tomography. Using the developed theory of DSI we demonstrate its capabilities of using non-identical objective lenses in both arms of the interference microscopy without degrading the interference fringe contrast and providing the flexibility to use user-defined microscope objective lens. It is also demonstrated that the interference fringes are not washed out over a large range of optical path difference (OPD) between the object and the reference arm providing competitive edge over low temporal coherence light sources. The theory and explanation developed here would enable wider penetration of DSI based QPM for applications in biology and material sciences.
A bio-inspired polymeric gradient refractive index (GRIN) human eye lens (2012)

A synthetic polymeric lens was designed and fabricated based on a bio-inspired, "Age=5" human eye lens design by utilizing a nanolayered polymer film-based technique. The internal refractive index distribution of an anterior and posterior GRIN lens were characterized and confirmed against design by µATR-FTIR. 3D surface topography of the fabricated aspheric anterior and posterior lenses was measured by placido-cone topography and exhibited confirmation of the desired aspheric surface shape. Furthermore, the wavefronts of aspheric posterior GRIN and PMMA lenses were measured and simulated by interferometry and Zemax software, respectively. Their results show that the gradient index distribution reduces the overall wavefront error as compared a homogenous PMMA lens of an identical geometry. Finally, the anterior and posterior GRIN lenses were assembled into a bio-inspired GRIN human eye lens through which a clear imaging was possible.
Hydration-Dependent Dynamical Modes in Xyloglucan from Molecular Dynamics Simulation of13C NMR Relaxation Times and Their Distributions (2018)

Macromolecular dynamics in biological systems, which play a crucial role for biomolecular function and activity at ambient temperature, depend strongly on moisture content. Yet, a generally accepted quantitative model of hydration-dependent phenomena based on local relaxation and diffusive dynamics of both polymer and its adsorbed water is still missing. In this work, atomistic-scale spatial distributions of motional modes are calculated using molecular dynamics simulations of hydrated xyloglucan (XG). These are shown to reproduce experimental hydration-dependent <sup>13</sup>C NMR longitudinal relaxation times ( T<sub>1</sub>) at room temperature, and relevant features of their broad distributions, which are indicative of locally heterogeneous polymer reorientational dynamics. At low hydration, the self-diffusion behavior of water shows that water molecules are confined to particular locations in the randomly aggregated XG network while the average polymer segmental mobility remains low. Upon increasing water content, the hydration network becomes mobile and fully accessible for individual water molecules, and the motion of hydrated XG segments becomes faster. Yet, the polymer network retains a heterogeneous gel-like structure even at the highest level of hydration. We show that the observed distribution of relaxations times arises from the spatial heterogeneity of chain mobility that in turn is a result of heterogeneous distribution of water-chain and chain-chain interactions. Our findings contribute to the picture of hydration-dependent dynamics in other macromolecules such as proteins, DNA, and synthetic polymers, and hold important implications for the mechanical properties of polysaccharide matrixes in plants and plant-based materials.
Broadband Athermal Waveguides and Resonators With Low Anomalous Dispersion (2020)

To mitigate the temperature sensitivity of photonic devices, materials with a negative thermo-optical coefficient (TOC) are integrated to optical waveguides. However, previously reported waveguides are made athermal at only one wavelength. In this paper, we theoretically propose a new broadband athermal waveguide, which consists of TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> with a negative TOC and SiC with a positive TOC in its core. This composite core shows a near-zero broadband effective TOC, i.e., ±1x10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-6</sup> /K over a 780-nm bandwidth from 1280 to 2060 nm. Furthermore, it also has low anomalous dispersion, from 66 to 329 ps/nm/km in the same wavelength range. This new athermal waveguide, when used to form microresonators, enables us to achieve broadband nonlinear applications with negligible intra-cavity thermal dynamics on a chip. We also show that the proposed waveguide can be tightly bent without suffering from a large bending loss/substrate leakage, which is suitable for dense integration.
Handover Management in 5G and Beyond: A Topology Aware Skipping Approach (2016)

