gebhart/patrepeval huggingface dataset:
Gold nanostructure microelectrode arrays for in vitro recording and stimulation from neuronal networks (2019)

An ideal microelectrode array (MEA) design should include materials and structures which exhibit biocompatibility, low electrode polarization, low impedance/noise, and structural durability. Here, the fabrication of MEAs with indium tin oxide (ITO) electrodes deposited with self-similar gold nanostructures (GNS) is described. We show that fern leaf fractal-like GNS deposited on ITO electrodes are conducive for neural cell attachment and viability while reducing the interfacial impedance more than two orders of magnitude at low frequencies (100-1000 Hz) versus bare ITO. GNS MEAs, with low interfacial impedance, allowed the detection of extracellular action potentials with excellent signal-to-noise ratios (SNR, 20.26 ± 2.14). Additionally, the modified electrodes demonstrated electrochemical and mechanical stability over 29 d in vitro.
Interactive Ray Tracing of Arbitrary Implicits with SIMD Interval Arithmetic (2007)

We present a practical and efficient algorithm for interactively ray tracing arbitrary implicit surfaces. We use interval arithmetic (IA) both for robust root computation and guaranteed detection of topological features. In conjunction with ray tracing, this allows for rendering literally any programmable implicit function simply from its definition. Our method requires neither special hardware, nor preprocessing or storage of any data structure. Efficiency is achieved through SIMD optimization of both the interval arithmetic computation and coherent ray traversal algorithm, delivering interactive results even for complex implicit functions.
The New "Great Work" (1998)

Retroviruses . John M. Coffin, Stephen H. Hughes, and Harold E. Varmus, Eds. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1998. 859 pp. $180. ISBN 0-87969-497-1. A benchmark reference written for the research community, with individual contributions intended to be independent and accessible in any order. Early chapters provide resolutely molecular descriptions of retrovirus structure, function, and replication; later ones consider pathogenesis, immune responses, and other aspects of the relationships between retroviruses and their hosts.
Efficient Human Germ Cell Specification from Stem Cells via Combinatorial Expression of Transcription Factors (2022)

Abstract Germ cells are the vehicle of human reproduction, arising early in embryonic development and developing throughout adult life until menopause onset in women. Primordial germ cells are the common precursors of germline cells in both sexes, undergoing sexual specification into oogonia or gonocytes which further develop into oocytes or spermatocytes during development. Methods for recapitulation of primordial germ cell and oogonia formation have been developed extensively in recent decades, but fundamental technical limitations in their methodologies, throughput, and yield limit their utilization. Recently, transcription factor (TF)-based methods for human primordial germ cell-like cell (hPGCLC) formation, mouse meiotic entry, and mouse oocyte maturation have demonstrated the feasibility of gene overexpression screening in identifying potent regulators of germ cell development. Here we screened 47 folliculogenesis-regulating TFs for their role in hPGCLC and oogonia formation, identifying DLX5, HHEX , and FIGLA whose individual overexpression enhances hPGCLC formation from hiPSCs. Additionally, we identify a set of three TFs, ZNF281, LHX8 , and SOHLH1 , whose combinatorial overexpression drives direct oogonia-like formation from hiPSCs in a four-day, feeder-free monolayer culture condition with additional feeder-free culture capabilities post-isolation. We characterize these TF-based germ cells via gene and protein expression analyses, and demonstrate their broad similarity to in vivo germ cells. Together, these results identify novel regulators of human germ cell development and establish new TF-based tools for human in vitro oogenesis research.
Study of upstream electromigration bimodality and its improvement in Cu low-k interconnects (2010)

The bimodality of upstream electromigration (EM) failures in the dual damascene structure of 45 nm Cu interconnection process with low-k material is investigated, and the improvement is demonstrated. Two major early failure modes with voids forming in via or at the chamfer of via-trench transition area are revealed and attributed to liner process weakness at the respective locations, which can be reduced and eliminated with optimized via and chamfer aspect ratios (ARs) defined by the dual damascene profile. Dielectric thickness, trench etch depth, via critical dimension (CD), chamfer of via-trench transition profile etc. can serve as the tuning factors for the upstream EM bimodality improvement. However, a balance between EM, time-dependent dielectric breakdown (TDDB) and resistance-capacitance (RC) performance need to be achieved.
ChemInform Abstract: Nonpeptide Arginine Vasopressin Antagonists for Both V1A and V2 Receptors: Synthesis and Pharmacological Properties of 4′‐(1,4,5,6‐Tetrahydroimidazo[4,5‐d] [1]benzoazepine‐6‐carbonyl)benzanilide Derivatives and 4′‐(5,6‐Dihydro‐4H‐thiazolo[5,4‐d] [1]benzoazepine‐6‐carbonyl)benzanilide Derivatives. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Space charge assisted evaluation method of the elasto-optic coefficients of electrooptic crystals (2020)

