gebhart/patrepeval huggingface dataset:
Transphosphorylation as a possible mechanism for insulin and epidermal growth factor receptor activation. (1990)

Fully functional chimeric receptors, consisting of major epidermal growth factor and insulin receptor domains, were co-expressed with kinase-negative epidermal growth factor and insulin receptor mutants in human kidney fibroblasts. Under these conditions, homologous extracellular and cytoplasmic domains mediated association of receptors and their precursors. The significance of receptor-receptor interaction was confirmed by transphosphorylation of kinase-negative receptors by ligand-activated chimeric receptors, which was observed between receptors sharing the same cytoplasmic domain as well as between receptors bearing only the same extracellular domain and containing heterologous kinases. Furthermore, the impaired ligand internalization capacity of a kinase-deficient insulin receptor was partially restored by transphosphorylation. Our experiments suggest interreceptor transphosphorylation and transactivation as a possible mechanism for signal amplification.
Evaluation of a Non-Proprietary, High-Tension, Four-Cable Median Barrier on Level Terrain (2012)

During the last decade, the use of cable median barriers has risen dramatically. Cable barriers are often utilized in depressed medians with widths ranging from 30 to 50 ft (9.1 to 15.2 m) and with fill slopes as steep as 4H:1V. A careful review of accident records has indicated that passenger vehicles occasionally penetrate through the standard three-cable median barrier and enter opposing traffic lanes. As a result, the Midwest States Regional Pooled Fund Program sponsored a research and development project to improve the safety performance of existing, non-proprietary, cable median barriers. These safety improvements included increased cable spacing, increased cable height, the use of four cables, increased cable tension, and optimized keyway bolts. For this study, one Test Level 3 (TL-3) full-scale crash test was performed on the improved high-tension, four-cable median barrier according to the Manual for Assessing Safety Hardware (MASH). The cable barrier system was configured with cable heights of 13½ in. (343 mm), 24 in. (610 mm), 34½ in. (876 mm), and 45 in. (1,143 mm) above the ground surface The improved barrier system was intended to satisfy impact safety standards when placed on either a 4H:1V slope or on level terrain. Because barrier penetration was a prime concern, the crash test utilized a 1500A full-sized passenger sedan to impact the barrier in order to investigate the significance of the 10½-in. (267-mm) cable spacing. The vehicle was contained by the barrier, but significant damage occurred to the occupant compartment. As such, the results from the crash test did not meet the MASH impact safety standards.
19.1 A 128Gb MLC NAND-Flash device using 16nm planar cell (2014)

The aggressive scaling of NAND Flash memory technology — one that is even outpacing Moore's Law — has enabled very rapid cost-per-bit reduction, resulting in an explosion of systems utilizing this versatile memory technology. From removable media and personal music players to smart phones, tablets, and now personal computers and data center applications employing client and enterprise solid state drives (SSDs), NAND technology is making solid-state memory-based storage affordable.
Tandem radical cyclization approach to angular triquinanes. A short synthesis of (.+-.)-silphiperfol-6-ene and (.+-.)-9-episilphiperfol-6-ene (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTandem radical cyclization approach to angular triquinanes. A short synthesis of (.+-.)-silphiperfol-6-ene and (.+-.)-9-episilphiperfol-6-eneDennis P. Curran and Shen Chun. KuoCite this: J. Am. Chem. Soc. 1986, 108, 5, 1106–1107Publication Date (Print):March 1, 1986Publication History Published online1 May 2002Published inissue 1 March 1986https://pubs.acs.org/doi/10.1021/ja00265a055https://doi.org/10.1021/ja00265a055research-articleACS PublicationsRequest reuse permissionsArticle Views755Altmetric-Citations63LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Design of Peptide Analogs (1984)

The application of modern theoretical techniques for the conformationally based design of peptide drugs is discussed. The early developments in the theoretical treatment of peptides and peptide hormones is briefly reviewed with emphasis on studies concerned with the enkephalins. A recent molecular dynamics simulation of Gonadotropin-Releasing Hormone (GnRH) is used to demonstrate the application of modern techniques. This allows us to treat highly flexible molecules such as GnRH, which is seen in the simulation to undergo large conformational fluctuations and major transitions from an extended to a folded state. The ability of a cyclic peptide to induce high energy conformational states in given residues is also discussed, and transitions in the phenylalanine residue in a molecular dynamics study of vasopressin are used to illustrate this behavior. From the wide range of conformations accessible to peptide hormones, as is found in these and other studies, it becomes clear that a rational, conformationally based approach to analog design requires supplementary information. We show how we have gone about this problem by incorporating theoretical simulations on additional constrained analogs, and developed a "template forcing" procedure to determine the conformational compatibility of these analogs. We also show how we designed a new analog, a highly constrained transannular bridged analog of a GnRH cyclic antagonist, using these methods and tested its proposed conformation theoretically. Other analogs are being designed by similar methods and routes for their synthesis are under study to test spectroscopically and biologically, the conformational predictions made through these studies.
FISH and chips: a review of microfluidic platforms for FISH analysis (2020)