Network densification is found to be a potential solution to meet 5G capacity standards. Network densification offers more capacity by shrinking base stations' (BSs) footprints, thus reduces the number of users served by each BS. However, the gains in the capacity are achieved at the expense of increased handover (HO) rates. Hence, HO rate is a key performance limiting factor that should be carefully considered in densification planning. This paper sheds light on the HO problem that appears in dense 5G networks and proposes an effective solution via topology aware HO skipping. Different skipping techniques are considered and compared with the conventional best connected scheme. To this end, the effectiveness of the proposed schemes is validated by studying the average user rate in the downlink single-tier and two-tier cellular networks, which are modeled using Poisson point process and Poisson cluster process, respectively. The proposed skipping schemes show up to 47% gains in the average throughput that would maximize the benefit of network densification.
It's OK to be a Control Freak: Deploying machine learning algorithms and model-based controllers for WRRF optimization (2022)

Hybrid models are powerful predictors of performance in Water Resource Recovery Facilities (WRRFs). When used in controllers, hybrid models can help inform manipulated variable setpoints in feedforward controllers. This idea was tested for chlorine disinfection and ammonia-based aeration control.
SUMO Wrestles with Mitophagy to Extend Lifespan (2020)

SUMOylation, a conserved protein post-translational modification that performs multiple functions including regulation of nuclear transport and transcription, is implicated in numerous biological processes including aging. RNAi knockdown of the sole Small Ubiquitin-like MOdifier (SUMO) gene, smo-1, in <i>Caenorhabditis elegans</i> shortened lifespan, whereas overexpression in the intestine modestly increased lifespan. Smo-1 is required for mitochondrial fission in a tissue-specific manner. Fission, in turn, is needed for mitophagy to maintain mitochondrial homeostasis during aging. SUMOlyation affects DAuer Formation (DAF)-16, which can be directly SUMOylated, and SKN-1, the homolog of mammalian Nrf2. These regulators play key roles in maintaining mitochondrial homeostasis. However, given the modest effect of overexpressing smo-1 on lifespan enhancement and potential interference with other genes that can promote increased lifespan, caution is advised in the translation of this study based on <i>C. elegans</i>. Although inhibitors of SUMOlyation have been developed for cancer and activators also have been identified, broad-acting biochemical pathway modifiers such as SUMO are often suboptimal drug targets and may not be as promising for antiaging applications as they first appear.
On the formation of stationary destructive cathode-side filaments in p<inf>+</inf>-n<inf>&#x2212;</inf>-n<sup>+</sup> diodes (2009)

Analyzing the dynamics of current filaments is essential for a correct understanding of SOA limitations. Current filaments can occur during the reverse-recovery period of p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-</sup> -n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> diodes. In this work, we apply the results from an analysis of the plasma-front dynamics for the one-dimensional case to conditions under which current filaments appear in the depletion layers due to dynamic avalanche. We show that the anode-side plasma front velocity is higher in the vicinity of the filament than far away from the filament center, favoring the evolution of a lateral traveling anode-side filament. Furthermore, we find that the cathode-side plasma front changes its vertical propagation direction when a dynamic avalanche in the cathode-side depletion layer causes current crowding. As a result, the cathode-side depletion layer in the vicinity of the filament decreases, favoring the formation of a standing cathode-side filament that may cause final destruction of the device. The analytical results are in good agreement with numerical simulations and results of previously published work.
A randomized phase 3 study of ixazomib–dexamethasone versus physician’s choice in relapsed or refractory AL amyloidosis (2021)

In the first phase 3 study in relapsed/refractory AL amyloidosis (TOURMALINE-AL1 NCT01659658), 168 patients with relapsed/refractory AL amyloidosis after 1-2 prior lines were randomized to ixazomib (4 mg, days 1, 8, 15) plus dexamethasone (20 mg, days 1, 8, 15, 22; n = 85) or physician's choice (dexamethasone ± melphalan, cyclophosphamide, thalidomide, or lenalidomide; n = 83) in 28-day cycles until progression or toxicity. Primary endpoints were hematologic response rate and 2-year vital organ deterioration or mortality rate. Only the first primary endpoint was formally tested at this interim analysis. Best hematologic response rate was 53% with ixazomib-dexamethasone vs 51% with physician's choice (p = 0.76). Complete response rate was 26 vs 18% (p = 0.22). Median time to vital organ deterioration or mortality was 34.8 vs 26.1 months (hazard ratio 0.53; 95% CI, 0.32-0.87; p = 0.01). Median treatment duration was 11.7 vs 5.0 months. Adverse events of clinical importance included diarrhea (34 vs 30%), rash (33 vs 20%), cardiac arrhythmias (26 vs 15%), nausea (24 vs 14%). Despite not meeting the first primary endpoint, all time-to-event data favored ixazomib-dexamethasone. These results are clinically relevant to this relapsed/refractory patient population with no approved treatment options.
Characterizing the Metal–SAM Interface in Tunneling Junctions (2015)

