gebhart/patrepeval huggingface dataset:
Circulating miR-106b-3p, miR-101-3p and miR-1246 as diagnostic biomarkers of hepatocellular carcinoma (2018)

Hepatocellular carcinoma (HCC) is the most common liver cancer and second leading cause of cancer related death worldwide. Most HCCs occur in a damaged cirrhotic background and it may be difficult to discriminate between regenerative nodules and early HCCs. No dependable molecular biomarker exists for the early detection of HCC. MicroRNAs (miRNAs) have attracted attention as potential blood-based biomarkers. To identify circulating miRNAs with diagnostic potential in HCC, we performed preliminary RNAseq studies on plasma samples from a small set of HCC patients, cirrhotic patients and healthy controls. Then, out of the identified miRNAs, we investigated miR-101-3p, miR-106b-3p, miR-1246 and miR-411-5p in plasma of independent HCC patients' cohorts. The use of droplet digital PCR (ddPCR) confirmed the aberrant levels of these miRNAs. The diagnostic performances of each miRNA and their combinations were measured using Receiver Operating Characteristic (ROC) curve analyses: a classifier consisting of miR-101-3p, miR-1246 and miR-106b-3p produced the best diagnostic precision in plasma of HCC vs. cirrhotic patients (AUC = 0.99). A similar performance was found when the levels of miRNAs of HCC patients were compared to healthy controls (AUC = 1.00). We extended the analyses of the same miRNAs to serum samples. In serum of HCC vs. cirrhotic patients, the combination of miR-101-3p and miR-106b-3p exhibited the best diagnostic accuracy with an AUC = 0.96. Thus, circulating miR-101-3p, miR-106b-3p and miR-1246, either individually or in combination, exhibit a considerable potential value as diagnostic biomarkers of HCC.
Ratios of biogenic elements for distinguishing recent from fossil microorganisms (2007)

The ability to distinguish possible microfossils from recent biological contaminants is of great importance to Astrobiology. In this paper we discuss the application of the ratios of life critical biogenic elements (C/O; C/N; and C/S) as determined by Energy Dispersive X-ray Spectroscopy (EDS) to this problem. Biogenic element ratios are provided for a wide variety of living cyanobacteria and other microbial extremophiles, preserved herbarium materials, and ancient biota from the Antarctic Ice Cores and Siberian and Alaskan Permafrost for comparison with macrofossils and microfossils in ancient terrestrial rocks and carbonaceous meteorites.
Analyses of truncated fibrillin caused by a 366 bp deletion in the FBN1 gene resulting in Marfan syndrome (1994)

We studied fibrillin synthesis in cultured fibroblasts from 11 members of a three-generation family with Marfan syndrome, caused by a large in-frame deletion in FBN1 (the fibrillin gene) leading to a loss of 366 bases in the corresponding fibrillin mRNA. Metabolic labelling with [35S]Met/Cys and SDS/PAGE allowed unequivocal identification of normal and truncated fibrillin in all cell strains harbouring the deletion. In culture medium, fibrillin and its truncated counterpart were predominant, whereas their respective larger precursors were found only in traces. This proportion, however, was markedly shifted towards the normal and truncated precursors by EGTA and reversed by the addition of calcium, which confirmed the existence of profibrillin and its probably calcium-dependent conversion into fibrillin. Tunicamycin caused increased electrophoretic mobility of normal and truncated molecules without changing their apparent size differences. Intracellularly, only profibrillin was found; in the mutant cells truncated and normal profibrillin molecules were present in similar amounts and both populations were secreted and deposited simultaneously into the extracellular matrix; there, however, truncated profibrillin only became easily detectable after treatment of cells with dextran sulphate, which increased the amount of extractable profibrillin. Immunofluorescence microscopy in patients' cultures identified fibrillin-containing microfibrils which appeared to be moderately reduced both in amount and diameter. Ultrastructural analysis by rotary-shadowing and immunogold electron microscopy demonstrated the presence of numerous beaded domains reacting with fibrillin antibodies, but no intact fibrillin microfibrils in patient's cell-layer extracts, in contrast with the extensive microfibrils elaborated by control cultures. Our findings suggest, that in the patients' cell cultures all microfibrils contained the truncated fibrillin molecules.
Catalytic Reduction of Oxygen by a Copper Thiosemicarbazone Complex (2020)

The new copper(II) thiosemicarbazone complex CuL (H 2 L = 4‐{bis[4‐( p ‐methoxyphenyl)‐thiosemicarbazone]}‐2,3‐butane) was synthesized and structurally characterized. Its electrochemical behavior in N,N ‐dimethylformamide (DMF) was examined. This complex proved active for homogeneous oxygen reduction reaction (ORR) in DMF in the presence of organic acids. The activity and selectivity for ORR were found to be dependent on the nature of the proton source (phenol or acetic acid). This study confirms the previously reported free energy linear correlation between selectivity and overpotential requirement [Passard et al., J. Am. Chem. Soc . 2016 , 138 , 2925–2928] and suggests that additional descriptors are required for a full understanding of the catalytic ORR behaviour.
Bayesian ontology querying for accurate and noise-tolerant semantic searches (2012)

