gebhart/patrepeval huggingface dataset:
Optimum Conditions for Novel One-Step Cleaning Method for Pre-Gate Oxide Cleaning Using Robust Design Methodology (2000)

A novel one-step cleaning method has been developed for pre-gate-oxide cleaning to replace the conventional RCA two-step cleaning process. Tetramethyl ammonium hydroxide (TMAH) and ethylenediamine tetraacetic acid (EDTA) are added into the RCA SC-1 cleaning solution to enhance cleaning efficiency. We adapt a robust design methodology (Genichi Taguchi method) to analyze the results of our experiments. Using this novel method, it is found that the optimum conditions are A 1 B 2 C 1 D 1 (A 1 : TMAH:NH 4 OH=1:50, B 2 : EDTA concentration is 100 ppm, C 1 : cleaning time is 5 min, and D 1 : cleaning temperature is 60°C). This novel one-step cleaning method is very promising for future large-sized silicon wafer cleaning processes because it has the advantages of reduced processing time and temperature, cost reduction due to reduced chemical usage and improved performance.
Kernelized Matrix Factorization for Collaborative Filtering (2016)

Matrix factorization (MF) methods have shown great promise in collaborative filtering (CF). Conventional MF methods usually assume that the correlated data is distributed on a linear hyperplane, which is not always the case. Kernel methods are used widely in SVMs to classify linearly non-separable data, as well as in PCA to discover the non-linear embeddings of data. In this paper, we present a novel method to kernelize matrix factorization for collaborative filtering, which is equivalent to performing the low-rank matrix factorization in a possibly much higher dimensional space that is implicitly defined by the kernel function. Inspired by the success of multiple kernel learning (MKL) methods, we also explore the approach of learning multiple kernels from the rating matrix to further improve the accuracy of prediction. Since the right choice of kernel is usually unknown, our proposed multiple kernel matrix factorization method helps to select effective kernel functions from the candidates. Through extensive experiments on real-world datasets, we show that our proposed method captures the nonlinear correlations among data, which results in improved prediction accuracy compared to the state-of-art CF models.
Simple Methodology for Heck Arylation at C‐8 of Adenine Nucleosides (2008)

Abstract A simple method for the arylation of 8‐vinyladenine nucleoside derivatives is reported. With a broad set of aryl iodides and bromides, the reaction is catalyzed by the simple combination palladium acetate/tris( o ‐tolyl)phosphine/triethylamine [Pd(OAc) 2 /( o ‐tol) 3 P/Et 3 N]. As expected, aryl chlorides are more difficult coupling partners but some undergo reactions with more exotic catalysts. Although trans ‐olefins are the major products, minor amounts of cis ‐isomers are detected in some cases, and a post ‐arylation mechanism for their formation is proposed. Finally, by subtle catalyst modulation chemoselective N ‐arylation of the nucleoside can be achieved in the presence of the vinyl moiety.
Abstract 3571: Precise somatic mutation prediction in the absence of matching normal DNA (2017)

