gebhart/patrepeval huggingface dataset:
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome (2023)

Previous urinary tract infections (UTIs) can predispose one to future infections; however, the underlying mechanisms affecting recurrence are poorly understood. We previously found that UTIs in mice cause differential bladder epithelial (urothelial) remodelling, depending on disease outcome, that impacts susceptibility to recurrent UTI. Here we compared urothelial stem cell (USC) lines isolated from mice with a history of either resolved or chronic uropathogenic Escherichia coli (UPEC) infection, elucidating evidence of molecular imprinting that involved epigenetic changes, including differences in chromatin accessibility, DNA methylation and histone modification. Epigenetic marks in USCs from chronically infected mice enhanced caspase-1-mediated cell death upon UPEC infection, promoting bacterial clearance. Increased Ptgs2os2 expression also occurred, potentially contributing to sustained cyclooxygenase-2 expression, bladder inflammation and mucosal wounding-responses associated with severe recurrent cystitis. Thus, UPEC infection acts as an epi-mutagen reprogramming the urothelial epigenome, leading to urothelial-intrinsic remodelling and training of the innate response to subsequent infection.
Constitutively activated CK2 potentially plays a pivotal role in Theileria-induced lymphocyte transformation (2005)

Activation of casein kinase II (CK2) was one of the first observations made on how Theileria parasites manipulate host cell signal transduction pathways and we argue that CK2 induction may in fact contribute to many of the different activation events that have been described since 1993 for Theileria-infected lymphocytes such as sustained activation of transcription factors c-Myc and NF-kappaB. CK2 also contributes to infected lymphocyte survival by inhibiting caspase activation and is probably behind constitutive PI3-K activation by phosphorylating PTEN. Finally, we also discuss how CK2A may act not only as a kinase, but also as a stimulatory subunit for the protein phosphatase PP2A, so dampening down the MEK/ERK and Akt/PKB pathways and for all these reasons we propose CK2 as a central player in Theileria-induced lymphocyte transformation.
DEVELOPMENT OF AN INSTRUMENTED ULNAR HEAD PROSTHESIS TO QUANTIFY LOAD TRANSFER IN-VITRO (2008)

Quantitative measurements of load transfer through the distal radioulnar joint (DRUJ) are limited. An instrumented ulnar head prosthesis was developed to measure bending and torsion moments about the three anatomic axes of the ulna. This device has shown repeatable loading data following insertion in a cadaveric specimen during active forearm rotation trials conducted in an in-vitro upper extremity joint simulator. The data acquired from this device will have important implications for upper extremity modeling, implant fixation and design, and optimizing surgical procedures related to DRUJ arthroplasty. To develop a system to quantify in-vitro load transfer through the distal radioulnar joint (DRUJ) following ulnar head arthroplasty during simulated active forearm rotation. Also, the effect of an eccentric ulnar head implant design was investigated. A load-measuring system was developed that was easily surgically inserted, and produced repeatable loading data. The instrumented implant developed in this study will contribute to the optimization of surgical procedures and implant design parameters related to distal ulnar arthroplasty. Four pairs of strain gauges were applied to the stem of an ulnar head prosthesis to measure bending and torsion moments about the three anatomic axes of the ulna. Three ulnar heads were machined with varying eccentricities (axisymmetric, 1.5 mm offset and 3.0 mm offset). The implant was inserted in one unpreserved cadaveric upper extremity and active forearm rotation induced using a computer controlled joint simulator. Repeatability (assessed using the maximum standard deviation over 5 trials of pronation and supination) was less than 9% of the output range for all loads. Bending and torsion moments between −0.4 and 0.5 Nm, correlating to joint loads between 0 and 50 N, were measured. The measured loads followed a consistent pattern with forearm position. Higher loads were noted for the eccentric implant heads compared to the axisymmetric head, especially at the extreme ranges of rotation. Clinical interpretation of these findings is difficult since the optimal loading scenario for distal ulnar implant longevity remains unknown. Please contact author for diagrams and graphs.
Physical properties of dense amorphous poly(vinyl alcohol) as revealed by molecular dynamics simulation (2002)