We developed a novel technique to evaluate the elasto-optic coefficients of electrooptic (EO) single crystals. Notably, this method uses the deformation of the crystal generated by the space charge formed by the electrons injected into the crystal. For the first time, to our knowledge, the coefficient p 12 was quantified separately from p 11 for KTa 1- x Nb x O 3 (KTN) with this method. Both the coefficients exhibit significant temperature dependence caused by polarization fluctuations. Genuine EO coefficients g g 11 and g g 12 were calculated by excluding photoelastic contributions from the nominal EO coefficients. g g 12 was negligibly small compared to the nominal coefficient before the exclusion. This indicates that the conventional nominal coefficient g n 12 is actually composed of strain-induced components but does not reflect the pure effect.
Towards a noise prediction model for in vivo neural recording (2012)

The signal-to-noise ratio of in vivo extracellular neural recordings with microelectrodes is influenced by many factors including the impedance of the electrode-tissue interface, the noise of the recording equipment and biological background noise from distant neurons. In this work we study the different noise sources affecting the quality of neural signals. We propose a simplified noise model as an analytical tool to predict the noise of an electrode given its geometrical dimensions and impedance characteristics. With this tool we are able to quantify different noise sources, which is important to determine realistic noise specifications for the design of electronic neural recording interfaces.
EFFICIENT SYNTHESIS OF THE 5-HT2C RECEPTOR AGONIST, ORG 37684 (2001)

Abstract An efficient synthesis of the 5-HT2C receptor agonist Org 37684 is presented. The synthesis utilises the regioselective demethylation of an arylether as the key step. ACKNOWLEDGMENTS We thank Dr. Ken Heatherington, Dr. Peter Clayton and Dr. Graeme Harden for performing the analysis on compounds 4 to 12. We also thank Dr. Ian Cliffe for helpful suggestions whilst preparing this manuscript and acknowledge the work of Mrs. Lyn Heaney in typing this paper.
Role of protein kinase Cδ in paraquat‐induced glial cell death (2008)

Paraquat (1,1'-dimethyl-4,4'-bipyridinium) is structurally similar to the neurotoxin 1-methyl-4-phenyl-4-phenylpyridium ion (MPP+), the active metabolite of the parkinsonism-inducing agent 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), which can induce the parkinsonism property in rodents, nonhuman primates, and human. In contrast to the neurotoxic effects of paraquat, little is known about its effects on glial cells. Here, we examined the mechanisms of paraquat toxicity in glial cells in culture. Paraquat treatment also reduced the viability of C6 glial cells in primary astrocyte cultures, and cell death was mostly apoptotic in nature. PKCdelta played a central role in the paraquat-induced glial cell death: (1) the PKCdelta-specific inhibitor rottlerin blocked paraquat-induced glial cell death; (2) paraquat induced tyrosine and threonine phosphorylation of PKCdelta; and (3) transfection of the dominant-negative mutant of PKCdelta attenuated paraquat toxicity. PKCdelta was also involved in the generation of reactive oxygen species (ROS), which mediated the paraquat toxicity. The nicotinamide adenine dinucleotide phosphate (reduced form) oxidase (NADPH oxidase) inhibitor diphenyleneiodonium blocked the paraquat-induced ROS production and subsequent cell death, indicating the involvement of NADPH oxidase in the cytotoxic action of paraquat in glia. PKCdelta was also important in glial cell death induced by MPP+ but not in that induced by rotenone. Last, Rac1 appeared to antagonize paraquat toxicity in glia. These results indicate a gliotoxic effect of paraquat and an opposing role of PKCdelta and Rac1 in paraquat-induced glial cell death.
Chemical Space Mimicry for Drug Discovery (2017)

We describe a new library generation method, Machine-based Identification of Molecules Inside Characterized Space (MIMICS), that generates sets of molecules inspired by a text-based input. MIMICS-generated libraries were found to preserve distributions of properties while simultaneously increasing structural diversity. Newly identified MIMICS-generated compounds were found to be bioactive as inhibitors of specific components of the unfolded protein response (UPR) and the VEGFR2 pathway in cell-based assays, thus confirming the applicability of this methodology toward drug design applications. Wider application of MIMICS could facilitate the efficient utilization of chemical space.
On Continuing DNN Accelerator Architecture Scaling Using Tightly Coupled Compute-on-Memory 3-D ICs (2023)

