gebhart/patrepeval huggingface dataset:
K-Ras Promotes Growth Transformation and Invasion of Immortalized Human Pancreatic Cells by Raf and Phosphatidylinositol 3-Kinase Signaling (2007)

Mutational activation of the K-Ras oncogene is well established as a key genetic step in the development and growth of pancreatic adenocarcinomas. However, the mechanism by which aberrant Ras signaling promotes uncontrolled pancreatic tumor cell growth remains to be fully elucidated. The recent use of primary human cells to study Ras-mediated oncogenesis provides important model cell systems to dissect this mechanism. We have used a model of telomerase-immortalized human pancreatic duct-derived cells (E6/E7/st) to study mechanisms of Ras growth transformation. First, we found that human papillomavirus E6 and E7 oncogenes, which block the function of the p53 and Rb tumor suppressors, respectively, and SV40 small t antigen were required to allow mutant K-Ras(12D) growth transformation. Second, K-Ras(12D) caused growth transformation in vitro, including enhanced growth rate and loss of density dependency for growth, anchorage independence, and invasion through reconstituted basement membrane proteins, and tumorigenic transformation in vivo. Third, we determined that the Raf, phosphatidylinositol 3-kinase (PI3K), and Ral guanine nucleotide exchange factor effector pathways were activated, although extracellular signal-regulated kinase (ERK) activity was not up-regulated persistently. Finally, pharmacologic inhibition of Raf/mitogen-activated protein kinase/ERK and PI3K signaling impaired K-Ras-induced anchorage-independent growth and invasion. In summary, our studies established, characterized, and validated E6/E7/st cells for the study of Ras-induced oncogenesis.
A Practical and Scalable Method for Manufacturing JAK Inhibitor ASP3627 (2019)

ASP3627 (1) is a potent Janus kinase inhibitor discovered and developed by Astellas Pharma Inc. Here, we report the development of a practical and scalable method for manufacturing ASP3627 featuring a six-reaction telescoping process consisting of DIBAL reduction, hydrolysis, Wittig reaction, cyclization, and a two-step sequence to remove the SEM group. In addition, a simple palladium removal procedure using l-cysteine is described. This method was used to successfully perform the first multikilogram synthesis of ASP3627, producing 30 kg with high purity in excellent overall yield.
Chemoinformatics and Artificial Intelligence Colloquium: Progress and Challenges to Develop Bioactive Compounds (2022)

We report the main conclusions of the first Chemoinformatics and Artificial Intelligence Colloquium, Mexico City, June 15-17, 2022. Fifteen lectures were presented during a virtual public event with speakers from industry, academia, and non-for-profit organizations. Twelve hundred and ninety students and academics from more than 60 countries. During the meeting, applications, challenges, and opportunities in drug discovery, de novo drug design, ADME-Tox (absorption, distribution, metabolism, excretion and toxicity) property predictions, organic chemistry, peptides, and antibiotic resistance were discussed. The program along with the recordings of all sessions are freely available at https://www.difacquim.com/english/events/2022-colloquium/
Interference cancellation architecture for full-duplex system with GFDM signaling (2016)

This paper concerns the design of in-band full-duplex transceivers that employ generalized frequency-division multiplexing (GFDM). The composite of these two timely concepts is a promising candidate technology for emerging 5G systems since the GFDM waveform is advantageous to flexible spectrum use whereas full-duplex operation can significantly improve spectral efficiency. The main technical challenge in full-duplex transceivers at large is to mitigate their inherent self-interference due to simultaneous transmission and reception. In the case of GFDM that is non-orthogonal by design, interference cancellation becomes even more challenging since the interfering signal is subject to intricate coupling between all subchannels. Thus, we first develop a sophisticated frequency-domain cancellation architecture for removing all the self-interference components. Furthermore, by exploiting the specific structure of the interference pattern, we further modify the scheme into one that allows flexible control and reduction of computational complexity. Finally, our simulation results illustrate the trade-off between cancellation performance and system complexity, giving insights into the implementation of interference cancellation when we aim at achieving both low error rate and low complexity.
Improvement of the I2t capability for xEV active short circuit protection by combination of RC-IGBT and Leadframe technologies (2018)