Dense amorphous poly(vinyl alcohol) (PVAL) built from a chain with 145 repeating units was studied by constant number of particles, pressure, and temperature-molecular dynamics simulations at temperatures between 400 and 527K. The results of the simulations were compared with pressure–volume–temperature data, solubility parameter, x-ray scattering pattern, and data for the characteristic ratio. The fractional free-volume distribution was computed and the diffusion characteristics of water in the polymer were studied. Experimental water desorption data were obtained and they were compared with the results obtained from the simulations. The AMBER-force field was initially adopted to generate the dynamics, but this force field yielded structures with too high specific volumes. The size of the oxygen atoms was then decreased until the maximum difference between experimental and simulated specific volumes was within 2.2%. This modification of the force field resulted in satisfactory agreement between experimental and simulated data for the volume expansion coefficient and the compressibility in the temperature range from 402 to 502K. The essential features in the local packing of the atoms as revealed by wide-angle x-ray scattering were also present in the simulated structures. Simulated values for the characteristic ratio were in agreement with earlier reported experimental values. The solubility parameter showed only minor deviations from reported experimental values. Water-molecule trajectories yielded diffusivity in accordance with the experimental zero-concentration diffusivity. The water molecule makes well-resolved jumps (cage-like penetrant motion) even at the highest temperature of simulation, 510K. The water molecule rotates much faster than it makes jumps in the PVAL matrix. The lifetimes of the hydrogen bonds between polymer chain segments were longer than for those of the hydrogen bonds formed between water and polymer chain segments. This finding suggests that the primary rate-controlling factor for water diffusion in this polymer is the constraining effect of hydrogen bonds formed between polymer chain segments.
Training Deep Normalizing Flow Models in Highly Incomplete Data Scenarios with Prior Regularization (2021)

Deep generative frameworks including GANs and normalizing flow models have proven successful at filling in missing values in partially observed data samples by effectively learning -- either explicitly or implicitly -- complex, high-dimensional statistical distributions. In tasks where the data available for learning is only partially observed, however, their performance decays monotonically as a function of the data missingness rate. In high missing data rate regimes (e.g., 60% and above), it has been observed that state-of-the-art models tend to break down and produce unrealistic and/or semantically inaccurate data. We propose a novel framework to facilitate the learning of data distributions in high paucity scenarios that is inspired by traditional formulations of solutions to ill-posed problems. The proposed framework naturally stems from posing the process of learning from incomplete data as a joint optimization task of the parameters of the model being learned and the missing data values. The method involves enforcing a prior regularization term that seamlessly integrates with objectives used to train explicit and tractable deep generative frameworks such as deep normalizing flow models. We demonstrate via extensive experimental validation that the proposed framework outperforms competing techniques, particularly as the rate of data paucity approaches unity.
The Method of Fundamental Solutions for the Impulse Responses Reconstruction in Arbitrarily Shaped Plates (2011)

International audience
Social Analysis and the COVID-19 Crisis (2020)

This book is a collective journal of the COVID-19 pandemic. With first-hand accounts of the pandemic as it unfolded, it explores the social and the political through the lens of the outbreak. Featuring contributors located in India, the United States, Brazil, the United Kingdom, Germany, and Bulgaria, the book presents us with simultaneous multiple histories of our time. The volume documents the beginning of social distancing and lockdown measures adopted by countries around the world and analyses how these bore upon prevailing social conditions in specific locations. It presents the authors' personal observations in a lucid conversational style as they reflect on themes such as the reorganization of political debates and issues, the experience of the marginalized, theodicy, government policy responses, and shifts into digital space under lockdown, all of these under an overarching narrative of the healthcare and economic crisis facing the world. A unique and engaging contribution, this book will be useful to students and researchers of sociology, public health, political economy, public policy, and comparative politics. It will also appeal to general readers interested in pandemic literature.
Exploring the impact of scenario and distance information on the reliability assessment of multi-sensor systems (2022)

With the growth of self-driving technologies, the reliability analysis of automated driving systems has received considerable attention from both academia and industry. Safety of the intended functionality (SOTIF) serves as one of the primary standards to assure the reliability and safety of the automated driving system. One of its key issues is the performance limitations of perception sensor systems. Generally, the reliability of the perception sensor system depends on the different scenarios of the driving environment. In this work, we investigate the sensor features and dependencies of the front camera and the top LiDAR of the nuTonomy scenes (nuScenes) dataset with respect to scenarios (e.g., rain and night) and distance information (e.g., two distance-based regions of interest). In addition, we apply the obtained parameters to a proven analytical reliability model to examine the impact of scenario and distance information on the reliability assessment.
Mechanical Shear Properties of Cell-Polymer Cartilage Constructs (1999)

