gebhart/patrepeval huggingface dataset:
Environmental Pseudomonads Inhibit Cystic Fibrosis Patient-Derived Pseudomonas aeruginosa (2016)

We demonstrate that clinical CF-derived isolates of P. aeruginosa are susceptible to competition in the presence of environmental pseudomonads. We observed that many diverse environmental strains exhibited varied antagonistic profiles against a panel of clinical P. aeruginosa isolates, suggesting the presence of distinct mechanisms of inhibition among these ecological strains. Understanding the properties of these antagonistic events offers the potential for discoveries of antimicrobial compounds or metabolic pathways important to the development of novel treatments for P. aeruginosa infections.
Toll-like receptor triggering in cord blood mesenchymal stem cells (2009)

Recently, the antagonizing effect on the differentiation of mesenchymal stem cells (MSCs) by toll-like receptor (TLR) ligands, was described.Our study shows that on more primitive cord blood derived MSCs, the expression of TLRs and ligand-induced triggering differs from that of bone marrow derived MSCs.At the RNA level, cord blood MSCs (unrestricted somatic stem cells; USSCs) express low levels of TLR1,3,5,9 and high levels of TLR4 and TLR6.At the protein level expression of TLR5 and very low expression of TLR4 was observed.NF-B translocation studies revealed that both TLR4 and TLR5 are functional, although signalling kinetics induced by the individual ligands differed.Stimulation of USSCs with either lipopolysaccharide (LPS) or flagellin resulted in a marked increase of interleukin (IL)-6 and/or IL-8 production although levels differed significantly between both stimuli.Interestingly, tumour necrosis factor (TNF)-␣ was undetectable after TLR stimulation, which appeared to be due to an inactivated TNF-␣ promoter in USSCs.Moreover, osteoblastic differentiation was enhanced after triggering USSCs with LPS and flagellin.In summary, TLR4 and 5 signalling in USSCs is slow and results in the up-regulation of a restricted number of pro-inflammatory cytokines and enhanced osteoblastic differentiation.Apparently, the outcome of TLR signalling depends on the cell type that expresses them.
Stratix 10 NX Architecture and Applications (2021)

The advent of AI has driven the adoption of high density low precision arithmetic on FPGAs. This has resulted in new methods in mapping both arithmetic functions as well as dataflows onto the fabric, as well as some changes to the embedded DSP Blocks. Technologies outside of the FPGA realm have also evolved, such as the addition of tensor structures for GPUs, and also the introduction of numerous AI ASSPs, all of which have a higher claimed performance and efficiency than current FPGAs. In this paper we will introduce the Stratix 10 NX device (NX), which is a variant of FPGA specifically optimized for the AI application space. In addition to the computational capabilities of the standard programmable soft logic fabric, a new type of DSP Block provides the dense arrays of low precision multipliers typically used in AI implementations. The architecture of the block is tuned for the common matrix-matrix or vector-matrix multiplications in AI, with capabilities designed to work efficiently for both small and large matrix sizes. The base precisions are INT8 and INT4, along with shared exponent support for support block floating point FP16 and FP12 numerics. All additions/accumulations can be done in INT32 or IEEE754 single precision floating point (FP32), and multiple blocks can be cascaded together to support larger matrices. We will also describe methods by which the smaller precision multipliers can be aggregated to create larger multiplier that are more applicable to standard signal processing requirements. In terms of overall compute throughput, Stratix 10 NX achieves 143 INT8/FP16 TOPs/FLOPs, or 286 INT4/FP12 TOPS/FLOPs at 600MHz. Depending on the configuration, power efficiency is in the range of 1-4 TOPs or TFLOPs/W.
Abstract LB-92: Loss of a single Hic1 allele accelerates polyp formation in Apc mice (2010)

Abstract Mutations in the Adenomatous Polyposis Colt (APC) gene have been implicated both in familial as well as sporadic gastrointestinal (GI) cancers. APC mutations are associated with autosomal dominant inheritance of disease in humans. Similarly, mice that contain a single mutant APC gene encoding a protein truncated at aa 716 (Ape716) develop multiple polyps throughout the GI tract as early as 4 weeks after birth. Inactivation of another tumor suppressor gene, Hypermethylated in Cancer 1 (HIC1) often occurs in human cancers, including GI, via CpG island hypermethylation. Homozygous deletion of Hic1 in mice results in major developmental defects and embryonic lethality. Hic1 heterozygotes have previously been shown to develop age dependent tumors of a variety of tissue types. We now report that loss of a single Hic1 allele can promote crypt dysplasia of the small intestine and further potentiate polyp formation in Apc716 mice. Hic1+/−, Apc716 double heterozygous mice develop increased numbers of polyps throughout the GI tract by 60 days. Hic1 expression is lost in polyps with a selective increase in DNA hypermethylation of this gene only in polyps from double-heterozygous mice. Immunohistochemical analyses of polyps show increases in markers such as -catenin, SIRT1, and Sox9, indicating aberrant Wnt and Hic1 signaling. Together, our data suggest that loss of a gene frequently silenced via epigenetic mechanisms, Hic1, can cooperate with loss of a gene often mutated in GI cancer, Apc, to promote tumorigenesis in an in-vivo model of multiple intestinal neoplasia. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-92.
Nfix Regulates Temporal Progression of Muscle Regeneration through Modulation of Myostatin Expression (2016)

