gebhart/patrepeval huggingface dataset:
Supplementary Tables S1-S12 from Comprehensive Genetic Characterization of Human Thyroid Cancer Cell Lines: A Validated Panel for Preclinical Studies (2023)

&lt;p&gt;Supplementary Table S1. Cell line authentication by Short Tandem Repeat Profiling (STR) Supplementary Table S2. Full list of genetic variants identified by MSK-IMPACT sequencing Supplementary Table S3. Details for identified high-confidence gene rearrangements resulting in in-frame fusion proteins Supplementary Table S4. Recurrent copy number alterations in thyroid cancer cell lines. Supplementary Table S5. Genes located within the recurrent copy number alteration regions. Supplementary Table S6. Differentially expressed genes, which are located within CNA regions. "Matching_CNA_type" column indicates whether the direction of the expression change corresponds to the CNA type (133 out of 134, overexpression for gene amplification and underexpression for gene deletions). Supplementary Table S7. Thyroid cancer cell lines gene expression data. Normalized gene expression values for all genes in the 44 cell lines assessed by Affymetrix expression microarray in this study ("CU" prefix, University of Colorado). Supplementary Table S8. Genes with differential expression in PTC vs. ATC cell lines. List of differentially expressed genes between PTC-derived vs. ATC-derived cell lines (limma, adjusted p-value&lt;0.05). Supplementary Table S9. Genes with differential expression in PTC vs. ATC tumors. List of top 1000 differentially expressed genes when comparing PTC vs. ATC tumors from other studies (19,20), assessed with the same platform used for cell line transcriptomic profiling. Supplementary Table S10. Thyroid differentiation score (TDS) in thyroid cancer cell lines and tissues. TDS values are calculated for 44 cell lines from this study ("CU" prefix, University of Colorado) and thyroid tissues from other studies, assessed with the same platform: 9 PTC-normal pairs ("He", (19)) 17 PDTCs and 20 ATCs ("Landa", (20)). Supplementary Table S11. Association of TDS16 and TDS13 with clinical and histopathologic characteristics of PTC tumors from the TCGA. P-values calculated with Kruskal-Wallis rank sum test are shown. Supplementary Table S12. BRAFV600E-RAS scores (BRS) and the sensitivity of thyroid cancer cell lines to trametinib and PD-0325901. Drug sensitivity is expressed as a relative area under the dose response curve.&lt;/p&gt;
Faculty Opinions recommendation of RGMA and IL21R show association with experimental inflammation and multiple sclerosis. (2010)

Rat chromosome 1 harbors overlapping quantitative trait loci (QTL) for cytokine production and experimental models of inflammatory diseases. We fine-dissected this region that regulated cytokine production, myelin oligodendrocyte glycoprotein (MOG)-induced experimental autoimmune encephalomyelitis (EAE), anti-MOG antibodies and pristane-induced arthritis (PIA) in advanced intercross lines (AILs). Analysis in the tenth and twelfth generation of AILs resolved the region in two narrow QTL, Eae30 and Eae31. Eae30 showed linkage to MOG-EAE, anti-MOG antibodies and levels of interleukin-6 (IL-6). Eae31 showed linkage to EAE, PIA, anti-MOG antibodies and levels of tumor necrosis factor (TNF) and IL-6. Confidence intervals defined a limited set of potential candidate genes, with the most interesting being RGMA, IL21R and IL4R. We tested the association with multiple sclerosis (MS) in a Nordic case-control material. A single nucleotide polymorphism in RGMA associated with MS in males (odds ratio (OR)=1.33). Polymorphisms of RGMA also correlated with changes in the expression of interferon-gamma (IFN-gamma) and TNF in cerebrospinal fluid of MS patients. In IL21R, there was one positively associated (OR=1.14) and two protective (OR=0.87 and 0.68) haplotypes. One of the protective haplotypes correlated to lower IFN-gamma expression in peripheral blood mononuclear cells of MS patients. We conclude that RGMA and IL21R and their pathways are crucial in MS pathogenesis and warrant further studies as potential biomarkers and therapeutic targets. PMID: 20072140
Front Matter: Volume 10231 (2017)

