gebhart/patrepeval huggingface dataset:
Cellular substrates for angiotensin1‐7 (Ang1‐7) action in the rostral ventro‐lateral medulla (RVLM) of the normotentsive and spontaneously hypertensive rat (SHR) (2009)

Ang1‐7 is an important component of the central renin‐angiotensin system and affects haemodynamics when injected into the RVLM. The cellular substrate(s) that Ang1‐7 targets in RVLM is unknown., We studied the effects of Ang1‐7 in organotypic brainstem slice cultures of Wistar rat (WR) and SHR. Using cell‐selective promoters incorporated into adeno viral vectors, we expressed green fluorescent protein in catecholaminergic (CA‐) neurones and non‐CA neurones and a Ca 2+ indicator Case12(1) in astroglia. . Ang1‐7 (200 nM) depolarised non‐CA neurones in both WR and SHR (by 5 and 4 mV, correspondingly; p&lt;0.05), which in SHR, but not WR, was accompanied by an increase in [Ca 2+ ]i of 61 ± 28% (P&lt;0.05). In contrast, Ang 1‐7 (200 nM) had no measurable effect on either membrane potential or [Ca 2+ ]i in CA neurones of either SHR or WR. In astrocytes Ang1‐7 also triggered increases in [Ca 2+ ]i: 200nM Ang1‐7 evoked increases of 62±23% in [Ca 2+ ]i in 26% of WR astrocytes whereas 600 nM Ang1‐7 activated more astrocytes (54%) but the average amplitude of response was similar. In SHR, Ang1‐7 effects were also similar. Effect of Ang1‐7 could be blocked by co‐application of its antagonist, A779 (200 nM) but not losartan (1 μM). We conclude that non‐CA neurones and glia in RVLM are the primary targets for Ang1‐7 and its effect on [Ca 2+ ]i in non‐CA neurones is enhanced in SHR. F.G. was supported by The Royal Society. SK and JFRP are supported by BHF. 1. Souslova EA et al. BMC Biotechnol 7:37, 2007
Regulating CRISPR/Cas9 Function through Conditional Guide RNA Control (2020)

Abstract Conditional control of CRISPR/Cas9 has been developed by using a variety of different approaches, many focusing on manipulation of the Cas9 protein itself. However, more recent strategies for governing CRISPR/Cas9 function are based on guide RNA (gRNA) modifications. They include control of gRNAs by light, small molecules, proteins, and oligonucleotides. These designs have unique advantages compared to other approaches and have allowed precise regulation of gene editing and transcription. Here, we discuss strategies for conditional control of gRNA function and compare effectiveness of these methods.
Addressing Challenges to Enhance the Bioactives ofWithania somniferathrough Organ, Tissue, and Cell Culture Based Approaches (2017)

<i>Withania somnifera</i> is a highly valued medicinal plant in traditional home medicine and is known for a wide range of bioactivities. Its commercial cultivation is adversely affected by poor seed viability and germination. Infestation by various pests and pathogens, survival under unfavourable environmental conditions, narrow genetic base, and meager information regarding biosynthesis of secondary metabolites are some of the other existing challenges in the crop. Biotechnological interventions through organ, tissue, and cell culture provide promising options for addressing some of these issues. <i>In vitro</i> propagation facilitates conservation and sustainable utilization of the existing germplasms and broadening the genetic base. It would also provide means for efficient and rapid mass propagation of elite chemotypes and generating uniform plant material round the year for experimentation and industrial applications. The potential of <i>in vitro</i> cell/organ cultures for the production of therapeutically valuable compounds and their large-scale production in bioreactors has received significant attention in recent years. <i>In vitro</i> culture system further provides distinct advantage for studying various cellular and molecular processes leading to secondary metabolite accumulation and their regulation. Engineering plants through genetic transformation and development of hairy root culture system are powerful strategies for modulation of secondary metabolites. The present review highlights the developments and sketches current scenario in this field.
Effects of interactions on the relaxation processes in magnetic nanostructures (2016)

