gebhart/patrepeval huggingface dataset:
A relaxed fusion of information from real and synthetic images to predict complex behavior (2011)

An important component of cognitive robotics is the ability to mentally simulate physical processes and to compare the expected results with the information reported by a robot's sensors. In previous work, we have proposed an approach that integrates a 3D game-engine simulation into the robot control architecture. A key part of that architecture is the Match-Mediated Difference (MMD) operation, an approach to fusing sensory data and synthetic predictions at the image level. The MMD operation insists that simulated and predicted scenes are similar in terms of the appearance of the objects in the scene. This is an overly restrictive constraint on the simulation since parts of the predicted scene may not have been previously viewed by the robot. In this paper we propose an extended MMD operation that relaxes the constraint and allows the real and synthetic scenes to differ in some features but not in (selected) other features. Image difference operations that allow a real image and synthetic image generated from an arbitrarily colored graphical model of a scene to be compared. Scenes with the same content show a zero difference. Scenes with varying foreground objects can be controlled to compare the color, size and shape of the foreground.
<title>State-of-the-art for large-area high-resolution gray-scale and full-color AC plasma flat panel displays</title> (1993)

A development status evaluation is presented for gas plasma display technology, noting how tradeoffs among the parameters of size, resolution, speed, portability, color, and image quality can yield cost-effective solutions for medical imaging, CAD, teleconferencing, multimedia, and both civil and military applications. Attention is given to plasma-based large-area displays' suitability for radar, sonar, and IR, due to their lack of EM susceptibility. Both monochrome and color displays are available.
Human mesenchymal stem cell-engineered hepatic cell sheets accelerate liver regeneration in mice (2015)

Mesenchymal stem cells (MSCs) are an attractive cell source for cell therapy. Based on our hypothesis that suppression of Wnt/β-catenin signal enhances hepatic differentiation of human MSCs, we developed human mesenchymal stem cell-engineered hepatic cell sheets by a small molecule compound. Screening of 10 small molecule compounds was performed by WST assay, TCF reporter assay, and albumin mRNA expression. Consequently, hexachlorophene suppressed TCF reporter activity in time- and concentration-dependent manner. Hexachlorophene rapidly induced hepatic differentiation of human MSCs judging from expression of liver-specific genes and proteins, PAS staining, and urea production. The effect of orthotopic transplantation of human mesenchymal stem cell-engineered hepatic cell sheets against acute liver injury was examined in one-layered to three-layered cell sheets system. Transplantation of human mesenchymal stem cell-engineered hepatic cell sheets enhanced liver regeneration and suppressed liver injury. The survival rates of the mice were significantly improved. High expression of complement C3 and its downstream signals including C5a, NF-κB, and IL-6/STAT-3 pathway was observed in hepatic cell sheets-grafted tissues. Expression of phosphorylated EGFR and thioredoxin is enhanced, resulting in reduction of oxidative stress. These findings suggest that orthotopic transplantation of hepatic cell sheets manufactured from MSCs accelerates liver regeneration through complement C3, EGFR and thioredoxin.
Integrated in silico and experimental assessment of disease relevance of PCDH19 missense variants (2021)

PCDH19 is a nonclustered protocadherin molecule involved in axon bundling, synapse function, and transcriptional coregulation. Pathogenic variants in PCDH19 cause infantile-onset epilepsy known as PCDH19-clustering epilepsy or PCDH19-CE. Recent advances in DNA-sequencing technologies have led to a significant increase in the number of reported PCDH19-CE variants, many of uncertain significance. We aimed to determine the best approaches for assessing the disease relevance of missense variants in PCDH19. The application of the American College of Medical Genetics and Association for Molecular Pathology (ACMG-AMP) guidelines was only 50% accurate. Using a training set of 322 known benign or pathogenic missense variants, we identified MutPred2, MutationAssessor, and GPP as the best performing in silico tools. We generated a protein structural model of the extracellular domain and assessed 24 missense variants. We also assessed 24 variants using an in vitro reporter assay. A combination of these tools was 93% accurate in assessing known pathogenic and benign PCDH19 variants. We increased the accuracy of the ACMG-AMP classification of 45 PCDH19 variants from 50% to 94%, using these tools. In summary, we have developed a robust toolbox for the assessment of PCDH19 variant pathogenicity to improve the accuracy of PCDH19-CE variant classification.
The Impact of Vehicle Structural Components on Radiation Patterns of a Window Glass Embedded FM Antenna (2011)

