gebhart/patrepeval huggingface dataset:
Abstract 4452: Musashi-2 regulates EGFR/HER3 expression in NSCLC, cell proliferation and response to EGFR inhibitors in EGFR-mutant NSCLC (2018)

Abstract Musashi-2 (MSI2) is an RNA-binding protein that regulates mRNA translation. We recently established that MSI2 is elevated in a subset of non-small cell lung cancer (NSCLC) tumors upon progression and drives NSCLC metastasis, in part based on activity supporting a TGF-beta/SMAD3/claudin signaling cascade. Here, reverse phase protein array (RPPA) analysis of MSI2-depleted versus control KrasLA1/+;P53R172HΔG/+ murine NSCLC cell lines identified a significant ~2.7-fold upregulation of HER3 (ERBB3) upon MSI2 depletion. Negative MSI2-dependent regulation of ERBB3 protein was confirmed in multiple NSCLC models, based on analysis of MSI2 depletion or overexpression. Further, MSI2 positively regulated expression of the epidermal growth factor receptor (EGFR) protein in the same models. Comparing EGFR and KRAS driven models, we found that MSI2 depletion significantly impairs cell proliferation only in EGFR-mutant NSCLC cell lines. Using RNA immunoprecipitation analysis coupled with qPCR, we show that MSI2 directly binds to EGFR and, to a lesser extent, to HER3 mRNA. MSI2 mRNA binding was approximately correlating with the presence of predicted MSI2 binding sites in corresponding mRNAs. NSCLC lung tissue microarray analysis revealed that MSI2 total positivity by H-score, 2+/3+ and 3+ positivity correlated with EGFR 3+ staining. Finally, EGFR inhibitors erlotinib and afatinib synergized with MSI2 depletion in EGFR mutant models, suggesting that therapeutic targeting of MSI2 could be of clinical value, especially in EGFR-mutant lung cancer. Citation Format: Peter Makhov, Alexander Kudinov, Alexander Deneka, Brian L. Egleston, Emmanuelle Nicolas, Kathy Q. Cai, Rohan Brebion, Eleanor Avril, Mark Hitrik, Anna S. Nikonova, Ilya G. Serebriiskii, Vladimir Khazak, Hossein Borghaei, Erica A. Golemis, Yanis Boumber. Musashi-2 regulates EGFR/HER3 expression in NSCLC, cell proliferation and response to EGFR inhibitors in EGFR-mutant NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4452.
Collectin Liver 1 and Collectin Kidney 1 of the Lectin Complement Pathway Are Associated With Mortality After Kidney Transplantation (2016)

Kidney transplanted patients still have significantly higher mortality compared with the general population. The innate immune system may play an important role during periods, with suppression of the adaptive immune system. In the present study, two soluble pattern recognition molecules of the innate immune system were investigated, collectin liver 1 (CL-L1) and collectin kidney 1 (CL-K1). Potential associations of their pretransplant levels and long-term graft and recipient survival were examined. The levels of CL-L1 and CL-K1 were measured at the time of transplantation in 382 patients (≥17 years) transplanted in 2000-2001. The cohort was subsequently followed until December 31, 2014. Data on patient and graft survival were obtained from the Norwegian Renal Registry. Both high CL-L1 (≥376 ng/mL) and high CL-K1 (≥304 ng/mL) levels were significantly associated with overall mortality in multivariate Cox analyses with hazard ration (HR) 1.50, 95% confidence interval (CI) 1.09-2.07, p = 0.013 and HR 1.43, 95% CI 1.02-1.99, p = 0.038, respectively. Moreover, high CL-K1 levels were significantly associated with cardiovascular mortality. No association between measured biomarkers and death-censored graft loss was found. Finally, there was a significant correlation between these two collectins, r = 0.83 (95% CI 0.80-0.86). In conclusion, CL-L1 and CL-K1 were significantly associated with mortality in kidney transplant recipients.
Matura Evaluation experiment based on human evaluation of machine translation (2010)