Abstract Accurate identification of somatic mutations is an essential first step for many cancer studies. It is usually done by comparing the genome of the tumour to the reference genome sequence derived from a normal tissue taken from the same donor. However, there are a number of possible scenarios in which matched normal tissues might be not available for comparisons. It is most commonly encountered when performing analysis on retrospective studies with human tissues from clinical trials or pathology archives when normal samples were not collected in the first place or patient consent precludes examination of normal tissue or germline variants. Another common scenario is the use of a cancer cell line as an experimental model, many of which have no information on the donor’s normal genome. In this work, we describe an algorithm to identify somatic single nucleotide variants (SNVs) in Next Generation Sequencing (NGS) data in the absence of normal samples using a machine learning approach. Our algorithm was evaluated using a family of supervised learning classifications across six different cancer types and ~1,600 samples, including cell lines, fresh frozen tissues, and formalin-fixed paraffin-embedded (FFPE) tissues. In addition, our algorithm was tested with both deep targeted sequencing and whole exome sequencing strategies. The algorithm correctly classified between 95% and 98% of somatic mutations with F1-measure ranges from 75.9% to 98.6% depending on the tumour type. We have released the algorithm as a software package called ISOWN (Identification of SOmatic mutations Without matching Normal tissues), which is available as Open Source under Apache License 2.0 from https://github.com/ikalatskaya/ISOWN. Citation Format: Irina Kalatskaya, Quang Trinh, Melanie Spears, John Bartlett, Lincoln Stein. Precise somatic mutation prediction in the absence of matching normal DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3571. doi:10.1158/1538-7445.AM2017-3571
Preparation of aryl chlorides from phenols (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation of aryl chlorides from phenolsElliott Bay, David A. Bak, Peter E. Timony, and Andrea Leone-BayCite this: J. Org. Chem. 1990, 55, 10, 3415–3417Publication Date (Print):May 1, 1990Publication History Published online1 May 2002Published inissue 1 May 1990https://pubs.acs.org/doi/10.1021/jo00297a087https://doi.org/10.1021/jo00297a087research-articleACS PublicationsRequest reuse permissionsArticle Views3932Altmetric-Citations20LEARN 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 Role of Doxycycline as a Matrix Metalloproteinase Inhibitor for the Treatment of Chronic Wounds (2009)

Many chronic wounds fail to heal with conventional therapy, resulting in disability and impaired quality of life. New technologies using recombinant growth factors, autologous growth factors, or bioengineered skin-tissue substitutes have been shown to be effective, but these treatments are costly. An effective, low-cost treatment to improve healing of chronic wounds is needed. The molecular environment of chronic wounds, like many other chronic inflammatory diseases, contains abnormally high levels of proinflammatory cytokines (tumor necrosis factor [TNF]-alpha and interleukin [IL]-1beta]) and matrix metalloproteinases (MMPs), which impair normal wound healing. In animal models and clinical studies of ulcerative diseases, doxycycline, an inexpensive and Food and Drug Administration (FDA)-approved antibiotic, appears to inhibit members of the MMP superfamily like MMPs and TNF-alpha-converting enzyme (TACE). This article provides an overview of the roles of MMPs and intrinsic tissue inhibitors of metalloproteinases (TIMPs) in wound healing and the damaging effects of chronically elevated levels of MMPSs in chronic wounds. It also explores the use of topical doxycycline, a synthetic MMP inhibitor (MMPI), to enhance healing of chronic wounds.
Isolable Pyridinium Trifluoromethoxide Salt for Nucleophilic Trifluoromethoxylation (2021)

An isolable pyridinium trifluoromethoxide salt is prepared from the reaction of 4-dimethylaminopyridine with the commercially available liquid 2,4-dinitro(trifluoromethoxy)benzene. The salt is an effective trifluoromethoxide source for S<sub>N</sub>2 reactions to form trifluoromethyl ethers.
Embryonic Germ Cells Are Capable of Adipogenic Differentiation In Vitro and In Vivo (2008)

There is an extensive clinical need for soft tissue filler materials, such as adipose tissue, for plastic and reconstructive surgery. Due to limitations with autologous adipose transplantation, engineered adipose tissue provides a potential alternative therapy. Embryonic germ cells form embryoid bodies and subsequent embryoid body-derived (EBD) cells have the ability to differentiate toward multiple tissue types. The objective of this study was to demonstrate that EBD cells were capable of adipogenic differentiation in vitro and in vivo using a poly(ethylene glycol)-based hydrogel scaffold. EBD cells underwent adipogenic differentiation in vitro and in vivo. Results were directly compared to adipogenic differentiation of adult bone marrow-derived mesenchymal stem cells (MSCs). Differentiated EBD cells in both monolayer and three-dimensional in vitro culture demonstrated fat granules by light microscopy, stained positive for lipids with oil red-O, and expressed adipocyte-specific genes (lipoprotein lipase [LPL], peroxisome proliferator activated receptor gamma2, and adipocyte-specific fatty acid binding protein [alphaP2]). In vivo constructs demonstrated adipogenic differentiation by alphaP2 and LPL gene expression and oil red-O staining of lipid granules. In conclusion, EBD cells are capable of differentiating toward an adipogenic lineage in vitro and in vivo. EBD cells' adipogenic differentiation is comparable to that of MSCs and demonstrate therapeutic potential for soft tissue augmentation and reconstruction.
Enhancing wireless performance using reflectors (2017)