The relative long wavelength of FM radio signals compared to a typical vehicle length means that a window glass-embedded FM band antenna couples strongly to vehicle structural components. Numerical simulations have been conducted to identify which key structural components in a full-size SUV have an effect on the average antenna gain patterns. In particular, it was found that the rear hatch and the seats of the SUV had a large effect on FM antenna gain patterns and thus required more careful modeling for the electromagnetic simulation. Also, it was found that the sunroof status, opened or closed, had a moderate effect on FM antenna gain patterns. Comparison with experimentally obtained FM antenna gain patterns demonstrated the importance of using the most detailed model possible when simulating patterns in the FM band.
610 Analysis of Turbulent Premixed Flames using DNS database (2000)

Direct numerical simulation of a turbulent premixed flame with single-step irreversible Arrhenius-type reaction is performed in order to evaluate turbulent transport properties. Because of reducing Reynolds number of inflowing turbulence, the calculation became stable and developed. The increase of the streamwise component of velocity fluctuation results in the increase of turbulent kinetic energy in the flame region. The x-component of velocity fluctuation increased twice as much as y, z-component. The mean pressure gradient term and the pressure work term in Favre averaged transport equation have an important role in production of turbulence. But in this case the mean pressure has fluctuation, so the effect of the pressure to turbulent kinetic energy couldn't be declared.
Saturn: a terabit packet switch using dual round-robin (2002)

Input-output buffering with a moderate speedup has been widely considered as the most feasible solution for large-capacity switches. We propose a new terabit/sec packet switch and call it the Saturn (Switch At Terabit Using dual Round-robiN) switch. It uses a simple dual round-robin arbitration scheme to schedule packet and achieves high throughput and low statistical delay bound. It employs a bit-sliced crossbar fabric to switch packets at 10 Gbit/s at inputs and outputs, and adopts a novel token-tunneling technique to arbitrate contending packets at high speed (e.g,, within 10 ns), thus achieving a switch capacity of more than one terabit/sec by existing electronic technology.
Enhanced survival of vascular smooth muscle cells accounts for heightened elastin deposition in arteries of neonatal spontaneously hypertensive rats (2009)

Abnormal stiffening and narrowing of arteries are characteristic features of spontaneously hypertensive rats (SHR). In this strain, we have previously demonstrated an increased elastin content and abnormal organization of lamellae in conduit and resistance arteries from neonatal rats that preceded the impending inward remodelling, increased vascular stiffness and development of hypertension. The aim of this study was to assess the mechanism responsible for such excessive and aberrant elastin deposition in SHR vessels during perinatal development. We compared elastin, collagen and fibronectin production (inmunocytochemistry and quantitative assay of metabolically labelled insoluble elastin), DNA content as well as cell proliferation (proliferative cellular nuclear antigen, bromodeoxyuridine incorporation) and death rates (propidium iodide exclusion test, terminal transferase nick and labeling (TUNEL) assay) in cultures of vascular smooth muscle cells (VSMC) derived from neonatal SHR and Wistar-Kyoto (WKY) control rats. Cultures of VSMC derived from neonatal SHR exhibited hypertrophy, produced more elastin, collagen and fibronectin and contained more DNA than equally plated WKY counterparts. Further analysis revealed that the higher net DNA content in SHR-derived cultures was due to increased diploidy, but not to a heightened cell multiplication. The SHR-derived VSMC also exhibited lower rates of cell death and apoptosis, which were associated with increased levels of the anti-apoptotic protein, survivin. We therefore conclude that the peculiar heightened survival of matrix-producing VSMC in neonatal SHR is responsible for accumulation of hard-wearing elastin and other extracellular matrix elements in the growing arteries, thereby contributing to the subsequent development of systemic hypertension.
Thermal Conductivity Measurements and Modeling of Phase-Change Ge2Sb2Te5Materials (2009)