Nfix belongs to a family of four highly conserved proteins that act as transcriptional activators and/or repressors of cellular and viral genes. We previously showed a pivotal role for Nfix in regulating the transcriptional switch from embryonic to fetal myogenesis. Here, we show that Nfix directly represses the Myostatin promoter, thus controlling the proper timing of satellite cell differentiation and muscle regeneration. Nfix-null mice display delayed regeneration after injury, and this deficit is reversed upon in vivo Myostatin silencing. Conditional deletion of Nfix in satellite cells results in a similar delay in regeneration, confirming the functional requirement for Nfix in satellite cells. Moreover, mice lacking Nfix show reduced myofiber cross sectional area and a predominant slow twitching phenotype. These data define a role for Nfix in postnatal skeletal muscle and unveil a mechanism for Myostatin regulation, thus providing insights into the modulation of its complex signaling pathway.
Modeling and Forecasting of Defect-Limited Yield in Semiconductor Manufacturing (2008)

A detailed cause-and-effect stochastic model is developed to relate the type, size, location, and frequency of observed defects to the final yield in IC manufacturing. The model is estimated on real data sets with a large portion of unclassified defects and un inspected layers, and in presence of clustering of defects. Results of this analysis are used for evaluating kill ratios and effects of different factors, identifying the most dangerous cases and the most probable causes of failures, forecasting the yield, and designing optimal yield-enhancement strategies.
Enhanced Radar Phase Measurements by means of Highly Dispersive Waveguides (2019)

In this contribution, we present a newly developed radar phase measurement principle that utilizes the natural dispersion inside of waveguides in close proximity to their cutoff frequency. Therefore, a model to describe the effect of the dispersion on the radar phase is set up which provides a basis for a robust phase evaluation process. The model and process are verified by three-dimensional electromagnetic field simulations as well as by measurements that are carried out of a prototype setup with a millimeter wave frequency modulated continuous wave radar system.
Adjuvant versus salvage radiation therapy for prostate cancer and the risk of death (2010)

Radiation therapy after PSA failure as compared with adjuvant RT was not associated with an increased risk of ACM in men with Gleason score ≤7 and pT3R0 or pT2R1 disease.
Nanomonitor: A Miniature Electronic Biosensor for Glycan Biomarker Detection (2010)

Based on its performance metrics, the NanoMonitor has excellent potential for development as a point-of-care handheld electronic biosensor device for routine detection of glycan biomarkers from clinical samples.
Structure and Properties of Butadiene-tert-Butyl Methacrylate and Butadiene/Styrene-tert-Butyl Methacrylate Triblock Copolymer Ionomers (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure and Properties of Butadiene-tert-Butyl Methacrylate and Butadiene/Styrene-tert-Butyl Methacrylate Triblock Copolymer IonomersDon Loveday, Garth L. Wilkes, Craig D. Deporter, and James E. McGrathCite this: Macromolecules 1995, 28, 23, 7822–7830Publication Date (Print):November 1, 1995Publication History Published online1 May 2002Published inissue 1 November 1995https://pubs.acs.org/doi/10.1021/ma00127a032https://doi.org/10.1021/ma00127a032research-articleACS PublicationsRequest reuse permissionsArticle Views192Altmetric-Citations8LEARN 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 Get e-Alerts
The orientation dependence of the hydrogen distribution within Mo/V (110) and (001) multilayered artificial superlattices (1997)

We have investigated the hydrogen distribution within multilayered Mo/V (110) and (001) artificial superlattices. The hydrogen concentration, determined by the nuclear resonance reaction, is found to decrease with decreasing layer thickness. The decrease is attributed to an interface region with reduced hydrogen content. The extension of this interface region is found to be two monolayers in Mo/V (110), compared to the previously reported three monolayers in Mo/V (001) superlattices. In the (110) oriented samples the relative amount of H in the interface region decreases with increasing average H content (H/V - 0.5). This effect is shown to be related to the orientation of the hydrogen planes with respect to the boundaries implied by the Mo/V interfaces. The hydrogen induced volume change, obtained by conventional x-ray diffraction (XRD) and reciprocal space mapping, is found to be smaller for the (110) samples than for the (001) oriented samples at room temperature.
Investigations of enhanced device characteristics in pentacene-based field effect transistors with sol-gel interfacial layer (2007)