Signal decay is the fundamental problem of wireless communications, especially in an indoor environment where line-of-sight (LOS) paths for signal propagation are often blocked and various indoor objects exacerbate signal fading. There are three reasons for signal decay: long transmission distance, signal penetration, and reflection. In this paper, we propose OptRe which optimally places metallic reflectors - providing a highly reflective surface that can reflect impinging signals almost 100% - in indoor environments to reduce the reflection loss and enhance wireless transmissions. It enhances both WiFi signal and low-power IoT devices without changing their configurations or network protocols. To enable OptRe, we first develop an empirical signal propagation model that can accurately estimate the signal strength and adapt itself to the reflectors' location. Using micro-benchmarks, our empirical signal propagation model is shown to be more accurate than the other existing path loss models. We also optimally place reflectors to maximize the worst-case signal coverage within the target indoor areas. Our extensive experimental evaluation results have shown OptRe to enhance signal strength for different types of wireless signals by almost 2x.
Anatomic Studies of the Miniature Swine Cornea (2018)

The domestic swine eye resembles the human eye both anatomically and physiologically. Xenotransplantation of the swine cornea to humans in need of full keratoplasty shows promise as a potential therapeutic strategy to restore vision in individuals with advanced corneal disease, especially those residing in developing nations. That said, we characterized the morphology of corneas from miniature swine, which are smaller in size, easier to handle, and more cost-effective compared to domestic swine. Eyes (N = 15) were harvested from miniature swine from different age groups: 1 month (N = 3), 2 month (N = 3), 4 month (N = 3), 8 month (N = 3), as well as 24 month old adult domestic swine (N = 3). They were immediately submerged in fixative and processed for histological examination at the light and transmission electron microscopic level. Gross anatomic measurements of the cornea were significantly less (P value ≤ 0.05) in miniature swine versus domestic swine. Corneal strata exhibited morphological characteristics similar to the domestic swine cornea. Adult miniature swine corneas show similar overall corneal thickness at 8 months of age versus domestic swine. Miniature swine exhibit similar corneal morphology with the domestic pig and humans, with the exception of Bowman's layer, which is absent in pigs. Therefore, miniature pigs may be a useful resource of corneal tissue for humans in need of full keratoplasty, as well as serve as a large eye model for ophthalmology residents to develop surgical skills and for development and testing of ocular therapeutic strategies that translate to humans. Anat Rec, 301:1955-1967, 2018. © 2018 Wiley Periodicals, Inc.
10.9 A 13.1-to-28GHz fractional-N PLL in 32nm SOI CMOS with a &#x0394;&#x03A3; noise-cancellation scheme (2015)

A key challenge in high-performance I/O, as well as in reconfigurable radio and radar applications, is the generation of a clean clock signal supporting a wide range of frequencies. The introduction of fractional-N synthesis capability for wide-tuning-range applications enables generation of arbitrary output frequencies within that range from a single choice of reference frequency. A critical challenge in fractional-N synthesizer design is the cancellation of the deterministic component of the fractional-N ΔΣ noise, allowing fractional-N solutions to be applied even in noise-sensitive contexts. In this work, we present a flexible, wide tuning range, fractional-N PLL implemented in 32nm SOI CMOS technology, introducing two separate methods - one in the proportional path and one in the integral path - to process and suppress ΔΣ noise. The demonstrated design includes an integrated automatic calibration loop to optimize noise suppression, uses a dual VCO complex to support generation of any output frequency from 13 to 28GHz from a reference clock in the range of 15 to 300 MHz, and also supports extended tuning down to 1GHz through the use of configurable output dividers.
An Experiment on Learning with Limited Information: Nonconvergence, Experimentation Cascades, and the Advantage of Being Slow (2012)