Phase-change technology has been widely used in rewritable disks for optical recording applications. Recently, it has also received attention as a candidate for future high-storage-density nonvolatile random access memory, due to its much longer cycle life (∼1013) and fast data access time (∼100 ns) compared with the existing flash memory technology. In this article, we present thermal conductivity data and models for phase-change GeSbTe material that would be helpful in performance optimization and improvement in the reliability of phase change–based data storage devices and systems. We present thermal conductivity data for a 40-nm-thick Ge2Sb2Te5 phase-change layer in both amorphous and crystalline states using electrical resistance joule heating and thermometry techniques. The limits of lattice and electronic thermal conductivities are investigated to determine their relative contributions to the total thermal conductivity as a function of tellurium concentration, crystalline structures, and temperature.
Application of a Broad-Range Resequencing Array for Detection of Pathogens in Desert Dust Samples from Kuwait and Iraq (2011)

A significant percentage of the human population is exposed to high levels of naturally occurring airborne dusts. Although the link between airborne particulate inhalation and a variety of respiratory diseases has long been established, little is known about the pathogenic role of the microbial component of the dust. In this study, we applied highly multiplexed PCR and a high-density resequencing microarray (RPM-TEI version 1.0) to screen samples of fine topsoil particles and airborne dust collected in 19 locations in Iraq and Kuwait for the presence of a broad range of human pathogens. The results indicated the presence of potential human pathogens, including Mycobacterium, Brucella, Coxiella burnetii, Clostridium perfringens, and Bacillus. The presence of Coxiella burnetii, a highly infectious potential biowarfare agent, was confirmed and detected in additional samples by use of a more sensitive technique (real-time PCR), indicating a high prevalence of this organism in the analyzed samples. The detection of potentially viable pathogens in breathable dusts from arid regions of Iraq and Kuwait underscores the importance of further study of these environments.
Isolation of the (+)-Pinoresinol-Mineralizing Pseudomonas sp. Strain SG-MS2 and Elucidation of Its Catabolic Pathway (2017)

Pinoresinol is a dimer of two β-β'-linked coniferyl alcohol molecules. It is both a plant defense molecule synthesized through the shikimic acid pathway and a representative of several β-β-linked dimers produced during the microbial degradation of lignin in dead plant material. Until now, little has been known about the bacterial catabolism of such dimers. Here we report the isolation of the efficient (+)-pinoresinol-mineralizing <i>Pseudomonas</i> sp. strain SG-MS2 and its catabolic pathway. Degradation of pinoresinol in this strain is inducible and proceeds via a novel oxidative route, which is in contrast to the previously reported reductive transformation by other bacteria. Based on enzyme assays and bacterial growth, cell suspension, and resting cell studies, we provide conclusive evidence that pinoresinol degradation in strain SG-MS2 is initiated by benzylic hydroxylation, generating a hemiketal via a quinone methide intermediate, which is then hydrated at the benzylic carbon by water. The hemiketal, which stays in equilibrium with the corresponding keto alcohol, undergoes an aryl-alkyl cleavage to generate a lactone and 2-methoxyhydroquinone. While the fate of 2-methoxyhydroquinone is not investigated further, it is assumed to be assimilated by ring cleavage. The lactone is further metabolized via two routes, namely, lactone ring cleavage and benzylic hydroxylation via a quinone methide intermediate, as described above. The resulting hemiketal again exists in equilibrium with a keto alcohol. Our evidence suggests that both routes of lactone metabolism lead to vanillin and vanillic acid, which we show can then be mineralized by strain SG-MS2.<b>IMPORTANCE</b> The oxidative catabolism of (+)-pinoresinol degradation elucidated here is fundamentally different from the reductive cometabolism reported for two previously characterized bacteria. Our findings open up new opportunities to use lignin for the biosynthesis of vanillin, a key flavoring agent in foods, beverages, and pharmaceuticals, as well as various new lactones. Our work also has implications for the study of new pinoresinol metabolites in human health. The enterodiol and enterolactone produced through reductive transformation of pinoresinol by gut microbes have already been associated with decreased risks of cancer and cardiovascular diseases. The metabolites from oxidative metabolism we find here also deserve attention in this respect.
Hair Regeneration from Transected Follicles in Duplicative Surgery (2009)