Pentacene films grown on sol-gel silica dielectrics showed a significant enhancement in field effect mobility, threshold voltages, and subthreshold swings. This letter investigates the contributing factors for the enhanced device characteristics. The smoother and more hydrophobic film surfaces of sol-gel silica (rms roughness of ∼1.9Å and water contact angle of ∼75°) induced larger pentacene grains, yielding mobilities in excess of ∼1cm2∕Vs at an operating voltage of −20V. Different sol-gel silica film thicknesses showed similar trends in improved performances, indicating that this phenomenon is clearly a semiconductor-dielectric interface phenomenon rather than a bulk dielectric effect.
OpenCL library of stream memory components targeting FPGAs (2015)

In recent years, high-level languages and compilers, such as OpenCL have improved both productivity and FPGA adoption on a wider scale. One of the challenges in the design of high-performance stream FPGA applications is iterative manual optimization of the numerous application buffers (e.g., arrays, FIFOs and scratch-pads). First, to achieve the desired throughput, the programmer faces the burden of analyzing the memory accesses of each application buffer, and based on observed data locality determines the optimal on-chip buffering, and off-chip read/write data access strategy. Second, to minimize throughput bottlenecks, the programmer has to carefully partition the limited on-chip memory resources among many application buffers. In this work we present an FPGA OpenCL library of pre-optimized stream memory components (SMCs). The library contains three types of SMCs, which implement frequently applied data transformations: 1) stencil, 2) transpose and 3) tiling. The library generates SMCs that are optimized both for the specific data transformation they perform as well as the user specified data set size. Further, to ease the partitioning of on-chip memory resources among many application memories, the library automatically maps application buffers to on-chip and off-chip memory resources. This is achieved by enabling the programmer to specify an on-chip memory budget for each component. In terms of on-chip memory, the SMCs perform data buffering to exploit data locality and maximize reuse. In terms of off-chip memory accesses, the SMCs optimize read/write memory operations by performing data coalescing, bursting and prefetching. We show that using the SMC library, the programmer can quickly generate scalable, pre-optimized stream application memory components, thus reaching throughput targets without time consuming manual memory optimization.
Demonstration of defect free EUV mask for 22nm NAND flash contact layer using electron beam inspection system (2011)

Fabrication of defect free EUV masks including their inspection is the most critical challenge for implementing EUV lithography into semiconductor high volume manufacturing (HVM) beyond 22nm half-pitch (HP) node. The contact to bit-line (CB) layers of NAND flash devices are the most likely the first lithography layers that EUV will be employed for manufacturing due to the aggressive scaling and the difficulty for making the pattern with the current ArF lithography. To assure the defect free EUV mask, we have evaluated electron beam inspection (EBI) system eXplore&trade; 5200 developed by Hermes Microvision, Inc. (HMI) [1]. As one knows, the main issue of EBI system is the low throughput. To solve this challenge, a function called Lightning Scan&trade; mode has been recently developed and installed in the system, which allows the system to only inspect the pattern areas while ignoring blanket areas, thus dramatically reduced the overhead time and enable us to inspect CB layers of NAND Flash device with much higher throughput. In this present work, we compared the Lightning scan mode with Normal scan mode on sensitivity and throughput. We found out the Lightning scan mode can improve throughput by a factor of 10 without any sacrifices of sensitivity. Furthermore, using the Lightning scan mode, we demonstrated the possibility to fabricate the defect free EUV masks with moderate inspection time.
Precise point positioning with multipath estimation (2016)

Precise Point Positioning with low-cost GNSS receivers is attractive for numerous applications, as it can provide centimeter-level positioning without the exchange of raw measurements from a reference station. However, pseudorange multipath has to be accurately considered for a reliable ambiguity fixing. In this paper, we derive a precise model for the pseudorange multipath from the received signal, the correlator and discriminator function. We consider multiple reflections with individual amplitudes, phasings, Doppler shifts and code delays. We estimate a pseudorange multipath parameter for each satellite in our precise position solution to exploit the temporal correlation of multipath and to prevent a mapping of multipath to other state parameters. The method was tested with real measurements from a low-cost receiver and SSR corrections and showed that a millimeter-level positioning accuracy is achievable.
Compounds and methods for improving plant performance (2023)

The invention is directed to methods and compositions for increasing a growth characteristic of a plant, increasing nutrient use efficiency of a plant, or improving a plant's ability to overcome stress comprising applying a composition comprising ketosuccinamate, a derivative thereof, or a salt thereof, to the plant or to a propagation material of the plant.
A Distal Locus Element Mediates IFN-γ Priming of Lipopolysaccharide-Stimulated TNF Gene Expression (2014)