The authors would like to thank Arthur Schram, Frans van Winden, Arno Riedl, Ronald Bosman, and the rest of the members of CREED at the University of Amsterdam for their hospitality; John Ledyard, Yan Chen, participants at the
Antiviral screening identifies adenosine analogs targeting the endogenous dsRNA Leishmania RNA virus 1 (LRV1) pathogenicity factor (2017)

The endogenous double-stranded RNA (dsRNA) virus Leishmaniavirus (LRV1) has been implicated as a pathogenicity factor for leishmaniasis in rodent models and human disease, and associated with drug-treatment failures in Leishmania braziliensis and Leishmania guyanensis infections. Thus, methods targeting LRV1 could have therapeutic benefit. Here we screened a panel of antivirals for parasite and LRV1 inhibition, focusing on nucleoside analogs to capitalize on the highly active salvage pathways of Leishmania, which are purine auxotrophs. Applying a capsid flow cytometry assay, we identified two 2'-C-methyladenosine analogs showing selective inhibition of LRV1. Treatment resulted in loss of LRV1 with first-order kinetics, as expected for random virus segregation, and elimination within six cell doublings, consistent with a measured LRV1 copy number of about 15. Viral loss was specific to antiviral nucleoside treatment and not induced by growth inhibitors, in contrast to fungal dsRNA viruses. Comparisons of drug-treated LRV1<sup>+</sup> and LRV1<sup>-</sup> lines recapitulated LRV1-dependent pathology and parasite replication in mouse infections, and cytokine secretion in macrophage infections. Agents targeting Totiviridae have not been described previously, nor are there many examples of inhibitors acting against dsRNA viruses more generally. The compounds identified here provide a key proof-of-principle in support of further studies identifying efficacious antivirals for use in in vivo studies of LRV1-mediated virulence.
Testosterone Suppresses Protective Responses of the Liver to Blood-Stage Malaria (2004)

Testosterone induces a lethal outcome in otherwise self-healing blood-stage malaria caused by Plasmodium chabaudi. Here, we examine possible testosterone effects on the antimalaria effectors spleen and liver in female C57BL/6 mice. Self-healing malaria activates gating mechanisms in the spleen and liver that lead to a dramatic reduction in trapping activity, as measured by quantifying the uptake of 3-mum-diameter fluorescent polystyrol particles. However, testosterone delays malaria-induced closing of the liver, but not the spleen. Coincidently, testosterone causes an approximately 3- to 28-fold depression of the mRNA levels of nine malaria-responsive genes, out of 299 genes tested, only in the liver and not in the spleen, as shown by cDNA arrays and Northern blotting. Among these are the genes encoding plasminogen activator inhibitor (PAI1) and hydroxysteroid sulfotransferase (STA2). STA2, which detoxifies bile acids, is suppressed 10-fold by malaria and an additional 28-fold by testosterone, suggesting a severe perturbation of bile acid metabolism. PAI1 is protective against malaria, since disruption of the PAI1 gene results in partial loss of the ability to control the course of P. chabaudi infections. Collectively, our data indicate that the liver rather than the spleen is a major target organ for testosterone-mediated suppression of resistance against blood-stage malaria.
FDTD modeling of the borehole EM response of a Conductive Ore deposit in a Lossy Dielectric (1998)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1998FDTD modeling of the borehole EM response of a Conductive Ore deposit in a Lossy DielectricAuthors: D. JohnsonC. FurseAlan C. TrippD. JohnsonUniversity of Utah, C. FurseUniversity of Utah, and Alan C. TrippUniversity of Utahhttps://doi.org/10.1190/1.1820600 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1820600FiguresReferencesRelatedDetailsCited byCross‐borehole delineation of a conductive ore deposit in a resistive host—experimental designDavid Johnson, Elena Cherkaev, Cynthia Furse, and Alan C. Tripp7 February 2012 | GEOPHYSICS, Vol. 66, No. 3Faster than Fourier: ultra-efficient time-to-frequency-domain conversions for FDTD simulationsIEEE Antennas and Propagation Magazine, Vol. 42, No. 6 SEG Technical Program Expanded Abstracts 1998ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1998 Pages: 2092 publication data© 1998 Copyright © 1998 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 06 Jan 2005 CITATION INFORMATION D. Johnson, C. Furse, and Alan C. Tripp, (1998), "FDTD modeling of the borehole EM response of a Conductive Ore deposit in a Lossy Dielectric," SEG Technical Program Expanded Abstracts : 794-796. https://doi.org/10.1190/1.1820600 Plain-Language Summary PDF DownloadLoading ...
Katalytische Flüssigphasenumwandlung oxygenierter Kohlenwasserstoffe aus Biomasse zu Treibstoffen und Rohstoffen für die Chemiewirtschaft (2007)