Cartilaginous constructs were created by using bovine chondrocytes on synthetic, biodegradable scaffolds made of fibrous polyglycolic acid (PGA). The constructs have previously been shown to resemble natural articular cartilage biochemically and histologically. The mechanical properties of articular cartilage mainly depend on the swollen extracellular matrix (ECM), which is a gel consisting of collagen fibers and proteoglycans in a fluid phase of water and electrolytes. The biomechanical properties of the constructs and the build-up of the ECM were studied using dynamic, nondestructive measurements in shear. A small, harmonic strain, lambda < or = 5 x 10(-4), was applied to the sample, and the resulting stress was recorded and used for calculating the complex shear modulus G*. The applied strain was much smaller than that used in confined compression. The shear modulus G* correlated well with both the collagen and glycosaminoglycan content of the constructs but did not reach the same level as in natural cartilage. Collagen is the dominant component contributing to the shear strength of cartilage, and G* was shown to depend approximately quadratically on the collagen content of the constructs. The difference in G* between the constructs and natural cartilage was shown to depend on both the biochemical composition and the microstructure of the constructs. () ()
Suppression and Activation of the Malignant Phenotype by Extracellular Matrix in Xenograft Models of Bladder Cancer: A Model for Tumor Cell “Dormancy” (2013)

A major problem in cancer research is the lack of a tractable model for delayed metastasis. Herein we show that cancer cells suppressed by SISgel, a gel-forming normal ECM material derived from Small Intestine Submucosa (SIS), in flank xenografts show properties of suppression and re-activation that are very similar to normal delayed metastasis and suggest these suppressed cells can serve as a novel model for developing therapeutics to target micrometastases or suppressed cancer cells. Co-injection with SISgel suppressed the malignant phenotype of highly invasive J82 bladder cancer cells and highly metastatic JB-V bladder cancer cells in nude mouse flank xenografts. Cells could remain viable up to 120 days without forming tumors and appeared much more highly differentiated and less atypical than tumors from cells co-injected with Matrigel. In 40% of SISgel xenografts, growth resumed in the malignant phenotype after a period of suppression or dormancy for at least 30 days and was more likely with implantation of 3 million or more cells. Ordinary Type I collagen did not suppress malignant growth, and tumors developed about as well with collagen as with Matrigel. A clear signal in gene expression over different cell lines was not seen by transcriptome microarray analysis, but in contrast, Reverse Phase Protein Analysis of 250 proteins across 4 cell lines identified Integrin Linked Kinase (ILK) signaling that was functionally confirmed by an ILK inhibitor. We suggest that cancer cells suppressed on SISgel could serve as a model for dormancy and re-awakening to allow for the identification of therapeutic targets for treating micrometastases.
Fluorescence‐Based Fibre Optic Arrays: A Universal Platform for Sensing (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Effects of advanced illumination schemes on design manufacturability and interactions with optical proximity corrections (2000)

As advanced source illumination options become available for production implementation, at the 150 nm and 130 nm technology nodes, non-linear effects are introduced in the design shrink- path. In previous technologies, in particular 250 and 180 nm, partial coherence settings are used as a method to control mono- dimensional CD variations among features with different pitches. Source optimization becomes a function of the design pattern to be imaged and of the OPC applied to this design. The advent of Quadrupole, Quasar and Custom Illumination Apertures enables and enhances the use of Optical Extension (OE) technique to image features down to half of the KrF wavelength, but imposes stringent geometrical restrictions on the design, which are not currently well understood. Our work presents a novel methodology for analyzing effects of source illumination variations on full chip design layouts, extending and generalizing the concept of process window. By combining a powerful full-chip imaging simulator and an illuminator design tool, a very large parameter space of design geometries can be explored. Comparison between the desired and the actually imaged patterns is performed, yielding statistically significant CD errors. The analysis of this very large number of printability data points, covering the whole design pattern, allows the classification of critical geometries, i.e. the portions of the design which are process window limiting. Our methodology not only provides an illumination optimization tool for the lithographer, but above all, highlights the need for manufacturability verification performed early at the physical layout stage of the semiconductor design process. In particular, a design verification application is shown, where progressive linear shrinks of a given layout are matched against optimal image settings. Quantitative analysis of the resulting pattern failure modes provides a direct feedback for the layout designer.
Osteochondral Lesions of the Tibial Plafond and Ankle Instability With Ankle Cartilage Lesions: Proceedings of the International Consensus Meeting on Cartilage Repair of the Ankle (2022)

Level V, mechanism-based reasoning.
Interaction of F/sub 2/ excimer laser light with various types of synthetic SiO/sub 2/ glasses: towards the 3rd generation of synthetic silica (2003)

The authors consider the VUV-UV optical transmission spectra of synthetic silica specimens before and after F/sub 2/ laser irradiation. The absorption edge in the specimens differs from sample to sample: the absorption edge of the F-doped specimen is located at a shorter wavelength (153 nn) compared with the wet SiO/sub 2/ (155 nm) or the dry SiO/sub 2/ (157nm).
Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS (2012)

Artículo escrito por un elevado número de autores, solo se referencian el que aparece en primer lugar, el nombre del grupo de colaboración, si le hubiere, y los autores pertenecientes a la UAM
Nanomechanical Characterization of Organic Surface Passivation Films on 50 nm Patterns during Area-Selective Deposition (2021)