Interferon γ (IFN-γ) priming sensitizes monocytes and macrophages to lipopolysaccharide (LPS) stimulation, resulting in augmented expression of a set of genes including TNF. Here, we demonstrate that IFN-γ priming of LPS-stimulated TNF transcription requires a distal TNF/LT locus element 8 kb upstream of the TNF transcription start site (hHS-8). IFN-γ stimulation leads to increased DNase I accessibility of hHS-8 and its recruitment of interferon regulatory factor 1 (IRF1), and subsequent LPS stimulation enhances H3K27 acetylation and induces enhancer RNA synthesis at hHS-8. Ablation of IRF1 or targeting the hHS-8 IRF1 binding site in vivo with Cas9 linked to the KRAB repressive domain abolishes IFN-γ priming, but does not affect LPS induction of the gene. Thus, IFN-γ poises a distal enhancer in the TNF/LT locus by chromatin remodeling and IRF1 recruitment, which then drives enhanced TNF gene expression in response to a secondary toll-like receptor (TLR) stimulus.
Diode pumped alkali lasers (DPALs): an overview (2008)

The concept of power-scalable, high beam-quality diode pumped alkali lasers was introduced in 2003 [Krupke, US Patent No. 6,643,311; Opt. Letters, 28, 2336 (2003)]. Since then several laboratory DPAL devices have been reported on, confirming many of the spectroscopic, kinetic, and laser characteristics projected from literature data. This talk will present an overview of the DPAL concept, summarize key relevant properties of the cesium, rubidium, and potassium alkali vapor gain media so-far examined, outline power scaling considerations, and highlight results of published DPAL laboratory experiments.
Theoretical and Experimental Investigation of Two-to-One Internal Resonance in MEMS Arch Resonators (2018)

We investigate theoretically and experimentally the two-to-one internal resonance in micromachined arch beams, which are electrothermally tuned and electrostatically driven. By applying an electrothermal voltage across the arch, the ratio between its first two symmetric modes is tuned to two. We model the nonlinear response of the arch beam during the two-to-one internal resonance using the multiple scales perturbation method. The perturbation solution is expanded up to three orders considering the influence of the quadratic nonlinearities, cubic nonlinearities, and the two simultaneous excitations at higher AC voltages. The perturbation solutions are compared to those obtained from a multimode Galerkin procedure and to experimental data based on deliberately fabricated Silicon arch beam. Good agreement is found among the results. Results indicate that the system exhibits different types of bifurcations, such as saddle node and Hopf bifurcations, which can lead to quasi-periodic and potentially chaotic motions.
Reduction of ureteral stent encrustation by modulating the urine pH and inhibiting the crystal film with a new oral composition: a multicenter, placebo controlled, double blind, randomized clinical trial (2020)

Abstract Background: Encrustation of ureteral double J stents is a common complication that may affect its removal. The aim of the proposed study is to evaluate the efficacy and safety of a new oral composition to prevent double J stent encrustation in indwelling times up to 8 weeks. Methods: A double-blinded, multicenter, placebo-controlled trial was conducted with 105 patients with indwelling double J stents enrolled across 9 public hospitals in Spain. The patients were randomly assigned (1:1) into intervention or placebo groups for 3 to 8 weeks and both groups self-monitored daily their morning urine pH levels. The primary outcome of analysis was the degree of stent ends encrustation, defined by a 4-point score (0 – none; 3 – global encrustation) using macroscopic and electron microscopy analysis of crystals, after 3 to 8-w indwelling period. Score was exponentially transformed according to calcium levels. Secondary endpoints included urine pH decrease, stent removal, and incidence of adverse events. Results: The intervention group benefits from a lower global encrustation rate of stent ends than placebo group (1% vs 8.2%; p &lt; 0.018). Mean encrustation score was 85.12 (274.5) in the intervention group and 18.91 (102.27) in the placebo group (p &lt; 0.025). Considering the secondary end points, treated patients reported greater urine pH decreases (p = 0.002). No differences in the incidence of adverse events were identified between the groups. Conclusions: Our data suggest that the use of this new oral composition is beneficial in the context of ureteral double J indwelling by decreasing mean, as well as global encrustation. Trial registration: This trial was registered at www.clinicaltrials.gov under the name “Combined Use of a Medical Device and a Dietary Complement in Patient Urinary pH Control in Patients With an Implanted Double J Stent” with date 2 nd November 2017, code NCT03343275, and URL: https://clinicaltrials.gov/ct2/show/record/NCT03343275?term=NCT03343275&amp;draw=2&amp;rank=1 Keywords: double J stent; encrustation; nutraceutical; L-methionine; phytin; pH.