This work identifies the architectural and design scaling limits of 2-D flexible interconnect deep neural network (DNN) accelerators and addresses them with 3-D ICs. We demonstrate how scaling up a baseline 2-D accelerator in the <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$X/Y$ </tex-math></inline-formula> dimension fails and how vertical stacking effectively overcomes the failure. We designed multitier accelerators that are <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1.67\times $ </tex-math></inline-formula> faster than the 2-D design. Using our 3-D architecture and circuit codesign methodology, we improve throughput, energy efficiency, and area efficiency by up to <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$5\times $ </tex-math></inline-formula> , <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1.2\times $ </tex-math></inline-formula> , and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$3.9\times $ </tex-math></inline-formula> , respectively, over 2-D counterparts. The IR-drop in our 3-D designs is within 10.7% of VDD, and the temperature variation is within 12 °C.
Reproducibility of Cold Uptake Radiomics in 99m Tc-Sestamibi SPECT Imaging of Renal Cell Carcinoma (2017)

<sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">99m</sup> Tc-Sestamibi SPECT/CT imaging of renal cell carcinoma (RCC) has recently shown significant promise to distinguish benign oncocytomas from malignant RCC, where the former appears as high uptake in SPECT images and the latter as cold uptake. We aim towards radiomics analysis of cold uptake in SPECT images for another significant yet more daunting task of discriminating between RCC subtypes. The first step we pursue in the present work is feature selection by assessing the reproducibility of radiomic features. <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">99m</sup> Tc-Sestamibi SPECT/CT images of 50 patients with renal mass, plus a contrast-enhanced CT or MRI, were used by a trained radiologist to segment the region of interest (ROI) on the SPECT image. The impact of segmentation on reproducibility was studied by generating three ROIs via removing one voxel-layer from, or appending 1 and 2 voxel-layers to the manual ROIs (ROI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> , ROI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sub> , ROI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+1</sub> , ROI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+2</sub> ). Images were then uniformly quantized with eight grey-levels (GL) (2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> -2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sup> ). A total of 363 radiomic features, verified within the Image Biomarker Standardization Initiative, were generated for all 50 patients/four ROIs/eight GLs. Voxel intensity in SPECT images is the number of counts, which is a patient-dependent non-normalized quantity. Thus, (i) fixed number of bin quantization must be chosen over fixed bin-width, and (ii) non-normalized statistical features should be excluded. The intra-class correlation (ICC) type C-1 calculated for all features between (a) all four ROIs and (b) between all except ROI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sub> showed 204 features with (a) ICC>0.7 and (b) ICC>0.85, respectively. However, a subset of 204 features with emphasis on high GLs across higher-order feature classes should be further excluded due to the scarce presence of voxels with high intensities that can appear due to mis-segmentation. Moreover, reproducibility analysis of quantization using Spearman rank-correlation showed GLs below 32 should be avoided due to high variation. The resulting features and settings are recommended for further investigation of predictive value.
Microfluidic Technology for Biofuels Applications (2009)

We are developing a suite of microfluidic technologies to address the throughput limitations of conventional approaches for biomass analysis.We have developed a microfluidic electrophoretic assay for rapid (< 1 min) and multiplexed analysis of lignocellulosic biomass samples.To address the low throughput of conventional enzyme screening approaches, we have developed a rapid (1-2 hr) integrated microscale platform for cell-free expression and activity analysis of thermophilic cellulases.We have also developed a high-throughput approach for saccharification studies of ionic-liquid pretreated solid biomass.Currently, we are integrating the above technologies to develop optimized cellulase cocktails for cost-effective production of biofuels from lignocellulosic feedstocks.
ChemInform Abstract: Synthesis, Biological Activity, and Molecular Modeling of Ribose‐Modified Deoxyadenosine Bisphosphate Analogues as P2Y1 Receptor Ligands. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Capacitor Voltage Ripple Reduction Methods of Modular Multilevel Converter under Unbalanced Fault Conditions: A Comparison (2018)

Modular Multilevel Converter (MMC) is one of the most promising converter topology in medium/high-voltage applications. Reduction of capacitor voltage ripple during unbalanced grid conditions is very important for stable operation. A comparison of capacitor voltage ripple suppression methods under unbalanced conditions is presented in this paper. Three methods are explained and compared in simulation: circulating current specific sequence elimination method (CCSSE), instantaneous circulating current optimization method (ICCO), and arm current control method (ACC). The simulation model of these three methods are achieved in PLECS, the results show that the ICCO has best submodules capacitors voltage ripple reduction effect, but it will increase the peak arm current and DC line current ripple. CCSSE and ACC methods balance three phase energy in different perspectives, but the essence of these two methods are same.
Azobenzene-Containing Polyamic Acid with Excellent Langmuir−Blodgett−Kuhn Film Formation Behavior Suitable for All-Optical Switching (2005)