A Web-based system for human evaluation of machine translation is presented in this paper. The system is based on comprehension tests similar to the ones used in Polish matura (secondary school-leaving) examinations. The results of preliminary experiments for Polish-English and English-Polish machine translation evaluation are presented and discussed.
Diels–Alder Reactions of 2‐Vinylindoles with Open‐Chain C=C Dienophiles (2006)

Abstract The synthesis of diastereoisomeric 3,4‐disubstituted 1,2,3,4‐tetrahydrocarbazoles by Diels–Alder cycloaddition reactions between [( E )‐2‐vinyl]indole‐1‐carboxylic acid ethyl esters and open‐chain C=C dienophiles is reported and discussed. The reactions proceed with high regioselectivity whereas the diastereoselectivity ranges from moderate to excellent depending on the substitution pattern on both the dienes and dienophiles and on the catalyst employed. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
New Approach to Preparation of N‐Acylphosphoramido(thio)(seleno)ates. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Gut barrier-microbiota imbalances in early life lead to higher sensitivity to inflammation in a murine model of C-section delivery (2023)

Early-life gut microbiota-host crosstalk alterations related to CSD could be the linchpin behind the phenotypic effects that lead to increased susceptibility to an induced inflammation later in life in mice. Video Abstract.
Study of the Normal Human Kidney and Kidney Cancer with Monoclonal Antibodies (1984)

The ability to establish immortal tissue culture lines of human renal cancer as well as short-term lines of autologous normal kidney epithelium offers a unique system to probe the differences between a neoplastic cell and its normal counterpart. Monoclonal antibodies have been prepared against cell surface differentiation antigens of normal and neoplastic human kidney. The detected antigens have been biochemically characterized, and the molecular phenotypes of these cells is being unraveled. Differences in gene expression are becoming apparent between the normal and neoplastic kidney cell. Preliminary results indicate that these differences appear to have clinical significance.
A Robust Statistical Estimation of Internet Traffic (2009)

Abstract. A new method of estimating flow characteristics in the Internet is developped in this paper. For this purpose, a new set of random variables (referred to as observables) is defined. When dealing with sampled traffic, these observables can easily be computed from sampled data. By adopting a convenient mouse/elephant dichotomy also dependent on traffic, it is shown how these variables give a robust statistical information of long flows. A mathematical framework is developed to estimate the accuracy of the method. As an application, it is shown how one can estimate the number of long TCP flows when only sampled traffic is available. The algorithm proposed is tested against experimental data collected from different types of IP traffic.
Lifetime of EUVL masks as a function of degree of carbon contamination and capping materials (2008)

Lifetime of EUVL masks which are intentionally contaminated with carbon is investigated by comparing Si and Ru capping layer. Carbon deposition is observed not only on the multilayer, but also on the absorber sidewall of the mask. Deposited carbon on the sidewall during EUV exposure gradually varies mask CD and also induces the changes in the wafer printability and dose in the scanner. In addition, we compare the effects of carbon contamination between Si and Ru capped blank. Ru capped blank shows longer mask mean time between cleaning (MTBC) than Si capped blank by 25% in our experiments.
Update on peptidylarginine deiminases and deimination in skin physiology and severe human diseases (2007)

Deimination (or citrullination) is a recently described post-translational modification, but its consequences are not yet well understood. It is catalysed by peptidylarginine deiminases (PADs). These enzymes transform arginyl residues involved in a peptidyl link into citrullyl residues in a calcium-dependent manner. Several PAD substrates have already been identified like filaggrin and keratins K1 and K10 in the epidermis, trichohyalin in hair follicles, but also ubiquitous proteins like histones. PADs act in a large panel of physiological functions as cellular differentiation or gene regulation. It has been suggested that deimination plays a role in many major diseases such as rheumatoid arthritis, multiple sclerosis, Alzheimer's disease and psoriasis. Five human genes (PADIs), encoding five highly conserved paralogous enzymes (PAD1-4 and 6), have been characterized. These genes are clustered in a single locus, at 1p35-36 in man. Only PAD1-3 are expressed in human epidermis. PADs seem to be controlled at transcriptional, translational and activity levels and they present particular substrate specificities. In this review, we shall discuss these main biochemical, genetic and functional aspects of PADs together with their pathophysiological implications.
A short report on optimization of nucleic acid probes by DNA microarray synthesis and next generation sequencing (2021)

