gebhart/patrepeval huggingface dataset:
Somatic mutation detection using various targeted detection assays in paired samples of circulating tumor DNA, primary tumor and metastases from patients undergoing resection of colorectal liver metastases (2016)

Assessing circulating tumor DNA (ctDNA) is a promising method to evaluate somatic mutations from solid tumors in a minimally-invasive way. In a group of twelve metastatic colorectal cancer (mCRC) patients undergoing liver metastasectomy, from each patient DNA from cell-free DNA (cfDNA), the primary tumor, metastatic liver tissue, normal tumor-adjacent colon or liver tissue, and whole blood were obtained. Investigated was the feasibility of a targeted NGS approach to identify somatic mutations in ctDNA. This targeted NGS approach was also compared with NGS preceded by mutant allele enrichment using synchronous coefficient of drag alteration technology embodied in the OnTarget assay, and for selected mutations with digital PCR (dPCR). All tissue and cfDNA samples underwent IonPGM sequencing for a CRC-specific 21-gene panel, which was analyzed using a standard and a modified calling pipeline. In addition, cfDNA, whole blood and normal tissue DNA were analyzed with the OnTarget assay and with dPCR for specific mutations in cfDNA as detected in the corresponding primary and/or metastatic tumor tissue. NGS with modified calling was superior to standard calling and detected ctDNA in the cfDNA of 10 patients harboring mutations in APC, ATM, CREBBP, FBXW7, KRAS, KMT2D, PIK3CA and TP53. Using this approach, variant allele frequencies in plasma ranged predominantly from 1 to 10%, resulting in limited concordance between ctDNA and the primary tumor (39%) and the metastases (55%). Concordance between ctDNA and tissue markedly improved when ctDNA was evaluated for KRAS, PIK3CA and TP53 mutations by the OnTarget assay (80%) and digital PCR (93%). Additionally, using these techniques mutations were observed in tumor-adjacent tissue with normal morphology in the majority of patients, which were not observed in whole blood. In conclusion, in these mCRC patients with oligometastatic disease NGS on cfDNA was feasible, but had limited sensitivity to detect all somatic mutations present in tissue. Digital PCR and mutant allele enrichment before NGS appeared to be more sensitive to detect somatic mutations.
Boolean Operations on 3D Selective Nef Complexes -- Data Structure, Algorithms, and Implementation (2003)

Abstract. We describe a data structure for three-dimensional Nef complexes, algorithms for boolean operations on them, and our implementation of data structure and algorithms. Nef polyhedra were introduced by W. Nef in his seminal 1978 book on polyhedra. They are the closure of half-spaces under boolean operations and can represent non-manifold situations, open and closed boundaries, and mixed dimensional complexes. Our focus lies on the generality of the data structure, the completeness of the algorithms, and the exactness and efficiency of the implementation. In particular, all degeneracies are handled. 1
A study of human lens cell growth in vitro. A model for posterior capsule opacification. (1996)

The model presented here for posterior capsule opacification shows many of the changes seen in vivo, including rapid lens cell growth, wrinkling, tensioning, and light scatter in the posterior capsule. It will be possible to develop strategies for inhibiting cell growth with this system.
Acrylate formation from CO<sub>2</sub> and ethylene: catalysis with palladium and mechanistic insight (2015)

We report the first catalyst based on palladium for the reaction of CO2, alkene and a base to form sodium acrylate and derivatives. A mechanism similar to a previously reported Ni(0)-catalyst is proposed based on stoichiometric in situ NMR experiments, isolated intermediates and a parent palladalactone. Our palladium catalyst was applied to the coupling of CO2 with conjugated alkenes.
Testability analysis of analog systems (1990)

A method is presented to analyze the testability of both linear and nonlinear analog systems. It combines a rank-test algorithm with statistical methods. The algorithm will find sets of dependent parameters and determine whether it is possible to calculate a certain parameter with sufficient accuracy. it also determines a subset of appropriate measurements if redundant measurements are present.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Payment Terminal Emulator (2020)