This paper investigates the influence of the interface between a gold or silver metal electrode and an n-alkyl SAM (supported on that electrode) on the rate of charge transport across junctions with structure Met(Au or Ag)(TS)/A(CH2)nH//Ga2O3/EGaIn by comparing measurements of current density, J(V), for Met/AR = Au/thiolate (Au/SR), Ag/thiolate (Ag/SR), Ag/carboxylate (Ag/O2CR), and Au/acetylene (Au/C≡CR), where R is an n-alkyl group. Values of J0 and β (from the Simmons equation) were indistinguishable for these four interfaces. Since the anchoring groups, A, have large differences in their physical and electronic properties, the observation that they are indistinguishable in their influence on the injection current, J0 (V = 0.5) indicates that these four Met/A interfaces do not contribute to the shape of the tunneling barrier in a way that influences J(V).
PET imaging of adenosine A(1) receptors with (11)C-MPDX as an indicator of severe cerebral ischemic insult. (2003)

The degree of decreased MPDX binding to A1-Rs after reperfusion was a sensitive predictor of severe ischemic insult. MPDX PET has good potential to become a suitable in vivo imaging technique for evaluating the function of adenosine and A1-Rs in relation to cerebral ischemia.
A semiclassical analysis of optical code division multiple access (1991)

A model noncoherent, optical, asynchronous, CDMA system is described. The error rate for a single-user matched-filter receiver that is valid for arbitrary photomultipliers and signature sequence sets, adheres to the semiclassical model of light, and does not depend on approximations for large user groups, strong received optical fields, or chip synchronism is analyzed. The exact minimum probability of error and optimal threshold are compared to those obtained with user-synchronism and multiple-access interference (MAI) distribution approximations. For the special case of unity-gain photodetectors and prime sequences, it is shown that the approximation of chip synchronism yields a weak upper bound on the exact error rate. It is demonstrated that the approximations of perfect optical-to-electrical conversion and Gaussian-distributed MAI yield a poor approximation to the minimum error rate and an underestimate of the optimal threshold. Arbitrarily tight bounds are developed on the error rate for unequal energies per bit. In the case when the signal energies coincide, these bounding expressions are considerably easier to compute than the exact error rate.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Orientation tuning of contour integration (2010)

There currently exists an extensive body of literature devoted to understanding how the visual system integrates spatially segmented elements into contours, either artificially generated, or modeled after the contour statistics of natural scene imagery. However, little is known about the orientation tuning of the integration mechanism and whether such tuning changes as a function of contour curvature. To address those issues, we employed stimuli consisting of texture fields made up of pseudo-randomly distributed band-pass filtered noise elements (band-pass in spatial frequency and orientation), some of which, by virtue of their orientation alignment, formed a contour path. The orientation bandwidth of all filtered noise elements was varied, and the local spatial orientation misalignment (element-to-path angle) between the local element orientation and the contour path itself was systematically manipulated. The task consisted of a standard psychophysical 2AFC paradigm where observers were required to indicate which stimulus interval contained a contour. The results indicated that the local element orientation bandwidth needed to integrate low curvature contours was quite broad (ranging between 40° to 60°). For contours possessing a high degree of curvature, this bandwidth was significantly narrower (ranging between 20° to 30). However, the element-to-path angle varied very little as a function of contour curvature, ranging between 15° to 25° for all curvatures. The results indicate that the local element orientation tuning of the human visual contour integration mechanism is dependent on contour curvature.
Correction: Corrigendum: Automated Axon Counting in Rodent Optic Nerve Sections with AxonJ (2016)

Scientific Reports 6: Article number: 26559; published online: 26 May 2016; updated: 19 October 2016 In the Supplementary Information file originally published with this Article, Supplemental Figure 1 was omitted. In addition, “Supplemental Software” was incorrectly given as “Software Legend” These errors have now been corrected in the Supplementary Information that now accompanies the Article.
The Study of Thermal Property at a Line and Vias in Embedded Device Package (2016)