This manuscript has been withdrawn by bioRxiv as it was submitted and made public without the full consent of all the authors. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author
Energy-Efficient and Metastability-Immune Timing-Error Detection and Instruction-Replay-Based Recovery Circuits for Dynamic-Variation Tolerance (2008)

Microprocessor clock frequency (FCLK) is traditionally determined based on maximum supply voltage (Vcc) droop and temperature specifications. Since typical usage patterns usually run at nominal Vcc and temperature, these infrequent dynamic variations severely limit FCLK. The concept of timing-error detection and correction in previous work by Ernst, D., et al, (2003) is extended and implemented in a test-chip in 65nm CMOS in Bai, P., et al, (2004) to explore the effectiveness of resilient circuits in eliminating Vcc and temperature FCLK guardbands as well as exploiting path-activation probabilities to maximize throughput (TP).
Function Cultivation of Transparent Oxides Utilizing Built-In Nanostructure (2006)

Abstract This review article describes recent progress in our research on cultivation of functionality in crystalline and amorphous transparent oxides utilizing nanostructures embedded in the material itself. It includes the background of our research and approach. Subjects included are material exploration and device application of transparent oxide semiconductors for transparent electronics, function emergence in nano-porous crystal 12CaO·7Al2O3 utilizing active anion species stabilized by sub-nanometer-sized cages, and modified silica glass for vacuum/deep ultraviolet lasers. Our description of each subject include: background and approach, material design concept, fabrication or modification method, properties, and device fabrication. Emphasis is placed on the importance of a variety of built-in nanostructures in transparent oxides for novel function realization and the high potential of transparent oxides as ingredients for an ubiquitous element strategy of material research in this century.
Generative Compression (2017)

Traditional image and video compression algorithms rely on hand-crafted encoder/decoder pairs (codecs) that lack adaptability and are agnostic to the data being compressed. Here we describe the concept of generative compression, the compression of data using generative models, and suggest that it is a direction worth pursuing to produce more accurate and visually pleasing reconstructions at much deeper compression levels for both image and video data. We also demonstrate that generative compression is orders-of-magnitude more resilient to bit error rates (e.g. from noisy wireless channels) than traditional variable-length coding schemes.
Trajectory Planning of Differentially Flat Systems with Dynamics and Inequalities (2001)

Trajectory planning of dynamic systems, in near real-time, is important for aerospace systems, specially, unmanned air vehicles and launched munitions. Trajectory plans that do not consider the governing dynamic equations, applicable path and actuator constraints may be unrealizable during execution. The purpose of this paper is to propose a trajectory planning scheme for a class of dynamic systems, referred to as differentially flat systems. The planner is motivated from on-line computations and is aimed to satisfy the state equations, path and actuator constraints, and given initial and terminal constraints. The essence of the approach is demonstrated by two examples: (i) a hardware implementation on a spring-mass-damper system to demonstrate real-time capabilities during pursuit; (ii) trajectory planning of a PVTOL to illustrate the application to nonlinear problems.
A new coherent optical pseudo-color encoder (1976)