This paper describes the investigation results of I <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> t capability for IGBT module used for xEV powertrain application. I <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> t experiments and simulation evaluations are done by RC-IGBT or the conventional FWD with bondwires structure. As a result, RC-IGBT(wire) has 80% higher I <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> t capability compared with FWD in the case of comparable diode active area. In addition, RC-IGBT(leadframe) and RC-IGBT(bondwires) are also evaluated by experimental and simulational approaches. As a result, RC-IGBT(leadframe) has additional 33% increase in I <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> t compared to RC-IGBT(wire). Over all, I <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> t of RC-IGBT (leadframe) is 2.4 times higher than that of FWD (bondwires).
Cardiovascular magnetic resonance imaging in suspected cardiac tumour: a multicentre outcomes study (2021)

In patients with suspected cardiac tumour, CMR has high diagnostic accuracy. Patients with CMR diagnoses of no mass, pseudomass, and benign tumour have similar long-term mortality. The CMR diagnosis is a powerful independent predictor of mortality incremental to clinical risk factors.
Novel Solid Redox Polymerization Electrodes: Electrochemical Properties (1991)

The generic redox reaction of a class of linear sulfur‐containing redox polymerization electrodes can be described as
Data from Cyclin-Dependent Kinase 5 Activity Controls Cell Motility and Metastatic Potential of Prostate Cancer Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;We show here that cyclin-dependent kinase 5 (CDK5), a known regulator of migration in neuronal development, plays an important role in prostate cancer motility and metastasis. P35, an activator of CDK5 that is indicative of its activity, is expressed in a panel of human and rat prostate cancer cell lines, and is also expressed in 87.5% of the human metastatic prostate cancers we examined. Blocking of CDK5 activity with a dominant-negative CDK5 construct, small interfering RNA, or roscovitine resulted in changes in the microtubule cytoskeleton, loss of cellular polarity, and loss of motility. Expression of a dominant-negative CDK5 in the highly metastatic Dunning AT6.3 prostate cancer cell line also greatly impaired invasive capacity. CDK5 activity was important for spontaneous metastasis &lt;i&gt;in vivo&lt;/i&gt;; xenografts of AT6.3 cells expressing dominant-negative CDK5 had less than one-fourth the number of lung metastases exhibited by AT6.3 cells expressing the empty vector. These results show that CDK5 activity controls cell motility and metastatic potential in prostate cancer. (Cancer Res 2006; 66(15): 7509-15) (Cancer Res 2006; 66(15): 7509-15)&lt;/p&gt;&lt;/div&gt;
A deep convolutional neural network approach for astrocyte detection (2017)

Abstract Astrocytes are involved in brain pathologies such as trauma or stroke, neurodegenerative disorders like Alzheimer’s and Parkinson’s disease, chronic pain, and many others. Determining cell density and timing of morphological and biochemical changes is important for a proper understanding of the role of astrocytes in physiological and pathological conditions. One of the most important of such analyses is astrocytes count within a complex tissue environment in microscopy images. The most widely used approaches for the quantification of microscopy images data are either manual stereological cell counting or semi-automatic segmentation techniques. Detecting astrocytes automatically is a highly challenging computational task, for which we currently lack efficient image analysis tools. In this study, we developed a fast and fully automated software that assesses the number of astrocytes using Deep Convolutional Neural Networks (DCNN). The method highly outperforms state-of-the-art image analysis and machine learning methods and provides detection accuracy and precision comparable to that of human experts. Additionally, the runtime of cell detection is significantly less than other three analyzed computational methods, and it is faster than human observers by orders of magnitude. We applied DCNN-based method to examine the number of astrocytes in different brain regions of rats with opioid-induced hyperalgesia/tolerance (OIH/OIT) as morphine tolerance is believed to activate glial cells in the brain. We observed strong positive correlation between manual cell detection and DCNN-based analysis method for counting astrocytes in the brains of experimental animals.
Progress Towards Control of a Mycobacterial Pathogen, <i>Mycobacterium aviumsubsp</i>. <i>paratuberculosis</i>, the Causative Agent of Johne’s Disease in Cattle and Humans (2018)