Controlling the relaxation of magnetization in magnetic nanostructures is key to optimizing magnetic storage device performance. This relaxation is governed by both intrinsic and extrinsic relaxation mechanisms and with the latter strongly dependent on the interactions between the nanostructures. In the present work we investigate laser induced magnetization dynamics in a broadband optical resonance type experiment revealing the role of interactions between nanostructures on the relaxation processes of granular magnetic structures. The results are corroborated by constructing a temperature dependent numerical micromagnetic model of magnetization dynamics based on the Landau-Lifshitz-Bloch equation. The model predicts a strong dependence of damping on the key material properties of coupled granular nanostructures in good agreement with the experimental data. We show that the intergranular, magnetostatic and exchange interactions provide a large extrinsic contribution to the damping. Finally we show that the mechanism can be attributed to an increase in spin-wave degeneracy with the ferromagnetic resonance mode as revealed by semianalytical spin-wave calculations.
Methods for modeling non-equilibrium degenerate statistics and quantum-confined scattering in 3D ensemble Monte Carlo transport simulations (2016)

Particle-based ensemble semi-classical Monte Carlo (MC) methods employ quantum corrections (QCs) to address quantum confinement and degenerate carrier populations to model tomorrow's ultra-scaled metal-oxide-semiconductor-field-effect-transistors. Here, we present the most complete treatment of quantum confinement and carrier degeneracy effects in a three-dimensional (3D) MC device simulator to date, and illustrate their significance through simulation of n-channel Si and III-V FinFETs. Original contributions include our treatment of far-from-equilibrium degenerate statistics and QC-based modeling of surface-roughness scattering, as well as considering quantum-confined phonon and ionized-impurity scattering in 3D. Typical MC simulations approximate degenerate carrier populations as Fermi distributions to model the Pauli-blocking (PB) of scattering to occupied final states. To allow for increasingly far-from-equilibrium non-Fermi carrier distributions in ultra-scaled and III-V devices, we instead generate the final-state occupation probabilities used for PB by sampling the local carrier populations as function of energy and energy valley. This process is aided by the use of fractional carriers or sub-carriers, which minimizes classical carrier-carrier scattering intrinsically incompatible with degenerate statistics. Quantum-confinement effects are addressed through quantum-correction potentials (QCPs) generated from coupled Schrödinger-Poisson solvers, as commonly done. However, we use these valley- and orientation-dependent QCPs not just to redistribute carriers in real space, or even among energy valleys, but also to calculate confinement-dependent phonon, ionized-impurity, and surface-roughness scattering rates. FinFET simulations are used to illustrate the contributions of each of these QCs. Collectively, these quantum effects can substantially reduce and even eliminate otherwise expected benefits of considered In0.53Ga0.47As FinFETs over otherwise identical Si FinFETs despite higher thermal velocities in In0.53Ga0.47As. It also may be possible to extend these basic uses of QCPs, however calculated, to still more computationally efficient drift-diffusion and hydrodynamic simulations, and the basic concepts even to compact device modeling.
Switching current of a Cooper pair transistor with tunable Josephson junctions (2002)

We investigate the switching current of a Cooper pair transistor with tunable Josephson energy. The junctions are fabricated in a superconducting quantum interference device (SQUID) geometry which allows for an in situ tunable effective Josephson energy by application of a magnetic field. We find a $2e$-periodic switching current versus gate charge. As the magnetic field is increased the switching current stays $2e$-periodic but the magnitude is suppressed. At a magnetic field of half a flux quantum through the SQUID's the switching current is minimum. We can theoretically model the experimental data by assuming a switching current which is proportional to the ideal critical current squarred. We show that such a dependence is expected in the limit where the effect of thermal fluctuations on the system is strong.
Blending Protein Separation and Peptide Analysis through Real-Time Proteolytic Digestion (2005)