Duplicative surgery might represent a successful alternative for hair transplantation, because both portions are capable of regenerating a healthy hair. Moreover, our results suggest the possible presence of stem cells in both halves of the follicle.
End-user interactions with intelligent and autonomous systems (2012)

Systems that learn from or personalize themselves to users are quickly becoming mainstream yet interaction with these systems is limited and often uninformative for the end user. This workshop focuses on approaches and challenges to explore making these systems transparent, controllable and ultimately trustworthy to end users. The aims of the workshop are to help establish connections among researchers and industrial practitioners using real-world problems as catalysts to facilitate the exchange of approaches, solutions, and ideas about how to better support end users.
Owning an Enterprise With Three Lines of Code (2019)

Today, Software is rarely developed the green field: software developers are composers that build new system by combining existing (Open Source) solutions. Custom code is, in many development projects, a curiosity.As a result, all software depends on open source projects, which, sometimes, are as small as three lines of code or as large as several millions lines of code. One the one hand, these projects speed up the development. On the other hand, their use requires trust and care: with a few lines of code in an installation script, your development system can be powned or a small vulnerability in a dependency can be the root cause of one of the largest data leaks of the last years.In this talk, I will discuss, using real world examples, the security threats of using software dependencies carelessly and provide recommendations that help to minimise this risk.
Optical modeling of waveguide coupled TES detectors towards the SAFARI instrument for SPICA (2012)

The next generation of space missions targeting far-infrared wavelengths will require large-format arrays of extremely sensitive detectors. The development of Transition Edge Sensor (TES) array technology is being developed for future Far-Infrared (FIR) space applications such as the SAFARI instrument for SPICA where low-noise and high sensitivity is required to achieve ambitious science goals. In this paper we describe a modal analysis of multi-moded horn antennas feeding integrating cavities housing TES detectors with superconducting film absorbers. In high sensitivity TES detector technology the ability to control the electromagnetic and thermo-mechanical environment of the detector is critical. Simulating and understanding optical behaviour of such detectors at far IR wavelengths is difficult and requires development of existing analysis tools. The proposed modal approach offers a computationally efficient technique to describe the partial coherent response of the full pixel in terms of optical efficiency and power leakage between pixels. Initial wok carried out as part of an ESA technical research project on optical analysis is described and a prototype SAFARI pixel design is analyzed where the optical coupling between the incoming field and the pixel containing horn, cavity with an air gap, and thin absorber layer are all included in the model to allow a comprehensive optical characterization. The modal approach described is based on the mode matching technique where the horn and cavity are described in the traditional way while a technique to include the absorber was developed. Radiation leakage between pixels is also included making this a powerful analysis tool.
A large family of ancient repeat elements in the human genome is under strong selection (2006)

Although conserved noncoding elements (CNEs) constitute the majority of sequences under purifying selection in the human genome, they remain poorly understood. CNEs seem to be largely unique, with no large families of similar elements reported to date. Here, we search for CNEs among the ancestral repeat classes in the human genome and report the discovery of a large CNE family containing >900 members. This family belongs to the MER121 class of repeats. Although the MER121 family members show considerable sequence variation among one another, the individual copies show striking conservation in orthologous locations across the human, dog, mouse, and rat genomes. The element is also present and conserved in orthologous locations in the marsupial, but its genome-wide dispersal postdates the divergence from birds. The comparative genomic data indicate that MER121 does not encode a family of either protein-coding or RNA genes. Although the precise function of these elements remains unknown, the evidence suggests that this unusual family may play a cis-regulatory or structural role in mammalian genomes.
A 100 kHz SiC Sparse Matrix Converter (2007)

