gebhart/patrepeval huggingface dataset:
ChemInform Abstract: Substituted 3‐((Z)‐2‐(4‐nitrophenyl)‐2‐(1H‐tetrazol‐5‐yl)vinyl)‐4H‐chromen‐4‐ones as Novel anti‐MRSA Agents: Synthesis, SAR, and in vitro Assessment. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary figure S4 from Targeting eIF4A-Dependent Translation of KRAS Signaling Molecules (2023)

&lt;p&gt;Supplementary figure S4&lt;/p&gt;
Use of next generation sequencing and quantitative mass spectrometry to determine HER2 status. (2016)

e23237 Background: Traditional methods for HER2 assessment such as IHC and FISH are semi-quantitative and often limited by reproducibility issues. This may be a problem in tumors with borderline HER2 expression. We propose that selected reaction monitoring mass spectrometry (SRM-MS) and next generation sequencing (NGS) can be utilized to assess HER2 status. Methods: HER2 status was determined as per ASCO/CAP 2013 guidelines. SRM-MS was utilized to quantify HER2 protein levels in FFPE tissue blocks and a value ≥ 740 amol/μg was considered as positive. The same samples were analyzed using a capture-based NGS assay (MSK-IMPACT) to exome sequence 410 cancer-related genes. The Spearman rank correlation coefficient was calculated to assess the relationship between HER2 protein level by SRM-MS and HER2 gene fold change (FC) by NGS. Receiver operator curve (ROC) analysis was conducted to obtain optimal HER2 FC predictive of HER2 status by IHC/FISH and SRM-MS. Results: A total of 26 cases tested by IHC/FISH were selected and subjected to NGS and SRM-MS analysis. HER2 FC by NGS was highly correlated with HER2 protein level by SRM-MS (Spearman ρ = 0.94, P < .0001). In the ROC analysis, an NGS amplification FC threshold of 2 showed 92% agreement with HER2 protein level by SRM-MS (24/26 cases, Specificity = 100%, P < .0001). This threshold showed an agreement of 85% with HER2 status per IHC/FISH. One discordant case was IHC 3+ with low expression of HER2 per SRM-MS and no amplification by NGS (FC = 1.6). The other three discordant cases had IHC 2+ with borderline FISH (ratio 2.1-2.2), relatively low expression of HER2 by SRM-MS (422-953 amol/μg) and NGS amplification levels below our arbitrary threshold (FC: 1.5-1.8). We are expanding the analysis to include more HER2 equivocal cases to assess the discriminatory value of NGS and SRM-MS. Conclusions: Capture exome sequencing of a limited number of genes is becoming the gold standard to guide targeted therapy against oncogene-driven tumors. Given that this technique also allows the assessment of HER2 gene copy number, we posit that together with SRM-MS HER2 quantification it could be used to define the HER2 status of samples with borderline IHC/FISH and, ultimately, substitute these traditional techniques.
Non-Binary Approaches for Classification of Amyloid Brain PET (2019)

Machine learning (ML) is increasingly used in medical imaging. This paper provides pilot data of decision trees and random forests (RFs) to predict if a <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">18</sup> F-florbetapir brain positron emission tomography (PET) is positive or negative for amyloid deposition based on quantitative data analysis. The dataset included 55 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">18</sup> F-florbetapir brain PETs in participants with severe white matter disease and mild cognitive impairment (MCI), early Alzheimer's disease (AD) or transient ischemic events. The Montreal Cognitive Assessment (MoCA) score was known for each participant. All PET images were processed using the MINC toolkit to extract standardized uptake value ratios (SUVRs) for 59 regions of interest (features). Each PET was clinically read by 2 dual certified radiology/nuclear medicine physicians with final interpretation based on consensus. An initial study of RFs using conventional binary decision trees and PET quantitation suggests this is a powerful algorithm for PET classification as positive or negative for amyloid deposition. Preliminary data did not show improved results when a ternary RF approach was used. Finally, a soft-decision approach may be helpful to predict the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$\mathbf{MoCA}$</tex> score.
Influence of post exposure bake time on EUV photoresist RLS trade-off (2017)