Fluorescence in situ hybridization (FISH) allows visualization of specific nucleic acid sequences within an intact cell or a tissue section. It is based on molecular recognition between a fluorescently labeled probe that penetrates the cell membrane of a fixed but intact sample and hybridizes to a nucleic acid sequence of interest within the cell, rendering a measurable signal. FISH has been applied to, for example, gene mapping, diagnosis of chromosomal aberrations and identification of pathogens in complex samples as well as detailed studies of cellular structure and function. However, FISH protocols are complex, they comprise of many fixation, incubation and washing steps involving a range of solvents and temperatures and are, thus, generally time consuming and labor intensive. The complexity of the process, the relatively high-priced fluorescent probes and the fairly high-end microscopy needed for readout render the whole process costly and have limited wider uptake of this powerful technique. In recent years, there have been attempts to transfer FISH assay protocols onto microfluidic lab-on-a-chip platforms, which reduces the required amount of sample and reagents, shortens incubation times and, thus, time to complete the protocol, and finally has the potential for automating the process. Here, we review the wide variety of approaches for lab-on-chip-based FISH that have been demonstrated at proof-of-concept stage, ranging from FISH analysis of immobilized cell layers, and cells trapped in arrays, to FISH on tissue slices. Some researchers have aimed to develop simple devices that interface with existing equipment and workflows, whilst others have aimed to integrate the entire FISH protocol into a fully autonomous FISH on-chip system. Whilst the technical possibilities for FISH on-chip are clearly demonstrated, only a small number of approaches have so far been converted into off-the-shelf products for wider use beyond the research laboratory.
Ramsey-Based Inclusion Checking for Visibly Pushdown Automata (2015)

Checking whether one formal language is included in another is important in many verification tasks. In this article, we provide solutions for checking the inclusion of languages given by visibly pushdown automata over both finite and infinite words. Visibly pushdown automata are a richer automaton model than the classical finite-state automata, which allows one, for example, to reason about the nesting of procedure calls in the executions of recursive imperative programs. The presented solutions do not rely on explicit automaton constructions for determinization and complementation. Instead, they are more direct and generalize the so-called Ramsey-based inclusion-checking algorithms, which apply to classical finite-state automata and proved to be effective there to visibly pushdown automata. We also experimentally evaluate these algorithms, demonstrating the virtues of avoiding explicit determinization and complementation constructions.
Volume Rise During Flexible Urethane Foaming (1993)

During the formation of flexible urethane foams, isocyanate and water react to form urea dimers and oligomers which eventually segregate as a microdisperse solid phase. The role that urea segregation plays on reaction kinetics and flowability during foaming is examined in this work. Temperature and volume rise profiles were measured for a series of foam systems by varying the amount of water (2-6 pphp), isocyanate (90, 110, 130 index), and amine or tin catalysts in the formulation. Model calculations showed that 84-90% conversion of isocyanate (NCO) groups was required to form a crosslinked polymer network. However, volume rise was found to stop at 40-70% NCO conversion. This indicates that gelation is due to phase separation rather than covalent crosslinking. A sudden acceleration in the rate of reaction (dT/dt), detected before foams reached a constant volume, is thought to indicate microphase separation during foaming. A mechanism is presented to correlate temperature and volume rise profiles with urea microphase segregation during reactive urethane foaming. The blowing efficiency during foaming ranges between 55-82% as the concentration of isocyanate (90-130 index) or tin catalyst (0.2-0.4 pphp) is increased in the formulation, although it appears relatively independent of the water or amine catalyst levels used in this study. It was also found that addition of glycerine to the foaming system disrupted the urea microphase separation process, and increased the blowing efficiency to 85%.
Exploring Big Data using Visual Analytics. (2014)