Typical liquid- or gel-based protein separations require enzymatic digestion as an important first step in generating protein identifications. Traditional protocols involve long-term proteolytic digestion of the separated protein, often leading to sample loss and reduced sensitivity. Previously, we presented a rapid method of proteolytic digestion that showed excellent digestion of resistant and low concentrations of protein without requiring reduction and alkylation. Here, we demonstrate on-line, real-time tryptic digestion in conjunction with reversed-phase protein separation. The studies were aimed at optimizing pH and ionic strength and the size of the digestion element, to produce maximal protein digestion with minimal effects on chromatographic integrity. Upon establishing optimal conditions, the digestion element was attached downstream from a capillary C4 reversed-phase column. A four-protein mixture was processed through the combined system, and the resulting peptides were analyzed on-line by electrospray mass spectrometry. Extracted ion chromatograms for protein chromatography based on peptide elution were generated. These were shown to emulate ion chromatograms produced in a subsequent run without the digestion element, based on protein elution. The methodology will enable rapid and sensitive analysis of liquid-based protein separations using the power of bottom-up proteomics methodologies.
Poxvirus Vectored Cytomegalovirus Vaccine to Prevent Cytomegalovirus Viremia in Transplant Recipients (2020)

National Cancer Institute and Helocyte.
A New Tin-Free Source of Amidyl Radicals (2002)

[reaction: see text] The readily available N-(O-ethyl thiocarbonylsulfanyl)amides are powerful amidyl radical precursors that undergo 5-exo cyclization to give pyrrolidinone derivatives via a radical-chain reaction initiated by a small amount of lauroyl peroxide.
Simple modeling for conducted common-mode current in switching circuits (2002)

Common mode current strongly depends on stray capacitance of each circuit node, especially those with high dv/dt and di/dt. To build a simple model for conducted common mode current in switching circuit a computer software based on partial element equivalent circuit (PEEC) method is used to calculate the parasitic elements of the printed circuit board (PCB). Simulation results agree well with experimental results up to 10 MHz.
Robust and User Friendly 3D Re-Construction of Neutron Tomographic Images (2018)

Three-dimensional (3D) reconstruction of neutron tomographic projection images is an important tool for research on animal and plant tissues. Neutron scattering images contain impulsive noise caused by background cosmic gamma radiation that can significantly affect the reconstruction quality. Common de-noising methods are computationally efficient, but may also blur edges in the signal reducing the quality of reconstruction and may require careful parameter selection. Moreover, prior to reconstruction we must correct for rotation axis misalignment during data acquisition and suppress statistical noise due to variations in the neutron source. Currently many of these steps require manual intervention and parameter selection to maximize reconstruction quality. We have developed a more automatic algorithm which performs comparably to the semi-automatic state-of-the-art process.
Capture and analysis of prostate cancer circulating tumor cells (CTCS) using geometrically enhanced differential immunocapture (GEDI). (2011)