To achieve high volume manufacturing, EUV photoresists need to push back the "RLS trade-off" by simultaneously improving Resolution, Line-Width Roughness and Sensitivity (exposure dose). Acid diffusion in chemically amplified resist is known to impact these performances. This work studies the diffusion of acid in chemically amplified resist by varying the post exposure bake duration while monitoring the evolution of CD and LWR for 6 chemically amplified EUV photoresists (CAR). We observed a first regime where both CD and LWR quickly decrease during the first 30s of post exposure bake (PEB). This can be related to the deprotection reaction taking place in the exposed part of the resist. After 60s the decrease in CD and LWR slows down significantly, likely related to a regime of acid diffusion from exposed to unexposed region, and acid-quencher neutralization at the interface of these two regions. We tested two resists with different protecting group and the one having lower activation energy shows a faster CD change in the second regime, resulting in a worsening of LWR for longer PEB time. On the contrary, a resist with a high quencher loading shows reduced net diffusion of acid towards the unexposed region and controls the resist edge profile. In other words longer PEB does not degrade LWR, but as it reduces the line CD, sensitivity is impacted. With an appropriate ratio selection of quencher to PAG, an EUV dose reduction of up to 12% can be achieved with a change from a standard 60 second to a 240 second PEB time, while keeping LWR and resolution constant and therefore pushing the RLS performances. Finally, we confirmed that the observations on positive tone development (PTD) resist could be applied to negative tone development (NTD) resist: with a high quencher NTD resist we observed a dose reduction of 8% for longer PEB time, keeping LWR and resolution constant.
Defining the comprehensive genomic landscapes of pancreatic ductal adenocarcinoma using real world endoscopic aspiration samples (2020)

Background Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis despite progress in clinically relevant molecular subtyping. Most patients are diagnosed with advanced disease at which point tumors are mostly unresectable. This leaves core biopsy or endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) as the sole source of tumor tissue for molecular characterization. Currently, these small tissue fragments are not considered suitable for genomic analysis, which is why this precious snapshot usually remains unexplored.
An Efficient Data Aggregation Scheme Using Degree of Dependence on Clusters in WSNs (2010)

Recently, much effort aiming at achieving ubiquitous networks has been made. A ubiquitous network refers to a network environment, which enables anytime and anywhere access, by possibly any given device or by any user. In a ubiquitous network, applications require many types of information such as temperature and so forth. A great deal of attention has been paid to aggregate this information in Wireless Sensor Networks (WSNs). A WSN consists of tiny nodes comprising sensing and communication devices. The information sensed by each node is relayed via other nodes in the WSN to the destination node called the ``sink''. One of the most significant challenges pertaining to any WSN is to reduce the energy consumption of its nodes, which run on scarce battery resources. An effective scheme to reduce this energy consumption is to exploit the sink node's mobility, which however presents new challenges to the sink node's routing and information aggregation. In this paper, we propose a new routing and data aggregation scheme based on clustering. Simulation results demonstrate that our scheme can provide better energy efficient data aggregation as compared to the KAT (K-means And Traveling salesman path) mobility.
Highly conductive nano-sized Magnéli phases titanium oxide (TiOx) (2017)

Despite the strong recent revival of Magnéli phase TiO<sub>x</sub> as a promising conductive material, synthesis of Magnéli phase TiO<sub>x</sub> nanoparticles has been a challenge because of the heavy sintering nature of TiO<sub>2</sub> at elevated temperatures. We have successfully synthesized chain-structured Magnéli phases TiO<sub>x</sub> with diameters under 30 nm using a thermal-induced plasma process. The synthesized nanoparticles consisted of a mixture of several Magnéli phases. A post-synthesis heat-treatment was performed to reduce the electrical resistivity without changing the particle morphology. The resistivity of the heat-treated particle was as low as 0.04 Ω.cm, with a specific surface area of 52.9 m<sup>2</sup> g<sup>-1</sup>. The effects of heat-treatment on changes in the crystal structure and their correlation with the electron conductivity are discussed based on transmission electron microscopy images, X-ray diffraction spectra, and X-ray adsorption fine structure spectra. Electrochemical characterization using cyclic voltammetry and potentiodynamic scan shows a remarkable electrochemical stability in a strongly oxidizing environment.
Crystallographic Studies of Phosphonate-Based α-Reaction Transition-State Analogues Complexed to Tryptophan Synthase, (1999)

In an effort to use a structure-based approach for the design of new herbicides, the crystal structures of complexes of tryptophan synthase with a series of phosphonate enzyme inhibitors were determined at 2.3 A or higher resolution. These inhibitors were designed to mimic the transition state formed during the alpha-reaction of the enzyme and, as expected, have affinities much greater than that of the natural substrate indole-3-glycerol phosphate or its nonhydrolyzable analogue indole propanol phosphate (IPP). These inhibitors are ortho-substituted arylthioalkylphosphonate derivatives that have an sp(3)-hybridized sulfur atom, designed to mimic the putative tetrahedral transition state at the C3 atom of the indole, and lack the C2 atom to allow for higher conformational flexibility. Overall, the inhibitors bind in a fashion similar to that of IPP. Glu-49 and Phe-212 are the two active site residues whose conformation changes upon inhibitor binding. A very short hydrogen bond between a phosphonate oxygen and the Ser-235 hydroxyl oxygen may be responsible for stabilization of the enzyme-inhibitor complexes. Implications for the mechanism of catalysis as well as directions for more potent inhibitors are discussed.
Light-extraction efficiency control in AlGaN-based deep-ultraviolet flip-chip light-emitting diodes: a comparison to InGaN-based visible flip-chip light-emitting diodes (2015)