Area-selective deposition (ASD) is a “bottom-up” substrate-selective material deposition process, considered as a promising alternative to current “top-down” pattering techniques. The most studied and successful ASD strategies envisage a combination of atomic layer deposition (ALD) and a passivation layer, which prevents material deposition on the non-growth areas. As ASD targets increasingly smaller dimensions, metrology challenges are prominent along with preserving confined film growth. For patterned substrates with nanometric critical dimensions, only a few characterization techniques can be employed to assess the ASD performance. However, these techniques provide no or little insight into the passivation layer. This is a crucial limitation as the blocking film plays a key role in the ASD process. In this work, pulsed force mode atomic force microscopy (AFM) is used to characterize and monitor the quality of the passivation films by measuring the surface energy fluctuations occurring on the patterned substrate undergoing ASD. As the evolution of the relative adhesion force distribution of the sample under ALD conditions is recorded, the octadecanethiol (ODT) coverage on non-growth areas is accurately estimated. The heavily temperature-dependent self-assembled monolayer degradation revealed by the nanomechanical characterization is supported by X-ray photoelectron spectroscopy. As Hf3N4 ALD is performed, the top-down scanning electron microscopy investigation is employed to show the strong relationship between ASD quality upon ALD and pulsed force AFM-derived ODT coverage.
Memory addressing organization for stream-based reconfigurable computing (2003)

The paper gives a survey on methods to cope with the memory bandwidth problem, especially in the context of data-stream-based computing systems, like reconfigurable (and hardwired) datapath arrays, introduced by R. Hartenstein (Proc. ICECS 2002) and elsewhere.
Evolutionary process development towards next generation crystalline silicon solar cells : a semiconductor process toolbox application (2012)

Bulk crystalline Silicon solar cells are covering more than 85% of the world’s roof top module installation in 2010. With a growth rate of over 30% in the last 10 years this technology remains the working horse of solar cell industry. The full Aluminum back-side field (Al BSF) technology has been developed in the 90’s and provides a production learning curve on module price of constant 20% in average. The main reason for the decrease of module prices with increasing production capacity is due to the effect of up scaling industrial production. For further decreasing of the price per wattpeak silicon consumption has to be reduced and efficiency has to be improved. In this paper we describe a successive efficiency improving process development starting from the existing full Al BSF cell concept. We propose an evolutionary development includes all parts of the solar cell process: optical enhancement (texturing, polishing, anti-reflection coating), junction formation and contacting. Novel processes are benchmarked on industrial like baseline flows using high-efficiency cell concepts like i-PERC (Passivated Emitter and Rear Cell). While the full Al BSF crystalline silicon solar cell technology provides efficiencies of up to 18% (on cz-Si) in production, we are achieving up to 19.4% conversion efficiency for industrial fabricated, large area solar cells with copper based front side metallization and local Al BSF applying the semiconductor toolbox.
Low Band Gap Cyanovinylene Polymers Based on Ethylenedioxythiophene (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTLow Band Gap Cyanovinylene Polymers Based on EthylenedioxythiopheneGregory A. Sotzing, Christopher A. Thomas, John R. Reynolds, and Peter J. SteelView Author Information Center for Macromolecular Science and Engineering, Department of Chemistry, University of Florida, Gainesville, Florida 32611 Department of Chemistry, University of Canterbury, Christchurch, New Zealand Cite this: Macromolecules 1998, 31, 11, 3750–3752Publication Date (Web):May 8, 1998Publication History Received26 August 1997Revised13 February 1998Published online8 May 1998Published inissue 1 June 1998https://pubs.acs.org/doi/10.1021/ma971290fhttps://doi.org/10.1021/ma971290frapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views700Altmetric-Citations68LEARN 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-Alertsclose SUBJECTS:Oxidation,Plastics,Polymerization,Polymers,Redox reactions Get e-Alerts
Power and Channel Allocation for Cooperative Relay in Cognitive Radio Networks (2010)

In this paper, we investigate power and channel allocation for cooperative relay in a three-node cognitive radio network. Different from conventional cooperative relay channels, cognitive radio relay channels can be divided into three categories: direct, dual-hop, and relay channels, which provide three types of parallel end-to-end transmission. In the context, those spectrum bands available at all three nodes may either perform relay diversity transmission or assist the transmission in direct or dual-hop channels. On the other hand, the relay node involves both dual-hop and relay diversity transmission. In this paper, we develop power and channel allocation approaches for cooperative relay in cognitive radio networks that can significantly improve the overall end-to-end throughput. We further develop a low complexity approach that can obtain most of the benefits from power and channel allocation with minor performance loss.