This PDF file contains the front matter associated with SPIE Proceedings Volume 10231, including the Title Page, Copyright information, Table of Contents, Introduction (if any), and Conference Committee listing.
Divide and Conquer. Pocket-Opening Mixed-Solvent Simulations in the Perspective of Docking Virtual Screening Applications for Drug Discovery (2022)

The existence of a druggable binding pocket is a prerequisite for computational drug-target interaction studies including virtual screening. Retrospective studies have shown that extended sampling methods like Markov State Modeling and mixed-solvent simulations can identify cryptic pockets relevant for drug discovery. Here, we apply a combination of mixed-solvent molecular dynamics (MD) and time-structure independent component analysis (TICA) to four retrospective case studies: NPC2, the CECR2 bromodomain, TEM-1, and MCL-1. We compare previous experimental and computational findings to our results. It is shown that the successful identification of cryptic pockets depends on the system and the cosolvent probes. We used alternative TICA internal features such as the unbiased backbone coordinates or backbone dihedrals versus biased interatomic distances. We found that in the case of NPC2, TEM-1, and MCL-1, the use of unbiased features is able to identify cryptic pockets, although in the case of the CECR2 bromodomain, more specific features are required to properly capture a pocket opening. In the perspective of virtual screening applications, it is shown how docking studies with the parent ligands depend critically on the conformational state of the targets.
Impact of Obesity on Short- and Intermediate-Term Outcomes in Inflammatory Bowel Diseases: Pooled Analysis of Placebo Arms of Infliximab Clinical Trials (2018)

Background and aimsTo assess whether obesity may affect natural history of inflammatory bowel diseases (IBD), we conducted an individual participant data (IPD) pooled analysis of placebo arms, using data from clinical trials of infliximab in IBD and using the Yale Open Data Access (YODA) Project.
A Three-Player GAN for Super-Resolution in Magnetic Resonance Imaging (2023)

Learning based single image super resolution (SISR) task is well investigated in 2D images. However, SISR for 3D Magnetics Resonance Images (MRI) is more challenging compared to 2D, mainly due to the increased number of neural network parameters, the larger memory requirement and the limited amount of available training data. Current SISR methods for 3D volumetric images are based on Generative Adversarial Networks (GANs), especially Wasserstein GANs due to their training stability. Other common architectures in the 2D domain, e.g. transformer models, require large amounts of training data and are therefore not suitable for the limited 3D data. However, Wasserstein GANs can be problematic because they may not converge to a global optimum and thus produce blurry results. Here, we propose a new method for 3D SR based on the GAN framework. Specifically, we use instance noise to balance the GAN training. Furthermore, we use a relativistic GAN loss function and an updating feature extractor during the training process. We show that our method produces highly accurate results. We also show that we need very few training samples. In particular, we need less than 30 samples instead of thousands of training samples that are typically required in previous studies. Finally, we show improved out-of-sample results produced by our model.
Different measurement methods for characterizing and detecting memory effects in non-linear RF power amplifiers (2007)

Memory effects exhibited in RF power amplifiers (PA) have been identified as a major source of performance degradation in modern digital communication systems. While advanced amplifier linearization schemes, such as a digital predistortion (DPD) and envelope elimination restoration, are being used to improve efficiency and linearity in modern digital communication systems, they can also expose communication networks to unwanted emissions from memory effects if not carefully designed and tested. This paper gives a brief description of origins of memory effects in RF power amplifiers. Available methods to quantify memory effects caused by such as parasitic elements are reviewed. Finally a new method based on digital phosphor display technology (DPX) on Real Time Spectrum Analyzers for detecting the presence the memory effects is introduced and its unique capabilities to perform time-correlated measurement results are presented.
Case studies of a robot enhanced walker for training of children with cerebral palsy (2013)

Cerebral palsy (CP) is a disorder of movement and posture in children caused by non-progressive insult of the immature brain. The characteristic features are weakness, spasticity, muscle contractures, and poor motor coordination. The gait patterns of children with CP are slow, uncoordinated, and unstable. Our hypothesis is that these impaired children will benefit from robot enhanced walkers to improve their balance, coordination, and speed during gait. In addition, this experience will also impact their clinical scores that relate to their functional performance and caregiver assistance. In this study, we used a specially-designed robotic walker which children used to perform a series of walking tasks, in increasing order of difficulty. This study was performed in 30 training sessions over a period of 3 months. Each training session lasted for 20 minutes. The outcome measures were variables recorded by the robot such as travel distance, average speed, and clinical measured variables that characterize their disability profiles.
Energy efficient delivery of immersive video centric services (2012)