We study light-extraction efficiency (LEE) of AlGaN-based deep-ultraviolet light-emitting diodes (DUV-LEDs) using flip-chip (FC) devices with varied thickness in remaining sapphire substrate by experimental output power measurement and computational methods using 3-dimensional finite-difference time-domain (3D-FDTD) and Monte Carlo ray-tracing simulations. Light-output power of DUV-FCLEDs compared at a current of 20 mA increases with thicker sapphire, showing higher LEE for an LED with 250-μm-thick sapphire by ~39% than that with 100-μm-thick sapphire. In contrast, LEEs of visible FCLEDs show only marginal improvement with increasing sapphire thickness, that is, ~6% improvement for an LED with 250-μm-thick sapphire. 3D-FDTD simulation reveals a mechanism of enhanced light extraction with various sidewall roughness and thickness in sapphire substrates. Ray tracing simulation examines the light propagation behavior of DUV-FCLED structures. The enhanced output power and higher LEE strongly depends on the sidewall roughness of the sapphire substrate rather than thickness itself. The thickness starts playing a role only when the sapphire sidewalls become rough. The roughened surface of sapphire sidewall during chip-separation process is critical for TM-polarized photons from AlGaN quantum wells to escape in lateral directions before they are absorbed by p-GaN and Au-metal. Furthermore, the ray tracing results show a reasonably good agreement with the experimental result of the LEE.
Importance of vegetation type in forest cover estimation (2012)

Forests are an important natural resource that play a major role in sustaining a number of vital geochemical and bioclimatic processes. Since damage to forests due to natural and anthropogenic factors can have long-lasting impacts on the health of the planet, monitoring and estimating forest cover and its losses at global, regional and local scales is of primary concern. Developing forest cover estimation techniques that utilize remote sensing datasets offers global applicability at high temporal frequencies. However, estimating forest cover using satellite observations is challenging in the presence of heterogeneous vegetation types, each having its unique data characteristics. In this paper, we explore techniques for incorporating information about the vegetation type in forest cover estimation algorithms. We show that utilizing the vegetation type improves performance regardless of the choice of input data or forest cover learning algorithm. We also provide a mechanism to automatically extract information about the vegetation type by partitioning the input data using clustering.
Automated nuclear segmentation in the determination of the Ki-67 labeling index in meningiomas. (2006)

The described method can reliably assess the Ki-67 LI much faster than conventional enumerating. The computerized method has the advantages of objectivity, accuracy, repeatability, and ease of use. There is no request for special stains nor special image acquiring systems. The plugin can be downloaded at the "Morphometrie" section of http://www.uniklinikum-saarland.de/neuropathologie.
Qualitative process automation (2003)

The authors address basic research in computer science, control theory and material processing science wherein the focus is to develop a process control system which enables in-situ process model development. A generic control system architecture using qualitative physics is described together with an explanation of the system operation involving multiple cooperating expert systems. Specific details involving development and application of the control system to autoclave curing of composites are presented together with recent research results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
NON-DEPLETING ANTIBODIES SPECIFIC FOR CD4, BUT NOT CD8, INDUCE LONG-TERM SURVIVAL OF LEWIS RAT HEARTS TRANSPLANTED INTO α1,3-GALACTOSYLTRANSFERASE KNOCKOUT (GT-KO) MICE (1999)

1008 Introduction: The generation of GT-KO mice has provided a new system for the study of anti-α1,3-Gal antibody (Ab) responses in rodents. We used the xenotransplantation model of baby Lewis rat hearts-to-GT-KO mice to study anti-α1,3-Gal Ab production in a xenotransplantation context. Specifically we investigated the ability of anti-CD4 and anti-CD8 Abs, at doses that have been reported as capable of inducing tolerance to heart allografts, to control xenograft rejection and anti-α1,3-Gal Ab production. Methods: Baby Lewis rat hearts (10-20 days old) were transplanted into 3-6 month old GT-KO mice. Immunosuppression with non-depleting anti-CD4 (YTS 177.9.6) or anti-CD8 Abs (YTS105.18.10) (generous gifts from Dr. H. Waldmann, Cambridge, UK) were administered daily, by intravenous injection, from day -2 to 0, then q.o.d. by intraperitoneal injection till day 22, at a dose of 1 mg/mouse/day. Titers of anti-α1,3-Gal Abs were determined by ELISA using BSA-α1,3-Gal as the specific substrate and BSA as negative controls. Results: 1. A 22 day treatment with anti-CD4, but not anti-CD8, was able to induce longterm xenograft survival. (Table)Table2. The titers of anti-α1,3-Gal IgM and IgG were elevated at the time of rejection of xenografts in all groups. However, in the anti-CD4 group, titers of anti-α1,3-Gal IgM and IgG were elevated by day 35 post-transplant, while the xenografts were rejected 32 to 35 days later. Conclusions: Non-depleting anti-CD4 Ab treatment alone is sufficient to induce the long-term survival of baby Lewis rat hearts transplanted into GT-KO mice. While xenograft rejection was always accompanied by elevated titers of anti-α1,3-Gal IgM and IgG, the presence of these antibodies per se did not necessarily result in acute xenograft rejection. These data suggest that rejection in this model is primarily dependent of CD4+ T cells.
Benzyltoluene/perhydro benzyltoluene – pushing the performance limits of pure hydrocarbon liquid organic hydrogen carrier (LOHC) systems (2022)