Since the discovery that Mycobacterium aviumsubsp. paratuberculosis(Map) is the causative agent of Johne’s disease (JD) in cattle at the end of the nineteenth century, movement of livestock latently infected with Map has led to the spread of JD throughout the world. A new form of enteritis with clinical features of JD in cattle appeared in humans concurrent with the appearance of Map as a disease problem in livestock. The demonstration that Map is a zoonotic pathogen and the causative agent of the new form of enteritis in humans, however, wasn’t recognized until late in the twentieth century when methods were developed to detect the presence Map in tissues from patients with the new form of clinical enteritis. The objective of this short review is to provide a brief history explaining how Map has become a major disease problem in livestock and humans and then provide a review of the progress that has been made in treating patients with an enteritis caused by Map and the strategies underway to develop a vaccine to control infection in livestock.
SARS-CoV-2-specific peripheral T follicular helper cells correlate with neutralizing antibodies and increase during convalescence (2020)

T-cell immunity is likely to play a role in protection against SARS-CoV-2 by helping generate neutralizing antibodies. We longitudinally studied CD4 T-cell responses to the M, N, and S structural proteins of SARS-CoV-2 in 21 convalescent individuals. Within the first two months following symptom onset, a majority of individuals (81%) mount at least one CD4 T-cell response, and 48% of individuals mount detectable SARS-CoV-2-specific peripheral T follicular helper cells (pTfh, defined as CXCR5+PD1+ CD4 T cells). SARS-CoV-2-specific pTfh responses across all three protein specificities correlate with antibody neutralization with the strongest correlation observed for S protein-specific responses. When examined over time, pTfh responses increase in frequency and magnitude in convalescence, and robust responses with magnitudes greater than 5% were detected only at the second convalescent visit, an average of 38 days post-symptom onset. These data deepen our understanding of antigen-specific pTfh responses in SARS-CoV-2 infection, suggesting that M and N protein-specific pTfh may also assist in the development of neutralizing antibodies and that pTfh response formation may be delayed in SARS-CoV-2 infection.
A rate control scheme for H.264/AVC CBR transmission (2007)

In many applications, video sequences must be transmitted constant bit rate channels (CBR). Therefore, rate control has to be used to regulate the variable bit rate of coded stream. In this paper, we propose an effective bit-rate control algorithm in H.264/AVC for CBR transmission. Our algorithm jointly decides mode and quantization using rate distortion optimization (RDO) technique. And to reduce computational complexity, the proposed algorithm uses modified version of rate and distortion model calculated from the histogram of DCT coefficients. Since the proposed algorithm induces the rate and distortion model from the current macroblock instead of the previous coded frame or macroblock, it can effectively prevents the fluctuation of the output bits especially when scene change occurs, while keeping the quality in same level. And it can not only achieve the improvement of the rate control but also meet the target bit rate more accurately.
Dopant Activation Depth Profiling for Highly Doped Si:P By Scanning Spreading Resistance Microscopy (SSRM) and Differential Hall Effect Metrology (DHEM) (2022)

Heavily P-doped epitaxial Si layers were deposited over counter-doped Si substrates. P dopant activation was studied as a function of various processes used to prepare the samples. For electrical characterization, depth profiles of carrier concentration values were obtained using SSRM and DHEM techniques. Samples studied included an in-situ doped sample, a sample that was spike annealed at 1000ºC, a sample that was first coated with a Ti/TiN stack and then annealed for silicide formation before the Ti/TiN stack was removed, and a sample that was spike annealed + coated with Ti/TiN + annealed for silicide formation before the removal of the Ti/TiN stack. DHEM analysis showed substantial increase in dopant activation for spike annealed samples. SSRM results suggested lower carrier concentration values and more limited degree of activation. Formation of Ti/TiN contacts and its removal did not affect the carrier concentration values for the as-deposited epi layer. Sample that was first spike annealed and then subjected to contact formation process displaced a reduction in carrier concentration values as measured by DHEM.
Generalized Rectifier Wavelet Covariance Models For Texture Synthesis (2022)