53 Background: EpCAM-based immunocapture of prostate cancer (PC) CTCs yields relatively low purity and specificity. We developed a geometrically enhanced differential immunocapture (GEDI) microfluidic device that incorporates flow dynamics and utilizes a mAb to prostate-specific membrane antigen (PSMA) to optimize isolation and analysis of CTCs from PC patients. Methods: GEDI microfluidic silicon chips, fabricated using standard photolithography techniques, were functionalized by chemical cross-linking ending with a neutravidin terminated surface to which anti-PSMA biotinylated-mAb J591 was bound. C4-2 (PSMA+) and PC-3 (PSMA-) cells were used for chip optimization. 1 mL of peripheral blood from PC patients was flowed (1mL/hour) over functionalized chips. Captured cells were washed with PBS × 30 min, fixed with 3.7% formaldehyde, immunofluorescently stained for DAPI, androgen receptor (AR), tubulin and EpCAM and analyzed by high resolution point-scanning confocal microscopy. PSMA+, DAPI+, and CD45- cells were manually scored. RNA was extracted from unfixed captured CTCs using lysis buffer flowed thru the chip. Results: ∼80% capture efficiency was achieved from 26 PSMA positive C4-2 cells spiked into 1 mL blood flowed through the GEDI chip. RNA extracted from 50 C4-2 cells in 1 mL blood flowed thru the chip detected a known AR point mutation by RT-PCR and Sanger sequencing. Immunofluorescence staining of PSMA+ cells captured on the chip detected changes in AR subcellular localization and microtubule structure following treatment with DHT or paclitaxel, respectively. 10 patients with metastatic PC were analyzed by CellSearch (range 0-201 cells/7.5 mL) and GEDI chip (range 35-&gt;1200 cells/mL) yielding a 7-&gt;350 fold enrichment using GEDI. Captured PC cells isolated from PC patient incubated in 50 nm paclitaxel (ex vivo) overnight demonstrated microtubule bundling, indicative of drug-target engagement. Conclusions: PSMA based GEDI microfluidic CTC capture is highly specific and sensitive in capturing PSMA positive PC CTCs; and allows detailed CTC analysis including protein expression and subcellular localization, mutational analysis and drug sensitivity assessment. [Table: see text]
Genetically engineered mice as animal models for NIDDM (1997)

Genetically engineered animals carrying defined alterations in their genome can represent invaluable tools for better understanding complex polygenic diseases such as non-insulin-dependent diabetes mellitus (NIDDM) at the molecular level. The structure or expression of a number of genes potentially involved in insulin action or pancreatic beta-cell function have recently been altered in the mouse using transgenic or gene-targeting approaches. The obtention of such mice is the first step towards the development of animal models carrying multiple gene defects which would be very useful in NIDDM research.
Glare and shadow reduction for desktop digital camera capture systems (2013)

The quality of images of objects with significant 3D structure, captured at close range under a flash, may be substantially degraded by glare and shadow regions. In this paper, we introduce an imaging system and corresponding algorithm to address this situation. The imaging system captures three frames of the stationary scene using a single camera in a fixed position, but an illumination source in three different positions, one for each frame. The algorithm includes two processes: shadow detection and image fusion. Through shadow detection, we can locate the area of shadows. After getting the shadow maps, we generate a more complete final image by image fusion. Our experimental results show that in most cases, the shadow and glare are markedly reduced.
Three-Step Room-Temperature Cleaning of Bare Silicon Surface for Radical-Reaction-Based Semiconductor Manufacturing (2008)

In this study, a cleaning method for pregate cleaning which can suppress the generation of the microroughness of silicon-wafer surfaces as well as remove various contaminations such as metallic impurities, organic materials, and particles has been investigated. Functional waters such as ozonized ultrapure water (-UPW), -added UPW (-UPW), and low-concentration HF and hydrogen peroxide solution have been used in this cleaning method at room temperature. The cleaning-process flow is as follows: (i) -UPW cleaning, (ii) diluted HF and mixture including surfactant molecules (FPMS) cleaning with megasonic, and (iii) 30%-isopropyl alcohol/UPW rinsing, i.e., realization of three-step cleaning. After the pregate cleaning, silicon substrates are set into the radical-reaction gate-insulator film-formation process using microwave-excited, high-density plasma equipment, where or ion bombardment onto the substrate surface has been introduced to eliminate absorbed surfactant molecules as well as hydrogen termination, before starting oxygen radical oxidation or radical nitridation . This advanced, three-step room-temperature cleaning is promising for future semiconductor manufacturing in conjunction with the newly developed radical-reaction-based semiconductor manufacturing.
Conformal hydrophobic coatings prepared using atomic layer deposition seed layers and non-chlorinated hydrophobic precursors (2005)