We examine the basic energy tradeoffs between video transport and video processing for services such as multi-view video (MVV) streaming, where multiple media streams are combined and processed to create an immersive and personalized user experience. We analyze and compare the energy efficiency of different architectural options for the location of video processing functions and illustrate how the architecture of choice is influenced by the network topology, the users' view preferences, and the relative transport-processing energy efficiency. We provide an integer linear programming formulation for the energy efficient functional resource allocation problem, which we show it can be solved as a linear program, and an easily implementable algorithm that generates optimal solutions in polynomial time.
Synthesis, Crystal Structure, and Activity of Pyrazole-Based Inhibitors of p38 Kinase (2007)

A series of pyrazole inhibitors of p38 mitogen-activated protein (MAP) kinase were designed using a binding model based on the crystal structure of 1 (SC-102) bound to p38 enzyme. New chemistry using dithietanes was developed to assemble nitrogen-linked substituents at the 5-position of pyrazoles. Calculated log D was used in tandem with structure-based design to guide medicinal chemistry strategy and improve the in vivo activity of a series of molecules. The crystal structure of an optimized inhibitor, 4 (SC-806), in complex with p38 enzyme was obtained to confirm the hypothesis that the addition of a basic nitrogen to the molecule induces an interaction with Asp112 of p38 alpha. A compound identified from this series was efficacious in an animal model of rheumatic disease.
Heterologous expression of a recombinant lactobacillal β-galactosidase in Lactobacillus plantarum: effect of different parameters on the sakacin P-based expression system (2015)

The over-expression of recombinant L. reuteri β-galactosidase in a food-grade host strain was optimized, which is of interest for applications of this enzyme in the food industry. The results provide more detailed insight into these lactobacillal expression systems and confirm the potential of the pSIP system for efficient, tightly controlled expression of enzymes and proteins in lactobacilli.
Infrared ellipsometry on hexagonal and cubic boron nitride thin films (1997)

Infrared spectroscopic ellipsometry (IRSE) over the wavelength range from 700 to 3000 cm−1 has been used to study and distinguish the microstructure of polycrystalline hexagonal and cubic boron nitride thin films deposited by magnetron sputtering onto (100) silicon. The IRSE data are sensitive to the thin-film layer structure, phase composition, and average grain c-axes orientations of the hexagonal phase. We determine the amount of cubic material in high cubic boron nitride content thin films from the infrared optical dielectric function using an effective medium approach.
Corrosion Properties of 3% Cr Steels in Oil and Gas Environments (2001)

Abstract Steels containing up to 5% Cr were investigated with respect to their corrosion performance in oil and gas environments. Steels containing 3%Cr or more showed improved corrosion performance over Cr free steel by a factor of two or more in a sweet corrosion environment. 5% Cr steel, however, showed deeper localized corrosion than 3% Cr steel under simulated seawater injection conditions with some oxygen contamination. Although Cr containing steels showed rather poor SSC resistance, the resistance was improved by Mo addition.
Antibodies to Keyhole Limpet Hemocyanin Cross-React with an Epitope on the Polysaccharide Capsule of Cryptococcus neoformans and Other Carbohydrates: Implications for Vaccine Development (2003)

Cryptococcus neoformans causes a life-threatening meningoencephalitis in AIDS patients. Mice immunized with a glycoconjugate vaccine composed of the glucuronoxylomannan (GXM) component of the cryptococcal capsular polysaccharide conjugated to tetanus toxoid produce Abs that can be either protective or nonprotective. Because nonprotective Abs block the efficacy of protective Abs, an effective vaccine must focus the Ab response on a protective epitope. Mice immunized with peptide mimetics of GXM conjugated to keyhole limpet hemocyanin (KLH) with glutaraldehyde developed Abs to GXM. However, control peptides P315 and P24 conjugated to KLH also elicited Abs to GXM. GXM-binding Abs from mice immunized with P315-KLH were inhibited by KLH treated with glutaraldehyde (KLH-g), but not by P315. Furthermore, KLH-g inhibited binding of GXM by serum of mice immunized with GXM-TT, indicating that glutaraldehyde treatment of KLH reveals an epitope(s) that cross-reacts with GXM. Vaccination with KLH-g or unmodified KLH elicited Abs to GXM, but did not confer protection against C. neoformans, suggesting the cross-reactive epitope on KLH was not protective. This was supported by the finding that 4H3, a nonprotective mAb, cross-reacted strongly with KLH-g. Sera from mice immunized with either native KLH or KLH-g cross-reacted with several other carbohydrate Ags, many of which have been conjugated to KLH for vaccine development. This study illustrates how mAbs can be used to determine the efficacy of potential vaccines, in addition to describing the complexity of using KLH and glutaraldehyde in the development of vaccines to carbohydrate Ags.
(Invited) Ionogels for Safer Energy Storage: The Determining Effect of the Interface (2018)