State-of-the-art maximum entropy models for texture synthesis are built from statistics relying on image representations defined by convolutional neural networks (CNN). Such representations capture rich structures in texture images, outperforming wavelet-based representations in this regard. However, conversely to neural networks, wavelets offer meaningful representations, as they are known to detect structures at multiple scales (e.g. edges) in images. In this work, we propose a family of statistics built upon non-linear wavelet based representations, that can be viewed as a particular instance of a one-layer CNN, using a generalized rectifier non-linearity. These statistics significantly improve the visual quality of previous classical wavelet-based models, and allow one to produce syntheses of similar quality to state-of-the-art models, on both gray-scale and color textures.
Impact of Somatic Mutation on the S107(T15) Heavy-chain V Region of Antibodies Reactive with Self and Nonself (1989)

In recent years, we have learned a great deal about how individual B cells use multiple germ-line genetic elements to create a very large repertoire of heavy- (H) and light- (L) chain variable (V) regions each with a unique amino acid sequence (Tonegawa 1983). On the basis of the number of different germ-line V, (diversity) D, and (joining) J region genes for the H chain and V and J region genes for the L chain, the potential for junctional diversity, the introduction of additional sequences during the joining of these elements, and the association of different H and L chains, it has been estimated that at least 108 to 1010 different antibody molecules can be generated in a single individual (Tonegawa 1983). Even this enormous sequence diversity is apparently not sufficient to provide us with the high-affinity antibodies we need to protect us from agents such as toxins and viruses,...
Fabrication of High Quality Quantum Emitters in Diamond Nanostructures (2019)

As the field of solid-state quantum engineering matures, it is increasingly necessary to produce quantum emitters with narrow optical transitions and long spin coherence times aligned to nanophotonic structures [1]. The nitrogen-vacancy (NV) defect center in diamond is a well-suited candidate owing to a spin ground state with a long coherence time [2], nearby nuclear spins for quantum memories [3], and spin-selective optical transitions allowing for efficient optical spin initialization and readout [4].
Kidney-derived c-kit+ progenitor/stem cells contribute to podocyte recovery in a model of acute proteinuria (2018)

Kidney-derived c-kit<sup>+</sup> cells exhibit progenitor/stem cell properties and can regenerate epithelial tubular cells following ischemia-reperfusion injury in rats. We therefore investigated whether c-kit<sup>+</sup> progenitor/stem cells contribute to podocyte repair in a rat model of acute proteinuria induced by puromycin aminonucleoside (PAN), the experimental prototype of human minimal change disease and early stages of focal and segmental glomerulosclerosis. We found that c-kit<sup>+</sup> progenitor/stem cells accelerated kidney recovery by improving foot process effacement (foot process width was lower in c-kit group vs saline treated animals, P = 0.03). In particular, these cells engrafted in small quantity into tubules, vessels, and glomeruli, where they occasionally differentiated into podocyte-like cells. This effect was related to an up regulation of α-Actinin-4 and mTORC2-Rictor pathway. Activation of autophagy by c-kit<sup>+</sup> progenitor/stem cells also contributed to kidney regeneration and intracellular homeostasis (autophagosomes and autophagolysosomes number and LC3A/B-I and LC3A/B-II expression were higher in the c-kit group vs saline treated animals, P = 0.0031 and P = 0.0009, respectively). Taken together, our findings suggest that kidney-derived c-kit<sup>+</sup> progenitor/stem cells exert reparative effects on glomerular disease processes through paracrine effects, to a lesser extent differentiation into podocyte-like cells and contribution to maintenance of podocyte cytoskeleton after injury. These findings have clinical implications for cell therapy of glomerular pathobiology.
Driven energy transfer between coupled modes in spin-torque oscillators (2017)