To generate command surfaces for all-optical switching, highly ordered polymeric Langmuir-Blodgett-Kuhn (LBK) multilayers were fabricated onto silicon substrates and gold-coated optical glass slides from novel azobenzene-bearing polyamic acid systems. Pronounced Bragg peaks and well-defined Kiessig fringes observed in the X-ray reflectivity measurement for samples on silicon substrates indicate that these films possess a regularly repeated Y-type LBK multilayer structure and ultrasmooth surfaces. Fourier transform infrared (FT-IR) spectra taken by grazing incidence reflection suggest specific orientations of the functional groups in the layers. The excellent film-forming properties of the polyamic acid allow for a smooth buildup of several hundreds of layers of the LBK films onto gold-coated glass slides, which in turn allows for determining the geometrical thickness and the anisotropic refractive indices of the films by using optical waveguide spectroscopy. Interestingly, the probe laser beam induced a distinct fluorescence signal from the films, which remained even after the film underwent a thermal imidization process at 160 degrees C for 8 h in vacuo. LBK films fabricated from these compounds can be successfully applied for all-optically switching the alignment of liquid crystals by irradiation with light of different wavelengths.
Marginal zone B-cell lymphoma of the conjunctiva (2010)

Lymphomas are the most common orbital malignancies, marginal zone B-cell lymphoma being the most common histotype. One quarter of these lymphomas exhibit conjunctival involvement, which is almost exclusively observed in indolent lymphomas (96% of conjunctival lymphomas). Primary conjunctival marginal zone B-cell lymphoma exhibits interesting and peculiar features, with some molecular, biological, clinical and prognostic differences from the rest of the ocular adnexal lymphomas. Recent studies demonstrate that chromosomal abnormalities, autoimmune disorders and infectious agents are variably associated with the development and behavior of this lymphoma. Conjunctival lymphomas are rarely lethal tumors and, in selected cases, may be managed without anti-tumor treatment. In other cases, conjunctival lymphomas cause symptoms that require immediate treatment. To date, no guidelines for the management of patients with conjunctival lymphoma exist. Surgical resection, radiotherapy and chemotherapy are the most common approaches to these malignancies, but the use of systemic immunotherapy, bacteria-eradicating antibiotic therapy and local treatments, such as intralesional injections of interferon or rituximab and eyedrops of cytostatics, is progressively growing.
Low tidal volume ventilation is associated with reduced mortality in HIV-infected patients with acute lung injury (2008)

Lower tidal volume ventilation is independently associated with reduced mortality in HIV-infected patients with acute lung injury and respiratory failure.
All-optical time domain 160 Gb/s ADD/DROP based on pump depletion and nonlinearities in a single PPLN waveguide (2009)

All-optical time-domain 160Gb/s add/drop scheme based on PPLN waveguide is demonstrated which exploits pump depletion in addition to sum and difference frequency generation. Less than 3.5dB penalty on dropped, survived and added channels is obtained.
Supplementary Figure 5 from Cancer-Associated Fibroblasts Expressing CXCL14 Rely upon NOS1-Derived Nitric Oxide Signaling for Their Tumor-Supporting Properties (2023)

&lt;p&gt;PDF file - 59KB, NO and glutathione protect CXCL14-fibroblasts.&lt;/p&gt;
Extrusion Shear Printing: Automatic Transformation of Membrane‐Type Electronic Devices into Complex 3D Structures via Extrusion Shear Printing and Thermal Relaxation of Acrylonitrile–Butadiene–Styrene Frameworks (Adv. Funct. Mater. 5/2020) (2020)

In article number 1907384, Heung Cho Ko and co-workers demonstrate a novel technology for automatic shape transformation of electronic devices from 2D to 3D via extrusion shear printing and thermal relaxation of acrylonitrile–butadiene–styrene (ABS) frameworks. The transition from the glassy to rubbery state and reflow of the ABS polymer chains provide mechanical and electrical stability of electronic devices during transformation to develop complex 3D forms.
Non‐Viral CRISPR/Cas Gene Editing In Vitro and In Vivo Enabled by Synthetic Nanoparticle Co‐Delivery of Cas9 mRNA and sgRNA (2016)

Abstract CRISPR/Cas is a revolutionary gene editing technology with wide‐ranging utility. The safe, non‐viral delivery of CRISPR/Cas components would greatly improve future therapeutic utility. We report the synthesis and development of zwitterionic amino lipids (ZALs) that are uniquely able to (co)deliver long RNAs including Cas9 mRNA and sgRNAs. ZAL nanoparticle (ZNP) delivery of low sgRNA doses (15 n m ) reduces protein expression by &gt;90 % in cells. In contrast to transient therapies (such as RNAi), we show that ZNP delivery of sgRNA enables permanent DNA editing with an indefinitely sustained 95 % decrease in protein expression. ZNP delivery of mRNA results in high protein expression at low doses in vitro (&lt;600 pM) and in vivo (1 mg kg −1 ). Intravenous co‐delivery of Cas9 mRNA and sgLoxP induced expression of floxed tdTomato in the liver, kidneys, and lungs of engineered mice. ZNPs provide a chemical guide for rational design of long RNA carriers, and represent a promising step towards improving the safety and utility of gene editing.