Nowadays, cash payments are becoming less popular and few understand, what a complicated process stands behind the habitual inserting the card into PoS (Point-of-Sale) terminal. This payment process are implemented by FinTech companies, that provide banks and merchants with ready-to-use PoS terminals. And the most expensive and time-consuming phase of payment solution integration is is the certification of terminal software. In this work we consider communication protocol between a smart card and a PoS terminal based on EMV (Europay Mastercard Visa) international standard, together with its known vulnerabilities. In order to improve the certification process in one Portuguese FinTech company, standalone software for emulation of full EMV transaction workflow is suggested. We present details about implementation of 3C Emulator application.
Decreased CNS inflammation and absence of clinical exacerbation of disease after six months oral administration of bovine myelin in diseased SJL/J mice with chronic relapsing experimental autoimmune encephalomyelitis (1996)

Murine chronic relapsing experimental autoimmune encephalomyelitis (CR-EAE) is a model of inflammatory demyelinating disease of the central nervous system (CNS) with similarity to multiple sclerosis (MS) in humans. Mice with confirmed neurologic deficits from CR-EAE were treated by oral administration of whole bovine myelin to investigate the effect of long-term oral delivery of myelin antigens on clinical disease and on the inflammatory response in the CNS. EAE-positive mice were fed doses of 1 mg, 10 mg, or 20 mg of bovine myelin every other day for 6 months. We found that prolonged oral delivery of neuroantigen suppressed inflammatory and demyelination foci in the CNS of myelin-treated mice with no exacerbation of clinical disease status compared with the control group. Analysis of histologic sections of brain and spinal cords with hematoxylin-eosin (H&E) and Luxol fast blue (LFB) staining showed a decrease in the inflammatory cell infiltration and active centers of demyelination, respectively. Furthermore, after 6 months of treatment, there was no increased sensitization to myelin antigens seen, as measured by antimyelin basic protein (MBP) or anti-proteolipid apoprotein (PLP) antibodies. These results demonstrate that prolonged oral administration of myelin antigens in diseased animals has an ameliorating effect on the pathologic process and supports its potential long-term use in humans with MS. © 1996 Wiley-Liss, Inc.
Electrochemistry of Conductive Polymers 39. Contacts between Conducting Polymers and Noble Metal Nanoparticles Studied by Current-Sensing Atomic Force Microscopy (2006)

Electrical properties of contacts formed between conducting polymers and noble metal nanoparticles have been examined using current-sensing atomic force microscopy (CS-AFM). Contacts formed between electrochemically prepared pi-conjugated polymer films such as polypyrrole (PPy), poly(3-methylthiophene) (P3MeT), as well as poly(3,4-ethylenedioxythiophene) (PEDOT) and noble metal nanoparticles including platinum (Pt), gold (Au), and silver (Ag) have been examined. The Pt nanoparticles were electrochemically deposited on a pre-coated PPy film surface by reducing a platinum precursor (PtCl62-) at a constant potential. Both current and scanning electron microscopic images of the film showed the presence of Pt islands. The Au and Ag nanoparticles were dispersed on the P3MeT and PEDOT film surfaces simply by dipping the polymer films into colloid solutions containing Au or Ag particles for specified periods (5 to approximately 10 min). The deposition of Au or Ag particles resulted from either their physical adsorption or chemical bonding between particles and the polymer surface depending on the polymer. When compared with PPy, P3MeT and PEDOT showed a stronger binding to Au or Ag nanoparticles when dipped in their colloidal solutions for the same period. This indicates that Au and Ag particles are predominantly linked with the sulfur atoms via chemical bonding. Of the two, PEDOT was more conductive at the sites where the particles are connected to the polymer. It appears that PEDOT has better aligned sulfur atoms on the surface and is strongly bonded to Au and Ag nanoparticles due to their strong affinity to gold and silver. The current-voltage curves obtained at the metal islands demonstrate that the contacts between these metal islands and polymers are ohmic.
RAISR: Rapid and Accurate Image Super Resolution (2016)