The mutual interaction between the different eigenmodes of a spin-torque oscillator can lead to a large variety of physical mechanisms from mode hopping to multimode generation, that usually reduce their performances as radio-frequency devices. To tackle this issue for the future applications, we investigate the properties of a model spin-torque oscillator that is composed of two coupled vortices with one vortex in each of the two magnetic layers of the oscillator. In such double-vortex system, the remarkable properties of energy transfer between the coupled modes, one being excited by spin transfer torque while the second one being damped, result into an alteration of the damping parameters. As a consequence, the oscillator nonlinear behavior is concomitantly drastically impacted. This efficient coupling mechanism, driven mainly by the dynamic dipolar field generated by the spin transfer torque induced motion of the vortices, gives rise to an unusual dynamical regime of self-resonance excitation. These results show that mode coupling can be leveraged for controlling the synchronization process as well as the frequency tunability of spin-torque oscillators.
Special-purpose optics to reduce power dissipation in computational sensing and imaging systems (2017)

The central insight in computational sensing and imaging is that the joint design of optics and digital signal processing can lead to electrooptical imaging systems that are superior to those created through sequential design (optics then signal processing). Here “superior” means requiring fewer optical elements, enabling a wider range of form factors, supporting improved performance for a given optics budget, or enabling new imaging functionalities. Merit functions governing joint design depend solely on the digital output; thus the intermediate optical image need not “look good” but merely contain the information such that the final digital output can be computed. This approach underlies a range of new sensing technologies, including lensless imaging based on diffractive optics.[1], [2].
Spray-combustion synthesis: Efficient solution route to high-performance oxide transistors (2015)

Metal-oxide (MO) semiconductors have emerged as enabling materials for next generation thin-film electronics owing to their high carrier mobilities, even in the amorphous state, large-area uniformity, low cost, and optical transparency, which are applicable to flat-panel displays, flexible circuitry, and photovoltaic cells. Impressive progress in solution-processed MO electronics has been achieved using methodologies such as sol gel, deep-UV irradiation, preformed nanostructures, and combustion synthesis. Nevertheless, because of incomplete lattice condensation and film densification, high-quality solution-processed MO films having technologically relevant thicknesses achievable in a single step have yet to be shown. Here, we report a low-temperature, thickness-controlled coating process to create high-performance, solution-processed MO electronics: spray-combustion synthesis (SCS). We also report for the first time, to our knowledge, indium-gallium-zinc-oxide (IGZO) transistors having densification, nanoporosity, electron mobility, trap densities, bias stability, and film transport approaching those of sputtered films and compatible with conventional fabrication (FAB) operations.
The Effects of Laryngoscope Shape and Needle Position on Distal Airway Pressure in Jet Ventilation (2020)

NA (Basic Research) Laryngoscope, 131:E354-E357, 2021.
Structural basis for reversible photoswitching in Dronpa (2007)

Dronpa is a novel GFP-like fluorescent protein with exceptional light-controlled switching properties. It may be reversibly switched between a fluorescent on-state and a nonfluorescent off-state by irradiation with light. To elucidate the molecular basis of the switching mechanism, we generated reversibly switchable Dronpa protein crystals. Using these crystals we determined the elusive dark-state structure of Dronpa at 1.95-A resolution. We found that the photoswitching results in a cis-trans isomerization of the chromophore accompanied by complex structural rearrangements of four nearby amino acid residues. Because of this cascade of intramolecular events, the chromophore is exposed to distinct electrostatic surface potentials, which are likely to influence the protonation equilibria at the chromophore. We suggest a comprehensive model for the light-induced switching mechanism, connecting a cascade of structural rearrangements with different protonation states of the chromophore.
Magnetoelectric Interactions in Composites of Ferrite Films on Lattice-Matched Substrates and Ferroelectrics (2019)

The converse magnetoelectric effect (CME, $i.e.$ the magnetic response to a static electric field) in ferrite-ferroelectric composites is important for an innovative class of voltage-tunable, high-frequency magnetic devices. Technical challenges persist, though, due to weak CME coupling, large ferromagnetic-resonance (FMR) linewidth, and the need for a large bias magnetic field. This study aims to overcome those challenges by using single-crystal-like nickel ferrite films exhibiting high magnetostriction and narrow FMR linewidth. These films present a very high growth-induced magnetic anisotropy field that eliminates the need for a bias field, and facilitates device integration.