Abstract Motivation: Ontologies provide a structured representation of the concepts of a domain of knowledge as well as the relations between them. Attribute ontologies are used to describe the characteristics of the items of a domain, such as the functions of proteins or the signs and symptoms of disease, which opens the possibility of searching a database of items for the best match to a list of observed or desired attributes. However, naive search methods do not perform well on realistic data because of noise in the data, imprecision in typical queries and because individual items may not display all attributes of the category they belong to. Results:: We present a method for combining ontological analysis with Bayesian networks to deal with noise, imprecision and attribute frequencies and demonstrate an application of our method as a differential diagnostic support system for human genetics. Availability: We provide an implementation for the algorithm and the benchmark at http://compbio.charite.de/boqa/. Contact: Sebastian.Bauer@charite.de or Peter.Robinson@charite.de Supplementary Information: Supplementary Material for this article is available at Bioinformatics online.
Silicon-on-lithium-niobate photonics for quantum electro-optic converters (Conference Presentation) (2017)

Lithium niobate (LN) is a well-understood and heavily used optical material with a variety of useful properties such as its linear electro-optic effect, chi(2) nonlinearity, and piezoelectric effect. However, LN is a difficult material to etch and patterning high quality optical devices is challenging. Here we present results on the design and fabrication of a photonic crystal cavity made in a hybrid silicon-on-lithium-niobate material system. This material system takes advantage of the useful properties of LN, while simultaneously leveraging expertise in silicon etching and removing the need to pattern LN. These devices use the index contrast between silicon and LN to guide and confine optical resonances in a thin film of silicon bonded on top of LN. The photonic crystals have optical wavelength scale mode volumes and simulated quality factors greater than 10^6, with measured quality factors above 10^5. Due to the electro-optic effect in LN, these devices exhibit coupling between the optical resonance frequency and the electric field of adjacent electrodes. We show that such a system can yield a simulated electro-optic coupling rate of 0.6 GHz/V (4 pm/V). We expect resonators of this type to have a wide range of applications, including achieving large coupling to isolated rare-earth ions (such as Er3+) at telecom frequencies, efficient three-wave mixing in resonant silicon devices, and sensitive acousto- and electro-optic modulation.
Linoleyl Alcohol. II. Preparation, Properties, and Rearrangement1 (1940)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLinoleyl Alcohol. II. Preparation, Properties, and Rearrangement1J. P. Kass and G. O. BurrCite this: J. Am. Chem. Soc. 1940, 62, 7, 1796–1798Publication Date (Print):July 6, 1940Publication History Published online1 May 2002Published inissue 6 July 1940https://pubs.acs.org/doi/10.1021/ja01864a042https://doi.org/10.1021/ja01864a042research-articleACS PublicationsRequest reuse permissionsArticle Views87Altmetric-Citations5LEARN 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 decapping scavenger enzyme DCS-1: A new modulator of miRNA turnover (2013)

Click to increase image sizeClick to decrease image sizeKeywords:: microRNADCS-1DcpSXRN-1XRN1decapping scavenger enzymemicroRNA stabilitymicroRNA turnover
Problem Statements of FlexE Interface Management (2019)

This document outlines the problem statements for FlexE interface
management; it also gives an analysis of configuration requirements
for Flex Ethernet (FlexE) interface management. Requirements on FlexE
interface management are summarized in the end.
Flight Trials of the Wide Area Augmentation System (WAAS) (1994)

The Wide-Area Augmentation System (WAAS) is being rapidly developed by the Federal Aviation Administration for supplemental operational use in 1997. In time, it will be a primary navigation aid for all phases of flight down to Category I precision approach. The WAAS will include a network of approximately 20 to 30 Wide-area Reference Stations (WRSs) distributed around the National Airspace System. These reference stations will observe all GPS satellites in view and send pseudorange and ionospheric observations back to one or more Widearea Master Stations (WMSs). The WMSs will use this data to form vector corrections for each GPS satellite. These vectors contain separate components for the satellite ephemeris, satellite clock and ionosphere. The corrections will be broadcast to WAAS users via a geostationary satellite, using a signal and data format, which has been designed by RTCA Special Committee 159. In the Summer of 1994, Stanford performed WAAS flight trials to provide WAAS operational experience as early as possible. Our flight trials used three WAAS Reference Stations (WRSs), which Stanford installed for the FAA in the Western United States. They also used an experimental WMS located at Stanford. The flights used Professor David Powell’s Piper Dakota to fly WAAS precision approaches to an uninstrumented airport (Palo Alto). The WAAS data dramatically improved the accuracy of the airborne GPS fix, and it drove an “ILS-like” display. This paper describes our experiment and reports the results of the flights.
Floquet vortex states induced by light carrying the orbital angular momentum (2021)