Given an image, we wish to produce an image of larger size with significantly more pixels and higher image quality. This is generally known as the Single Image Super-Resolution (SISR) problem. The idea is that with sufficient training data (corresponding pairs of low and high resolution images) we can learn set of filters (i.e. a mapping) that when applied to given image that is not in the training set, will produce a higher resolution version of it, where the learning is preferably low complexity. In our proposed approach, the run-time is more than one to two orders of magnitude faster than the best competing methods currently available, while producing results comparable or better than state-of-the-art. A closely related topic is image sharpening and contrast enhancement, i.e., improving the visual quality of a blurry image by amplifying the underlying details (a wide range of frequencies). Our approach additionally includes an extremely efficient way to produce an image that is significantly sharper than the input blurry one, without introducing artifacts such as halos and noise amplification. We illustrate how this effective sharpening algorithm, in addition to being of independent interest, can be used as a pre-processing step to induce the learning of more effective upscaling filters with built-in sharpening and contrast enhancement effect.
Derivative Thermoanalytical Techniques. Instrumentation and Applications to Thermogravimetry and Differential Thermal Anaylsis (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDerivative Thermoanalytical Techniques. Instrumentation and Applications to Thermogravimetry and Differential Thermal AnaylsisClement. Campbell, Saul. Gordon, and C. L. SmithCite this: Anal. Chem. 1959, 31, 7, 1188–1191Publication Date (Print):July 1, 1959Publication History Published online1 May 2002Published inissue 1 July 1959https://doi.org/10.1021/ac60151a034RIGHTS & PERMISSIONSArticle Views120Altmetric-Citations9LEARN 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 InReddit PDF (453 KB) Get e-Alertsclose Get e-Alerts
ChemInform Abstract: Synthesis and Initial Structure—Activity Relationships of a Novel Series of Imidazolo[1,2‐a]pyrimid‐5‐ones as Potent GnRH Receptor Antagonists (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Chemical Visualization of Asphaltenes Aggregation Processes Studied in Situ with ATR-FTIR Spectroscopic Imaging and NMR Imaging (2015)

Crude oil phase behavior and asphaltene precipitation have been studied by two complementary chemical imaging methods for the first time. ATR-FTIR spectroscopic imaging approach has revealed the chemical composition of agglomerated and precipitated asphaltenes upon dilution with a flocculant. Asphaltenes, containing oxygen and nitrogen heteroatomic functional groups, have been detected to be least stable. Aromatic abundant asphaltenes have been observed to have relatively high solubility in crude oil/heptane blends. NMR imaging approach, capable of imaging in the bulk of crude oil samples, has demonstrated that n-heptane causes aggregation which can lead to the stable suspension or to the sedimentation followed by the formation of deposits, depending on flocculant concentration. These processes have been monitored for small and large amounts of heptane added to crude oil. The data obtained by ATR-FTIR spectroscopic imaging and NMR imaging have been correlated to propose a possible link between the chemical structure of asphaltenes and a mechanism of the formation of deposits.
Fluorimetric Determination of Creatine (1960)

Abstract A new fluorimetric method for determining creatine in serum, blood, and urine is described. The method is based upon the coupling of guanidine compounds with ninhydrin in alkaline solution to produce highly fluorescent products. In degree of sensitivity and simplicity the method possesses several advantages over currently used colorimetric methods, and creatine can be determined in concentrations as low as 1.0 X 10-7M. The serum creatine concentration was found to be 0.41 mg.% in normal adult males, who excrete only small amounts of creatine in the urine.
Mgmt deficiency alters the in vivo mutational spectrum of tissues exposed to the tobacco carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) (2008)