A new and simple method for pseudo-coloring a photograph in a coherent optical processing system, utilizing a newly developed technique of half-tone screens, is described. By selective spatial filtering of the high diffraction orders in the Fourier plane of a coherent optical system, images with up to ten contours of constant brightness have been generated on a picture from a single half-tone copy of that picture. The pseudo-coloring of the picture is achieved by mixing the high-diffraction-order outputs generated by lasers of different wavelengths. In the experiment described herein, an argon laser and a He-Ne laser were used. The experimental results demonstrate that the method has considerable flexibility. A discussion of the theory, the method, and potential applications is given.
Rankine cycle waste heat recovery system and method with improved EGR temperature control (2023)

A waste heat recovery (WHR) system and method for regulating exhaust gas recirculation (EGR) cooling is described. More particularly, a Rankine cycle WHR system and method is described, including an arrangement to improve the precision of EGR cooling for engine efficiency improvement and thermal management.
Testing of the A6 magnetron with radial extraction on the pulserad electron beam accelerator (2015)

Summary form only given. The Pulserad electron beam accelerator at the University of New Mexico (UNM) was refurbished and reconfigured to provide a voltage pulse with a very fast risetime, inspired by simulation results that indicated that the magnetron output characteristic was very sensitive to the voltage risetime. The modified Pulserad has a 2 ns risetime after which it maintains a flat-top for 30 ns and is capable of providing 350 kV into a matched load of 20 Ω. The main contributing factor for such a fast risetime is the low inductance oil breakdown switch located between the pulse forming line and the transmission line. Additionally, a low inductance transition region between oil and vacuum was designed to keep the degradation to the risetime minimal.
Infrared spectroscopic investigation of titanium in zeolites. A new assignment of the 960 cm–1band (1993)

The formation of Si–O–defect groups due to the incorporation of Ti in the framework of zeolites is evidenced by means of solid-state tetraethylammonium (TEA) cation exchange; a new assignment for the infrared (IR) band in both β-Ti and TS-1 is presented.
Identification and Analysis of the Georgia 98 Serotype, a New Serotype of Infectious Bronchitis Virus (2001)

Twenty-five field infectious bronchitis viruses (IBVs) similar to, but genetically distinct from, the DE072 serotype were isolated from several states in the United States from 1990 through 1999 and were examined molecularly and antigenically. A 421-bp sequence in the hypervariable region of the S1 gene was examined, and phylogenetic analysis on that region indicated that these viruses are closely related but fall into unique groups. Cross-virus neutralization testing and entire S1 sequence analysis on selected isolates further confirmed that fact, and we divided the viruses into the DE072 serotype and two other unique groups. In a vaccine protection trial, the commercially available DE072 vaccine showed less than 50% protection against viruses in one of the groups. The majority of the recent isolates belong to that group and share very low antigenic relatedness to the DE072 strain as well as other serotypes of IBV. Consequently, we designated this group as a new serotype, Georgia 98. We developed a restriction fragment length polymorphism analysis that can differentiate this new serotype from all other serotypes of IBV.
A Schumann Resonance-based Quantity for Characterizing Day-to-day Changes in Global Lightning Activity (2023)

The importance of lightning has long been recognized from the point of view of climate-related phenomena. However, the detailed investigation of lightning on global scales is currently hindered by the incomplete and spatially uneven detection efficiency of ground-based global lightning detection networks and by the restricted spatio-temporal coverage of satellite observations. We are developing different methods for investigating global lightning activity based on Schumann resonance (SR) measurements. SRs are global electromagnetic resonances of the Earth-ionosphere cavity maintained by the vertical component of lightning. Since charge separation in thunderstorms is gravity-driven, charge is typically separated vertically in thunderclouds, so every lightning flash contributes to the measured SR field. This circumstance makes SR measurements very suitable for climate-related investigations. In this study, 19 days of global lightning activity in January 2019 are analyzed based on SR intensity records from 18 SR stations and the results are compared with independent lightning observations provided by ground-based (WWLLN, GLD360 and ENTLN) and satellite-based (GLM, LIS/OTD) global lightning detection. Daily average SR intensity records from different stations exhibit strong similarity in the investigated time interval. The inferred intensity of global lightning activity varies by a factor of 2-3 on the time scale of 3-5 days which we attribute to continental-scale temperature changes related to cold air outbreaks from polar regions. While our results demonstrate that the SR phenomenon is a powerful tool to investigate global lightning, it is also clear that currently available technology limits the detailed quantitative evaluation of lightning activity on continental scales.
Performance Analysis of Distributed Single Carrier Systems With Distributed Cyclic Delay Diversity (2017)