Recently, Power devices have gotten a lot of attention in order to achieve low power consumption and downsizing for electrical equipment. Under such conditions, power packages are strongly required to have high heat dissipation structure with low on-state resistance and low inductance to decrease low power loss and high-speed switching noise. Panel Level Package (PLPTM) gives advantages on productivity, reliability and high-speed transmission characteristics. In this paper, we observed temperature rise at a line and vias during applying current of over 100 A to understand their design in PLPTM. We also simulated temperature distribution of the same model to research thermal behavior and compared with observed result.
Intraoperative Neuromonitoring and Lumbar Spinal Instrumentation: Indications and Utility (2021)

Multimodal intraoperative neurophysiologic monitoring (IONM) can be utilized as an adjunct to lumbar spinal instrumentation in order to aid with avoidance of neurologic complications. The most commonly utilized modalities include somatosensory-evoked potentials, motor-evoked potentials, and electromyography. Somatosensory-evoked potentials (SSEPs) allow for continuous assessment of the dorsal columns of the spinal cord and are therefore most useful during procedures with a posterior approach to the cervical and thoracic spine. Motor-evoked potentials (MEPs) and electromyography (EMG) can be applied intermittently to assess motor nerve function. The utility of each individual modality can be largely dependent on the surgical approach. Approaches to lumbar spinal instrumentation can be generally categorized as anterior, lateral, and posterior. For lateral approaches, electromyography can be helpful in identifying neural structures crossing the surgical field to prevent injury. In posterior and anterior approaches, somatosensory-evoked potentials and motor-evoked potentials can be used to assess nerve injury during and after maneuvers for decompression and instrumentation. Additionally, during the placement of pedicle screws, direct stimulation with triggered electromyography can be used to detect the pedicle cortex's breach. The efficacy of intraoperative neuromonitoring is dependent on prompt and accurate recognition of changes in signals. This is then followed by accurate recognition of the cause for these changes and appropriate responses by the surgeon, anesthesiologist, and monitoring personnel to correct the change.
Zeolite-modified electrodes and electrode-modified zeolites (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleZeolite-modified electrodes and electrode-modified zeolitesDebra R. RolisonCite this: Chem. Rev. 1990, 90, 5, 867–878Publication Date (Print):July 1, 1990Publication History Published online1 May 2002Published inissue 1 July 1990https://doi.org/10.1021/cr00103a011RIGHTS & PERMISSIONSArticle Views1774Altmetric-Citations253LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (3 MB) Get e-Alerts Get e-Alerts
Perturbation of D 1 Dopamine and AT 1 Receptor Interaction in Spontaneously Hypertensive Rats (2003)

The dopaminergic and renin-angiotensin systems interact to regulate blood pressure. Because this interaction may be perturbed in genetic hypertension, we studied D1 dopamine and AT1 angiotensin receptors in immortalized renal proximal tubule (RPT) and A10 aortic vascular smooth muscle cells. In normotensive Wistar-Kyoto (WKY) rats, the D1-like agonist fenoldopam increased D1 receptors but decreased AT1 receptors. These effects were blocked by the D1-like antagonist SCH 23390 (10(-7) mol/L per 24 hours). In spontaneously hypertensive rat (SHR) RPT cells, fenoldopam also decreased AT1 receptors but no longer stimulated D1 receptor expression. Basal levels of AT1/D1 receptor coimmunoprecipitation were greater in WKY RPT cells (29+/-2 density units, DU) than in SHR RPT cells (21+/-2 DU, n=7 per group, P<0.05). The coimmunoprecipitation of D1 and AT1 receptors was increased by fenoldopam (10(-7) mol/L per 24 hours) in WKY RPT cells but decreased in SHR RPT cells. The effects of fenoldopam in RPT cells from WKY rats were similar in aortic vascular smooth muscle cells from normotensive BD IX rats, that is, fenoldopam decreased AT1 receptors and increased D1 receptors. Our studies show differential regulation of the expression of D1 and AT1 receptors in RPT cells from WKY and SHR. This regulation and D1/AT1 receptor interaction are different in RPT cells of WKY and SHR. An altered interaction of D1 and AT1 receptors may play a role in the impaired sodium excretion and enhanced vasoconstriction in hypertension.