It has been proposed that O(6)-methylguanine DNA methyltransferase (MGMT) gene silencing in premalignant lesions and cancers of the lung might result in the acquisition of a 'mutator' phenotype. Previously, however, we found that Mgmt(-/-) mouse DNA failed to show an increase in spontaneous mutations. We thus hypothesized that only during exposure to specific environmental carcinogens would the consequences of MGMT deficiency become evident. Metabolism of the tobacco-derived nitrosamine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) generates alkylating species that can react with the O(6) position of deoxyguanine, thereby yielding substrates for MGMT-mediated repair. To investigate how MGMT might regulate the mutational effects of NNK, Mgmt(-/-) mice were crossed with a lacI-based transgenic reporter line (Big Blue) thus enabling an assessment of the in vivo mutagenic effects of this agent. We observed the induction of a complex spectrum of NNK-dependent lacI mutations in both control and Mgmt(-/-) tissues, but only a trend in the mutant frequency increases that could be attributed to MGMT deficiency. The mutational spectra of NNK-treated Mgmt(-/-) lungs revealed an increase in the absolute number of G:C to A:T changes accompanied by a shift in these from CpG to GpG sites, consistent with an S(N)1 alkylation mechanism. In keeping with the high levels of MGMT expressed in the liver, more pronounced mutagenic effects and greater differences in O(6) position of deoxyguanosine adduct levels following NNK were observed in Mgmt(-/-) versus wild-type mice. Extrapolating to humans, MGMT-deficient cells would likely exhibit an increased mutational burden, but only following exposures to specific environmental mutagens such as NNK.
Comparative Effects of All-trans β-Carotene vs. 9-cis β-Carotene on Carcinogen-Induced Neoplastic Transformation and Connexin 43 Expression in Murine 10T1/2 Cells and on the Differentiation of Human Keratinocytes (2000)

9-cis beta-Carotene was extracted from a commercial extract of the algae Dunaliella salina (Betatene), and its actions on proliferation and gene expression were examined in murine 10T1/2 cells and human HaCaT keratinocytes. The 9-cis isomer was less active than all-trans beta-carotene in reducing proliferation and in upregulating expression of connexin 43 in 10T1/2 cells. However, it had comparable ability to suppress carcinogen-induced neoplastic transformation. When tested in HaCaT cells in organotypic culture, it was less active in inducing connexin 43 expression and suppressing expression of keratin K1. In this assay the all-trans isomer was highly active at 10(-6) M, whereas 10(-5) M 9-cis beta-carotene was required to produce a comparable effect. Only small reductions in expression of the basal keratin 5 were seen. All-trans and 9-cis retinoic acids, potential metabolites of beta-carotene isomers, were studied in the same systems. In contrast to the carotenoids, the 9-cis isomer of retinoic acid was approximately 10-fold more active in suppressing neoplastic transformation and inducing connexin 43 expression in both cell types than the all-trans isomer. The retinoic acid isomers were about equipotent in suppressing K1 expression. Cellular levels of 9-cis beta-carotene were approximately 3.5-fold lower than levels of all-trans beta-carotene, suggesting that part, but not all, of this decreased activity of the 9-cis isomer was due to decreased cell uptake. Thus 9-cis beta-carotene is consistently less active than the all-trans isomer; that 9-cis retinoic acid is, in general, much more potent than the all-trans isomer suggests little or no conversion from the carotenoid to the retinoid under these culture conditions.
High-Resolution Spectral Analysis of Individual SERS-Active Nanoparticles in Flow (2010)