This study presents benzyltoluene/perhydro benzyltoluene as a very favourable liquid organic hydrogen carrier (LOHC) system for potential industrial applications.
Synthesis, molecular modeling, 2-D NMR, and biological evaluation of ILV mimics as potential modulators of protein kinase C (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis, molecular modeling, 2-D NMR, and biological evaluation of ILV mimics as potential modulators of protein kinase CAlan P. Kozikowski, Dawei Ma, Yuan Ping Pang, Patrick Shum, Vladimir Likic, Prasanna K. Mishra, Slobodan Macura, Alakananda Basu, John S. Lazo, and Richard G. BallCite this: J. Am. Chem. Soc. 1993, 115, 10, 3957–3965Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://pubs.acs.org/doi/10.1021/ja00063a015https://doi.org/10.1021/ja00063a015research-articleACS PublicationsRequest reuse permissionsArticle Views765Altmetric-Citations33LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Acute right heart failure after hemorrhagic shock and trauma pneumonectomy—a management approach (2016)

These data indicate that by decreasing PVR, iNO decreased RV afterload, preserved RV and LV function, and tissue oxygenation in this hemorrhagic shock and pneumonectomy model. This suggests that iNO may be a useful clinical adjunct to mitigate right heart failure and improve survival when trauma pneumonectomy is required.
Heterogeneous Expression of Recombination Activating Genes and Surface CD5 in CD3low CD4+CD8+ Thymocytes (1996)

Clonal selection in the thymus occurs mostly in the CD4+ CD8+ (double positive; DP) stage. Within DP thymocytes, cells in the CD3low subset are believed to be involved in clonal selection, and this subset is generally considered as a homogeneous population. T-cell antigen-receptor (TCR) signals on DP thymocytes are known to (i) down-regulate recombination activating gene (RAG) expression; and (ii) up-regulate the expression of T-cell function-associated molecules, including the cell surface glycoprotein CD5. The present study examined the expression of RAG and CD5 molecules among the subpopulations of normal adult DP thymocytes. DP thymocytes were fractionated according to their cell surface expression levels of TCR-CD3 complex into CD3dim, CD3lo, CD3med, and CD3hi cells, since TCR expression is known to increase during thymocyte maturation. Down-regulation of RAG mRNA was located between the CD3low and CD3med DP populations. However, within the DP CD3low subpopulation, we found that CD5 varies from low to high expression levels. Upon fractionation of DP CD3low thymocytes into CD5low and CD5high subsets, we were able to detect down-regulation of RAG transcripts within the CD3low subpopulation. Thus, by the criteria of CD5 surface expression and RAG mRNA expression levels, DP CD3low thymocytes can be considered a heterogeneous thymocyte subpopulation.
High Precision Hybrid RF and Ultrasonic Chirp-based Ranging for\n Low-Power IoT Nodes (2020)

Hybrid acoustic-RF systems offer excellent ranging accuracy, yet they\ntypically come at a power consumption that is too high to meet the energy\nconstraints of mobile IoT nodes. We combine pulse compression and synchronized\nwake-ups to achieve a ranging solution that limits the active time of the nodes\nto 1 ms. Hence, an ultra low-power consumption of 9.015 {\\mu}W for a single\nmeasurement is achieved. Measurements based on a proof-of-concept hardware\nplatform show median distance error values below 10 cm. Both simulations and\nmeasurements demonstrate that the accuracy is reduced at low signal-to-noise\nratios and when reflections occur. We introduce three methods that enhance the\ndistance measurements at a low extra processing power cost. Hence, we validate\nin realistic environments that the centimeter accuracy can be obtained within\nthe energy budget of mobile devices and IoT nodes. The proposed hybrid signal\nranging system can be extended to perform accurate, low-power indoor\npositioning.\n