Ionogels represent a route to biphasic materials, for the use of ionic liquids (ILs) for all-solid devices. Confining ILs within host networks enhances their averaged dynamics, resulting in improved charge transport. Fragility, short relaxation times, low viscosity, and good ionic conductivity, all them appear to be related to the IL / host network interface. The presence of ILs at interface neighborhood leads to the breakdown of aggregated, structured regions that are systematically found in bulk ILs. This “destructuration”, 1 as well as segregative interactions at interface, 2 coupled with percolation of the bicontinuous solid/liquid interface, 3 make these materials very competitive among the existing solid electrolytes. Such approach could provide (i) a route to lower locally the viscosity of ILs, and (ii) an easier pathway for diffusion of charged species. Several types of ionogels demonstrate this effect, taking into account of fully inorganic, hybrid, polymeric or organic-inorganic host networks . This “all-solid” approach can be applied to several electrochemical energy storage sources, including lithium batteries (Fig 1) 2,4 and supercapacitors (Fig. 2). 5 Strikingly, high performance were shown on these devices, thanks to interfacial effects of confined ILs, with sometimes heightened properties of the chosen ILs as referred to their bulk properties. 2,3,6 Such solid electrolytes are particularly well suited for microdevices that we have been or are being developed (Fig. 3). 5,6 Herein we will emphasize the results of a systematic study of the effect of size of confinement. References: [1] A. Guyomard-Lack et al., Phys. Chem. Chem. Phys., 16 (2014) 23639-23645. [2] A. Guyomard-Lack et al., New J. Chem., 40 (2016) 4269-4276. [3] C. V. Cerclier et al., Phys. Chem. Chem. Phys., 17 (2015) 29707—29713 [4] D. Aidoud et al., J. Power Sources, 330 (2016) 92-103 [5] M. Brachet et al., J. Mater. Chem. A, 4 (2016) 11835-11843. [6] E. Eustache et al., Adv. Energy Mater., 5 (2015) 1500680 Figure 1
Abstract 14422: Molecular Pathogenesis of Cardiac Microthrombi in Fatal Covid-19: Insights from Clinico-histopathologic and Single Nuclei RNA Sequencing Analyses (2021)

Cardiac microthrombi are postulated to underlie cardiac injury in critical COVID-19. To determine pathogenic mechanism(s) of cardiac injury in fatal COVID-19, we conducted a single-center prospective cohort study of 69 consecutive COVID-19 decedents. Microthrombi was the most commonly detected acute cardiac histopathologic feature (n=48, 70%). We tested associations of cardiac microthrombi with biomarkers of inflammation, cardiac injury, and fibrinolysis and with in-hospital antiplatelet therapy, therapeutic anticoagulation, and corticosteroid treatment, while adjusting for multiple clinical factors, including COVID-19 therapies. Higher peak ESR and CRP during hospitalization were independently associated with higher odds of microthrombi (ESR, P non-linearity 0.015, P association =0.008; CRP per 20mg/L increase, OR 1.17, 95%CI 1.00-1.36). Using single nuclei RNA-sequence analysis, we discovered an enrichment of prothrombotic, anti-fibrinolytic, and extracellular matrix signaling amongst cardiac fibroblasts in microthrombi-positive COVID-19 hearts, compared with microthrombi-negative COVID-19 hearts and non-COVID-19 donor hearts. Our cumulative findings identify these specific transcriptomic changes in cardiac fibroblasts as salient features of COVID-19-associated cardiac microthrombi.
Highly-Ordered Supportless Three-Dimensional Nanowire Networks with Tunable Complexity and Interwire Connectivity for Device Integration (2011)