This paper investigates a distributed cyclic delay diversity (CDD) transmission scheme for cyclic-prefixed single carrier systems in non-identically and identically distributed frequency selective fading channels. The distinguishable feature of the proposed scheme lies in providing a transmit diversity gain while reducing the burden of estimating the channel state information, which is a challenging task in distributed and cooperative systems. To effectively use the distributed CDD scheme at the transmitters, two sufficient conditions are derived to eliminate the intersymbol interference at the receiver and leveraged to convert the multi-input single-output channel into a single-input single-output channel. These conditions allow the system to achieve the maximum diversity for frequency selective fading channels at a full rate. To achieve this maximum diversity, a fixed number of CDD transmitters are selected based on the channel conditions, symbol block size, and maximum time dispersion of the channel, and a new two-stage transmission mode is proposed. Based on the distributed CDD and the proposed selection schemes, a new expression for the signal-to-noise ratio at the receiver is obtained with the aid of order statistics, and then closed-form expressions for the outage probability and average symbol error rate (ASER) are derived. As far as the identically distributed frequency selective fading channel model is concerned, the achievable maximum diversity gain is proved, with the aid of asymptotic analysis, to be equal to the product of the total number of transmitters in the system and the number of multipath components. Link-level simulations are also conducted to validate the analytical expressions for outage probability, ASER, and maximum achievable diversity gain.
Graphene p-n junction photo-responsivity enhanced with gap-plasmons (Conference Presentation) (2019)

Graphene photodetectors’ intrinsically low responsivity (sensitivity) has been a long-standing issue that overshadows graphene’s other excellent optical properties as a photodetection material. The key to improving the graphene photodetector responsivity lies in enhancing the photothermoelectric (PTE) effect, which has already been demonstrated to be the dominant photocarrier generation mechanism. To maximize the PTE current, one would need a strong optically-induced temperature gradient to overlap with a graphene p-n junction spatially. Here, the temperature gradient drives the charge carrier movement, while the graphene p-n junction separates the different charge carrier types (electrons and holes) and makes them drift in opposite directions. In this work, we show that these two conditions can be met simultaneously in a meticulously designed device, combining a gap plasmon structure and a pair of split-gates. The gap plasmon structure absorbs 71% of incident light creating localized heating (thereby large temperature gradient), and the split-gates create a p-n junction at the center of the localized thermal gradient. We fabricated a graphene photodetector with the proposed configuration, and experimentally verified the dominance of PTE effect in photocurrent generation in good agreement with theoretical calculations. More importantly, we obtained a responsivity 70 times higher than the previously reported value from a similar device without plasmon-enhancement. Moreover, originating from the combination of gap plasmon-enhanced optical absorption and optimized p-n junction, our responsivity is 5~7 times higher than reported values for other graphene photodetectors with different types of plasmon-enhancement and no junction control.
Minimizing Wafer Surface Damage and Chamber Material Contamination in New Plasma Processing Equipment (1990)

Magnetic enhancement was determined to be effective in reduction of the plasma potential. In extremely high-excitation-frequency plasma, the self-bias voltage of the electrode was substantially reduced, while the plasma potential remained constant. The plasma potential was effectively controlled by utilizing a DC-biased shield electrode, and found to be very effective in minimizing the chamber material contamination. The dual rf excitation plasma processing equipment was proposed and found to be capable of controlling the self-bias of the substrate without altering the target self-bias voltage.