Abstract Für die moderne Industriegesellschaft hat Biomasse ein enormes Potenzial als nachhaltiger Energieträger und Quelle organischen Kohlenstoffs. Ziel dieses Aufsatzes ist es, eine Übersicht über katalytische Reaktionen in der flüssigen Phase zu geben, in denen Sauerstoff‐haltige Rohstoffe aus Biomasse (vor allem Zucker und Zuckeralkohole) in wertvollere Chemikalien und Treibstoffe umgewandelt werden, wobei ein besonderer Schwerpunkt auf solchen katalytischen Transformationen liegt, die aus einem Verständnis der fundamentalen Reaktionsmechanismen abgeleitet wurden. Die Schlüsselreaktionen bei der chemischen Umwandlung von Biomasse sind Hydrolyse, Dehydratisierung, Isomerisierung, Aldolkondensation, Reformierung, Hydrierung und Oxidation. Ferner wird diskutiert, wie aus grundlegenden chemischen und katalytischen Konzepten Strategien für die Steuerung von Reaktionsverläufen und Prozessbedingungen erarbeitet werden können. Als Beispiele dienen dabei die Herstellung von H 2 /CO 2 ‐ oder H 2 /CO‐Gasmischungen durch Reformierung in der wässrigen Phase, die Produktion von Furanen durch selektive Dehydratisierung von Kohlenhydraten und die Erzeugung flüssiger Alkane durch Kombination der Aldolkondensation mit Dehydratisierungs‐ und Hydrierungsprozessen.
Responses to iron limitation are impacted by light quality and regulated by RcaE in the chromatically acclimating cyanobacterium Fremyella diplosiphon (2014)

Photosynthetic organisms adapt to environmental fluctuations of light and nutrient availability. Iron is critical for photosynthetic organismal growth, as many cellular processes depend upon iron cofactors. Whereas low iron levels can have deleterious effects, excess iron can lead to damage, as iron is a reactive metal that can result in the production of damaging radicals. Therefore, organisms regulate cellular iron levels to maintain optimal iron homeostasis. In particular, iron is an essential factor for the function of photosystems associated with photosynthetic light-harvesting complexes. Photosynthetic organisms, including cyanobacteria, generally respond to iron deficiency by reduced growth, degradation of non-essential proteins and in some cases alterations of cellular morphology. In response to fluctuations in ambient light quality, the cyanobacterium Fremyella diplosiphon undergoes complementary chromatic adaptation (CCA). During CCA, phycobiliprotein composition of light-harvesting antennae is altered in response to green light (GL) and red light (RL) for efficient utilization of light energy for photosynthesis. We observed light-regulated responses to iron limitation in F. diplosiphon. RL-grown cells exhibited significant reductions in growth and pigment levels, and alterations in iron-associated proteins, which impact the accumulation of reactive oxygen species under iron-limiting conditions, whereas GL-grown cells exhibited partial resistance to iron limitation. We investigated the roles of known CCA regulators RcaE, RcaF and RcaC in this light-dependent iron-acclimation response. Through comparative analyses of wild-type and CCA mutant strains, we determined that photoreceptor RcaE has a central role in light-induced oxidative stress associated with iron limitation, and impacts light-regulated iron-acclimation responses, physiologically and morphologically.