Ultrathin and conformal films deposited using atomic layer deposition (ALD) can enhance the reliability and performance of micro-electro-mechanical systems (MEMS) devices. Al2O3 ALD films are particularly useful because the Al2O3 ALD surface chemistry is very favorable and amenable to growth on a wide variety of substrates. Al2O3 ALD can be utilized to deposit robust and reliable hydrophobic coatings. A thin Al2O3 ALD film is deposited and is used as a seed layer to prepare and optimize the MEMS surface for the subsequent attachment of the hydrophobic precursors. Once the Al2O3-coated surface is prepared, non-chlorinated alkylsilanes are chemically bonded to the surface hydroxyl groups on the ALD seed layer. The film growth was monitored using an in situ quartz crystal microbalance, Fourier transform infrared spectroscopy and ex situ Auger electron spectroscopy. This deposition technique results in a dense and conformal hydrophobic film with a water contact angle of 108 ± 2°. When annealed in air to 300 °C for 10 min, the hydrophobic ALD films remained hydrophobic with a contact angle greater than 90°. Using MEMS cantilever beam arrays, hydrophobic ALD-coated beams were determined to have an adhesion energy of 0.11 ± 0.03 mJ m−2 at 100% humidity as compared with an adhesion energy of 12 ± 1 mJ m−2 for the same beams without any coating.
<title>Micro-optics in VCSEL and solid state laser resonators</title> (1998)

Several unconventional laser resonators are described, and their application to various laser systems is explored. Spatial mode control of vertical cavity surface emitting lasers is enhanced by two spatial filtering methods. The first employs a GRIN lens with a patterned mirror designed to reflect power only from desired modes. The angular selectivity of a Fabry-Perot etalon is used in the second system to improve spatial modal discrimination. Diffractive optical elements are used with a solid-state laser for beam shaping and aberration correction. An analysis of the effects of fabrication errors shows that higher-order diffraction terms and phase errors can result in distorted modes. However, proper cavity design can help to reduce these effects and insure proper mode shape.© (1998) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
A Vacuum-Compatible Air Bearing: Design Analysis and Optimization (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Supplementary Table S1 from A Small-Molecule Modulator of the Tumor-Suppressor miR34a Inhibits the Growth of Hepatocellular Carcinoma (2023)

&lt;p&gt;Supplementary Table S1. Primer sequences used for qRT-PCR.&lt;/p&gt;
A monolithically-integrated optical transmitter and receiver in a zero-change 45nm SOI process (2014)

An optical transmitter and receiver with monolithically-integrated photonic devices and circuits are demonstrated together for the first time in a commercial 45nm SOI process, without any process changes. The transmitter features an interleaved-junction carrier-depletion ring modulator and operates at 3.5Gb/s with an 8dB extinction ratio and combined circuit and device energy cost of 70fJ/bit. The optical receiver connects to an integrated SiGe detector designed for 1180nm wavelength and performs at 2.5Gb/s with 15μA sensitivity and energy cost of 220fJ/bit.
Synthetic turbulence using artificial boundary layers (2009)

Turbulent vortices in fluid flows are crucial for a visually interesting appearance. Although there has been a significant amount of work on turbulence in graphics recently, these algorithms rely on the underlying simulation to resolve the flow around objects. We build upon work from classical fluid mechanics to design an algorithm that allows us to accurately precompute the turbulence being generated around an object immersed in a flow. This is made possible by modeling turbulence formation based on an averaged flow field, and relying on universal laws describing the flow near a wall. We precompute the confined vorticity in the boundary layer around an object, and simulate the boundary layer separation during a fluid simulation. Then, a turbulence model is used to identify areas where this separated layer will transition into actual turbulence. We sample these regions with vortex particles, and simulate the further dynamics of the vortices based on these particles. We will show how our method complements previous work on synthetic turbulence, and yields physically plausible results. In addition, we demonstrate that our method can efficiently compute turbulent flows around a variety of objects including cars, whisks, as well as boulders in a river flow. We can even apply our model to precomputed static flow fields, yielding turbulent dynamics without a costly simulation.