A Sparse Matrix Converter (SMC) is a direct AC/AC converter that contains no large energy storage components. A 100 kHz, 1.5 kW SiC SMC is presented, which uses 1300 V, 4 A SiC JFET cascode devices. The SMC is operated from a 50 Hz, 230 V mains supply and has a predicted efficiency of 94%. A tower-like construction results in a volume of 1 liter and a power density of 1.5 kW/liter (25 W/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ). The measured waveforms verify matrix operation and show that the SiC JFET cascode devices have turn-on switching times of 30 ns. Analysis shows that the SMC heat sink and EMI filter volume can be minimized to 0.14 liters if the switching frequency is reduced to 40 kHz.
Structure‐Activity Relationship of Phenylpyrazolones against Trypanosoma cruzi (2020)

Chagas disease is a neglected parasitic disease caused by the parasitic protozoan Trypanosoma cruzi and currently affects around 8 million people. Previously, 2-isopropyl-5-(4-methoxy-3-(pyridin-3-yl)phenyl)-4,4-dimethyl-2,4-dihydro-3H-pyrazol-3-one (NPD-0227) was discovered to be a sub-micromolar inhibitor (pIC<sub>50</sub> =6.4) of T. cruzi. So far, SAR investigations of this scaffold have focused on the alkoxy substituent, the pyrazolone nitrogen substituent and the aromatic substituent of the core phenylpyrazolone. In this study, modifications of the phenyldihydropyrazolone scaffold are described. Variations were introduced by installing different substituents on the phenyl core, modifying the geminal dimethyl and installing various bio-isosteres of the dihydropyrazolone group. The anti T. cruzi activity of NPD-0227 could not be surpassed as the most potent compounds show pIC<sub>50</sub> values of around 6.3. However, valuable additional SAR data for this interesting scaffold was obtained, and the data suggest that a scaffold hop is feasible as the pyrazolone moiety can be replaced by a oxazole or oxadiazole with minimal loss of activity.
Coordination of CcpA and CodY regulators in Staphylococcus aureus USA300 strains (2022)

Abstract The complex crosstalk between metabolism and gene regulatory networks makes it difficult to untangle individual constituents and study their precise roles and interactions. To address this issue, we modularized the transcriptional regulatory network (TRN) of the Staphylococcus aureus USA300 strain by applying Independent Component Analysis (ICA) to 385 RNA sequencing samples. We then combined the modular TRN model with a metabolic model to study the regulation of carbon and amino acid metabolism. Our analysis showed that regulation of central carbon metabolism by CcpA and amino acid biosynthesis by CodY are closely coordinated. In general, S. aureus increases the expression of CodY-regulated genes in the presence of preferred carbons sources such as glucose. This transcriptional coordination was corroborated by metabolic model simulations that also showed increased amino acid biosynthesis in the presence of glucose. Further, we found that CodY and CcpA cooperatively regulate the expression of ribosome hibernation promoting factor, thus linking metabolic cues with translation. In line with this hypothesis, expression of CodY-regulated genes is tightly correlated with expression of genes encoding ribosomal proteins. Together, we propose a coarse-grained model where expression of S. aureus genes encoding enzymes that control carbon flux and nitrogen flux through the system is coregulated with expression of translation machinery to modularly control protein synthesis. While this work focuses on three key regulators, the full TRN model we present contains 76 total independently modulated sets of genes, each with the potential to uncover other complex regulatory structures and interactions. Importance Staphylococcus aureus is a versatile pathogen with an expanding antibiotic resistance profile. The biology underlying its clinical success emerges from an interplay of many systems such as metabolism and gene regulatory networks. This work brings together models for these two systems to establish fundamental principles governing the regulation of S. aureus central metabolism and protein synthesis. Studies of these fundamental biological principles are often confined to model organisms such as Escherichia coli . However, expanding these models to pathogens can provide a framework from which complex and clinically important phenotypes such as virulence and antibiotic resistance can be better understood. Additionally, the expanded gene regulatory network model presented herein can deconvolute the biology underlying other important phenotypes in this pathogen.