Never before in history data is generated and collected at such high volumes as it is today. For the exploration of large data sets to be e↵ective, it is important to include the human in the data exploration process and combine the flexibility, creativity, and general knowledge of the human with the enormous storage capacity and the computational power of today’s computers. Visual Analytics helps to deal with the flood of information by integrating the human in the data analysis process, applying its perceptual abilities to the large data sets. Presenting data in an interactive, graphical form often fosters new insights, encouraging the formation and validation of new hypotheses for better problem-solving and gaining deeper domain knowledge. Visual analytics techniques have proven to be of high value in exploratory data analysis. They are especially powerful for the first steps of the data exploration process, namely understanding the data and generating hypotheses about the data, but they also significantly contribute to the actual knowledge discovery by guiding the search using visual feedback. In putting visual analysis to work on big data, it is not obvious what can be done by automated analysis and what should be done by interactive visual methods. In dealing with massive data, the use of automated methods is mandatory and for some problems it may be su cient to only use fully automated analysis methods, but there is also a wide range of problems where the use of interactive visual methods is necessary. The presentation discusses when it is useful to combine visualization and analytics techniques and it will also discuss the options how to combine techniques from both areas. Examples from a wide range of application areas illustrate the benefits of visual analytics techniques. (c) 2014, Copyright is with the authors. Published in the Workshop Proceedings of the EDBT/ICDT 2014 Joint Conference (March 28, 2014, Athens, Greece) on CEUR-WS.org (ISSN 1613-0073). Distribution of this paper is permitted under the terms of the Creative Commons license CCby-nc-nd 4.0. Short Bio DANIEL A. KEIM is professor and head of the Information Visualization and Data Analysis Research Group in the Computer Science Department of the University of Konstanz, Germany. He has been actively involved in data analysis and information visualization research for about 20 years and developed a number of novel visual analysis techniques for very large data sets. He has been program co-chair of the IEEE InfoVis and IEEE VAST as well as the ACM SIGKDD conference, and he is member of the IEEE VAST as well as EuroVis steering committees. Dr. Keim got his Ph.D. and habilitation degrees in computer science from the University of Munich. Before joining the University of Konstanz, Dr. Keim was associate professor at the University of Halle, Germany and Senior Technology Consultant at AT&T Shannon Research Labs, NJ, USA.
Readings in agents (1997)

Chapter 1 Agents and Multiagent Systems: Themes, Approaches, and Challenges Chapter 2 Applications Chapter 3 Architectures and Infrastructure Chapter 4 Models of Agency
Action of Dipeptidyl Peptidase‐4 Inhibitors on SARS‐CoV‐2 Main Protease (2020)

In a recent publication, Eleftheriou et al. proposed that inhibitors of dipeptidyl peptidase-4 (DPP-4) are functional inhibitors of the main protease (M<sup>pro</sup> ) of SARS-CoV-2. Their predictions prompted the authors to suggest linagliptin, a DPP-4 inhibitor and approved anti-diabetes drug, as a repurposed drug candidate against the ongoing COVID-19 pandemic. We used an enzymatic assay measuring the inhibition of M<sup>pro</sup> catalytic activity in the presence of four different commercially available gliptins (linagliptin, sitagliptin, alogliptin and saxagliptin) and several structural analogues of linagliptin to study the binding of DPP-4 inhibitors to M<sup>pro</sup> and their functional activity. We show here that DPP-4 inhibitors like linagliptin, other gliptins and structural analogues are inactive against M<sup>pro</sup> .
Performance effect of unintended polarization on clutter attenuation (2019)

Various parameters can affect the ground moving target indicator (GMTI) radar performance. One such parameter that may often be overlooked is that of the unintended polarization of the antenna, e.g., the cross-polarization response. This paper discusses the issue of cross-polarization on clutter attenuation performance for GMTI radars.
Heparanase Expression and Function During Early Pregnancy in Mice1 (2007)

Embryo implantation is a complex process that involves interactions between cell-surface and extracellular components of the blastocyst and the uterus, including blastocyst adhesion to the uterine luminal epithelium, epithelial basement membrane penetration and stromal extracellular matrix remodeling, angiogenesis, and decidualization. These processes all involve interactions with heparan sulfate (HS) proteoglycans, which harbor various growth factors and cytokines and support cell adhesion. Heparanase (HPSE) is an endo-beta-glucuronidase that cleaves HS at specific sites. HPSE also can act as an adhesion molecule independent of its catalytic activity. Thus, HPSE is a multifunctional molecule contributing to and modulating HS-dependent processes. Exogenously added HPSE improves embryo implantation in mice; however, no information is available regarding the normal pattern of HPSE expression and activity during the implantation process in any system. Using several approaches, including real-time RT-PCR, in situ hybridization, and immunohistochemistry, we determined that uterine HPSE expression increases dramatically during early pregnancy in mice. Heparanase mRNA and protein were primarily expressed in decidua and were rapidly induced at the implantation site. Uterine HPSE activity was characterized and demonstrated to increase >40-fold during early pregnancy. Finally, we demonstrate that the HPSE inhibitor PI-88 severely inhibits embryo implantation in vivo. Collectively, these results indicate that HPSE plays a role in blastocyst implantation and complements previous studies showing a role for HS-dependent interactions in this process.
Supplementary Video 1 from Unexpected Dissemination Patterns in Lymphoma Progression Revealed by Serial Imaging within a Murine Lymph Node (2023)