Nanoparticle spectroscopic tags based on surface enhanced Raman scattering (SERS) are playing an increasingly important role in bioassay and imaging applications. The ability to rapidly characterize large populations of such tags spectroscopically in a high-throughput flow-based platform will open new areas for their application and provide new tools for advancing their development. We demonstrate here a high-resolution spectral flow cytometer capable of acquiring Raman spectra of individual SERS-tags at flow rates of hundreds of particles per second, while maintaining the spectral resolution required to make full use of the detailed information encoded in the Raman signature for advanced multiplexing needs. The approach allows multiple optical parameters to be acquired simultaneously over thousands of individual nanoparticle tags. Characteristics such as tag size, brightness, and spectral uniformity are correlated on a per-particle basis. The tags evaluated here display highly uniform spectral signatures, but with greater variability in brightness. Subpopulations in the SERS response, not apparent in ensemble measurements, are also shown to exist. Relating tag variability to synthesis parameters makes flow-based spectral characterization a powerful tool for advancing particle development through its ability to provide rapid feedback on strategies aimed at constraining desired tag properties. Evidence for single-tag signal saturation at high excitation power densities is also shown, suggesting a role for high-throughput investigation of fundamental properties of the SERS tags as well.
Safety of a Novel Botanical Extract Formula for Ameliorating Allergic Rhinitis (2003)

Allergic rhinitis (also known as hay fever) is the most commonly occurring immunological disorder, and it affects 40 million men, women, and children in the United States. Symptomatically, it is an inflammation and irritation of the mucous membranes that line the nose. Allergy is defined as a state of hypersensitivity or hyperimmunity caused by exposure to a particular antigen (allergen) that results in increased reactivity upon subsequent exposure. A novel botanical formulation, Aller-7/NR-A2, was developed for the treatment of allergic rhinitis; it is a combination of medicinal plant extracts from Phyllanthus emblica, Terminalia chebula, Terminalia bellerica, Albizia lebbeck, Piper nigrum, Zingiber officinale, and Piper longum. This novel formulation has demonstrated potent antihistaminic, anti-inflammatory, antispasmodic, antioxidant, and mast-cell-stabilization activities. All of the doses for these toxicity studies were selected according to the guidelines of the Organization for Economic Cooperation and Development, the World Health Organization, and the Environmental Protection Agency. Acute toxicity of Aller-7 was evaluated in Swiss Albino mice at doses of 125, 250, 500, 1000, and 1500 mg/kg. After 15 days of treatment, the animals were sacrificed. No histopathological changes were observed in major vital organs. A similar study was conducted in Albino Wistar rats, which were sacrificed at the end of 15 days. No histopathological changes or toxicity was observed at up to 2 g/kg body weight. Subacute toxicity was conducted in Albino Wistar rats at a dose of 90 mg/kg body weight for 3 days, then at 180 mg/kg for the next 3 days, and then at 270 mg/kg for 3 weeks. After 28 days, the animals were sacrificed and tested; no toxicity was observed. In a subchronic toxicity study, there was no observed adverse effect level at 1 g/kg body weight in rats. In a teratological assay, at doses of 3.0 g/kg (20 times the recommended dose) and 1.8 g/kg, respectively, no visceral or skeletal anomalies were observed in the fetuses. No maternal changes were observed when Aller-7 was administered during gestation and lactation. No evidence of mutagenicity was observed at doses up to 5000 mug per plate of Aller-7 in Salmonella typhimurium cells. The present study evaluated the safety of Aller-7 by conducting several in vitro and in vivo studies. Further studies of the 90-day chronic toxicity of Aller-7 are currently in progress.
Using In-Process Testing Metrics to Estimate Post-Release Field Quality (2007)

In industrial practice, information on the software field quality of a product is available too late in the software lifecycle to guide affordable corrective action. An important step towards remediation of this problem lies in the ability to provide an early estimation of post-release field quality. This paper evaluates the Software Testing and Reliability Early Warning for Java (STREW-J) metric suite leveraging the software testing effort to predict post-release field quality early in the software development phases. The metric suite is applicable for software products implemented in Java for which an extensive suite of automated unit test cases are incrementally created as development proceeds. We validated the prediction model using the STREW-J metrics via a two-phase case study approach which involved 27 medium-sized open source projects, and five industrial projects. The error in estimation and the sensitivity of the predictions indicate the STREW-J metric suite can be used effectively to predict post-release software field quality.