The fabrication of three-dimensional assemblies consisting of large quantities of nanowires is of great technological importance for various applications including (electro-)catalysis, sensitive sensing, and improvement of electronic devices. Because the spatial distribution of the nanostructured material can strongly influence the properties, architectural design is required in order to use assembled nanowires to their full potential. In addition, special effort has to be dedicated to the development of efficient methods that allow precise control over structural parameters of the nanoscale building blocks as a means of tuning their characteristics. This paper reports the direct synthesis of highly ordered large-area nanowire networks by a method based on hard templates using electrodeposition within nanochannels of ion track-etched polymer membranes. Control over the complexity of the networks and the dimensions of the integrated nanostructures are achieved by a modified template fabrication. The networks possess high surface area and excellent transport properties, turning them into a promising electrocatalyst material as demonstrated by cyclic voltammetry studies on platinum nanowire networks catalyzing methanol oxidation. Our method opens up a new general route for interconnecting nanowires to stable macroscopic network structures of very high integration level that allow easy handling of nanowires while maintaining their connectivity.
Application de la Fluorescence Induite par Laser dans les Plasmas Poussiéreux (2012)

Poster
TIR domains of plant immune receptors are NAD + -cleaving enzymes that promote cell death (2019)

Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors activate cell death and confer disease resistance by unknown mechanisms. We demonstrate that plant Toll/interleukin-1 receptor (TIR) domains of NLRs are enzymes capable of degrading nicotinamide adenine dinucleotide in its oxidized form (NAD<sup>+</sup>). Both cell death induction and NAD<sup>+</sup> cleavage activity of plant TIR domains require known self-association interfaces and a putative catalytic glutamic acid that is conserved in both bacterial TIR NAD<sup>+</sup>-cleaving enzymes (NADases) and the mammalian SARM1 (sterile alpha and TIR motif containing 1) NADase. We identify a variant of cyclic adenosine diphosphate ribose as a biomarker of TIR enzymatic activity. TIR enzymatic activity is induced by pathogen recognition and functions upstream of the genes <i>enhanced disease susceptibility 1</i> (<i>EDS1</i>) and <i>N requirement gene 1</i> (<i>NRG1</i>), which encode regulators required for TIR immune function. Thus, plant TIR-NLR receptors require NADase function to transduce recognition of pathogens into a cell death response.
Conduction disturbances caused by high current density electric fields. (1990)

During internal defibrillation, potential gradients greater than 100 V/cm occur near defibrillation electrodes. Such strong fields may cause deleterious effects, including arrhythmias. This study determined 1) the effects of such strong fields on the propagation of activation and 2) whether these effects were different for monophasic and biphasic shocks. Voltages and potential gradients during the shock, as well as activation sequences before and after the shock, were mapped from 117 epicardial electrodes placed over a 3 x 3-cm area on the right ventricle in six dogs. Pacing at a cycle length of 350 msec was given from a long narrow electrode on the right side of the mapped area to generate parallel activation isochrones. A monophasic shock, 10 msec in duration, or a biphasic shock with both phases 5 msec in duration was delivered 300 msec after the last paced stimulus via a mesh electrode on the left side of the mapped area as the cathode, with the anode on the right atrium. Shocks of 70-850 V were given, and the potential gradient and current density at each recording electrode were calculated from the measured potentials and fiber orientation by using a finite element method. Pacing was resumed 200 msec after the shock, and activation sequences were mapped for up to 5 minutes. Potential gradients ranged from 1 to 189 V/cm with high fields on the left side and low fields on the right side of the mapped area. Where the potential gradient was weak, the first activation sequence after the shock was similar to that before the shock, but activation blocked without conducting into areas where the gradient was greater than 64 +/- 4 (mean +/- SD) V/cm for monophasic and greater than 71 +/- 6 V/cm for biphasic shocks. These values are significantly different (p less than 0.003). The higher the potential gradient, the longer was the duration of block before conduction returned. Block duration, however, was generally shorter for biphasic than for monophasic waveforms of the same field strength. In conclusion, conduction block can follow either waveform, but biphasic waveforms cause less block than monophasic waveforms. This effect may partially explain the increased defibrillation efficacy of biphasic shocks.