&lt;p&gt;MOV file - 7.7MB, Procedure of implantation of LNIWC: A 6 week old C57BL/6 mouse was used for this LNIWC implantation&lt;/p&gt;
Self-Alignment of Interference Arising From Hallway Guidance of Diffuse Fields (2014)

Propagation theory is developed to get analytic expressions for both guided and diffusely scattered 3-D fields in common indoor environments, with access points (APs) placed along a hallway and mobile nodes in the rooms. Resulting predictions agree with measurements of both path loss and single-user multiple-input-multiple-output link capacity. In particular, the model reproduces the observed reduction in normalized channel capacity with increasing range. This effect, occurring in a common indoor environment, can be beneficial. Interfering APs, which tend to be further away, occupy channel dimensions corresponding to low-order hallway modes, causing total interference to concentrate in a small subset of the channel dimensions, in a manner reminiscent of interference alignment. The channel for the desired signal has a greater number of effective degrees of freedom (EDOFs) due to a shorter distance from its serving AP. The disparity in the number of EDOFs between the signal and the interference leads to higher rates, which can be further increased through water filling applied individually to each link, with no interlink coordination. The resulting rates are on the order of 30% greater than would be anticipated in range-independent scattering models.
A New Wireless Power Transfer Circuit With a Single-Stage Regulating Rectifier for Flexible Sensor Patches (2020)

Abstract A new wireless power transfer circuit with a single-stage regulating rectifier is designed and validated with satisfactory efficiency for flexible sensor patches. Since the battery is bulky and cannot be fabricated on a flexible substrate, the power source of the electronic patch is realized by wireless power transfer. Magnetic resonance transmission power at 13.56 MHz in the ISM band is adopted to make possible wireless power transfer. Furthermore, for high conversion efficiency, a new single-stage regulating rectifier is designed and implemented at the receiver side of the sensor patch. An active switching full-wave bridge rectifier is designed to reduce conduction loss and increase the voltage-conversion rate. A delay lock loop feedback controller overcomes the switching delays at high frequencies that significantly undermine power conversion efficiency. The voltage rectification and regulation are achieved simultaneously in a single-stage rectifier through 1X/0X mode control. The PFM control is adopted to select the switching frequency of the system in order to maximize the transient response during heavy load and to minimize the switching power losses during light load. The circuit is fabricated via the TSMC 0.35 μm process. The output efficiency of the circuitry was improved by 5–10% in light load as compared with the circuit without PFM control, while the peak efficiency reaches favorable 86%.
AB291. SPR-18 Correlation of sacral nerve lead targeting and urological efficacy: motor mapping, electrode position, and stimulation amplitude (2016)

Objective: Sacral neuromodulation (SNM) is a clinically used therapy for refractory urge frequency and incontinent patients. Using a recently developed sheep model, this preclinical study retrospectively evaluated the relationship between implanted sacral lead locations, motor threshold (MT) values, motor mapping, and acute urological efficacy to determine if acute location and physiological measurements are correlated. Methods: Twelve female polypay sheep were implanted with bilateral InterStim® devices (Model 3058) connected to quadripolar leads (model 3889) placed in the S2-4 foramina with S3 as the ideal target. CT scans at post-op and ≥12 months later were used for 3D rendering using MedCAD points placed on the sacrum and lead contacts to compare coordinates across animals. Acute cystometry was performed to test responses to SNM (0.21 ms PW, 10 Hz) at maximum tolerable amplitude (MTA). MT values were obtained by visual identification of the first motor response and the motor reflex was mapped to an anatomical map. Results: Sheep were categorized as responders (n=6; 50%) or non-responders (n=6; 50%) based on ≥50% increase in bladder capacity to acute SNM. There was a significant difference in motor mapping areas between responders (peri-anal contacts) and non-responders (activation of leg) (chi-square; P<0.05). Higher MTA values correlated with larger bladder capacity increases (Pearson correlation; P<0.05). Contact position correlated with urological response (ANOVA; P<0.05). A generalized Procrustes analysis on the 17 leads in S3 (remainder in S2 or S4) showed variability of distributions was higher in distal contacts (0 & 1, mean distance to center 7.3±1.8 mm, left & 6.8±1.3 mm, right) than proximal (2 & 3, mean distance to center 5.8±0.86 mm, left & 4.3±0.35 mm, right (ANOVA; alpha =0.05; F(3,64) =20.55; P<0.0001). Conclusions: (I) Responder sheep showed motor responses in peri-anal areas significantly more often than non-responders; (II) MTA weakly correlated with increased bladder capacity; (III) activation of lead contacts proximal to the sacral foramen produced more reliable urological results than did activation of distal contacts. These results suggest well-positioned leads will elicit specific responses that could be essential to effective SNM therapy. Future work will characterize changes over time to provide a temporal correlation of this relationship. Funding Source(s): Medtronic