We propose a scheme to create an electronic Floquet vortex state by irradiating a two-dimensional semiconductor with the laser light carrying non-zero orbital angular momentum. We analytically and numerically study the properties of the Floquet vortex states, with the methods analogous to the ones previously applied to the analysis of superconducting vortex states. We show that such Floquet vortex states are similar to the superconducting vortex states, and they exhibit a wide range of tunability. To illustrate the potential utility of such tunability, we show how such states could be used for quantum state engineering.
Modeling of molecular weight distribution and microstructure of copolymers prepared in emulsion (1990)

Abstract A stochastic model for evaluating Molecular Weight Distribution (MWD) and Chain Composition Distribution (CCD) of copolymers prepared in emulsion is applied to a “zero‐one‐two” binary system, i.e. with no more than two active chains per particle. Model predictions are compared with those by widely applied literature models based on bulk polymerization equations for evaluating CCD and on simplifying approaches for MWD (Refs. 5 and 6). For the particular system under examination, the range of reliable applicability of these approximated models is limited to high molecular weights (average degrees of polymerization larger than about 500 units), while for shorter chains the model here reported has to be used.
Reactivity of 4‐phenylthiazoles in ruthenium catalyzed direct arylations (2019)

The reactivity of the phenyl substituent of 4‐phenylthiazoles in Ru‐catalyzed direct arylation was studied. 4‐Phenylthiazole was found to be unreactive; whereas, the introduction of an aryl unit at C5‐position of 4‐phenylthiazole enhances its reactivity, allowing the selective mono‐arylation of the phenyl unit of 4‐phenylthiazoles in moderate to high yields using 5 mol% of [Ru( p ‐cymene)Cl 2 ] 2 catalyst precursor associated to KOPiv as base. These results reveal that the conformation and electronic properties of 4‐phenylthiazoles are crucial to allow the formation of suitable intermediates in the course of the catalytic cycle. The reaction tolerated both electron‐rich and electron‐poor aryl bromides allowing the straightforward tuning of the electronic properties of the arylated 2‐methyl‐4‐phenyl‐5‐arylthiazoles.
Drilling With a One-Step Solids-Control Technique (1989)

Summary The objectives of this paper are to report a new philosophy in solids control and field practice, referred to as fluid conditioning, to make a comparative evaluation of surface solids-control equipment, and to show details of a comprehensive mineralogical and physicochemical analysis of removed solids. For brevity, only a few field results are emphasized. For example, in a weighted mud system of 15.2 lbm/gal [18.2 × 102 kg/cm3], the adjustable concentric device of fluid conditioner rejects a greater percentage of 0.5- to 1.0-μm solids than a centrifuge. In an unweighted mud system of 9.5 lbm/gal [11.4 × 102 kg/m3], fluid contaminants such as calcite, dolomite, and salt are rejected through underflow. Another field example based on microscopic and scanning electron microscopic (SEM) size analysis showed that in a 12-lbm/gal [14.4 × 102-kg/m3] mud system, it is necessary to increase the operating pressure by a few psi to reduce the amount of 6-μm material. Our research in the area of particle size analysis of small, oilfield particles—e.g., smectite, sepiolite, Wyoming bentonite, and barite from bags of dust collectors—reveals that a quick-fix Fraunhofer diffraction analysis in the range of 10 μm and less is totally invalid in quantitative works. Finally, through the analysis of fluid rejects, we concluded that after the rig shaker (assuming that the rig shaker performs well), the one-step solids-control fluid conditioning can deliver desirable rheological properties and a reasonable size range for the suspended material.
A Comprehensive Evaluation of Reservoir Inflow and Wellbore Behavior in Intelligent Wells (2011)

Intelligent well technology is a relatively new technology that has been adopted&#13;\nby many operators in recent years to improve oil and gas recovery. Because of its&#13;\ncomplexity, accurate modeling of the reservoir and wellbore performance in the&#13;\nmultilateral well application is critical to optimize well production. Little work has been&#13;\nperformed on understanding the flow behavior through the main component of the&#13;\nintelligent well, the inflow control valve. This study presents a comprehensive model to&#13;\nquantify the reservoir and well performance in the horizontal laterals of the intelligent&#13;\nmultilateral well. Moreover, it combines this model with equations to evaluate the flow&#13;\nrate and pressure profile through the inflow control valves. As a result of this study, the&#13;\nwell performance of intelligent wells can be predicted and optimized.
A type-theoretic approach to higher-order modules with sharing (1994)

The design of a module system for constructing and maintaining large programs is a difficult task that raises a number of theoretical and practical issues. A fundamental issue is the management of the flow of information between program units at compile time via the notion of an interface. Experience has shown that fully opaque interfaces are awkward to use in practice since too much information is hidden, and that fully transparent interfaces lead to excessive interdependencies, creating problems for maintenance and separate compilation. The “sharing” specifications of Standard ML address this issue by allowing the programmer to specify equational relationships between types in separated modules, but are not expressive enough to allow the programmer complete control over the propagation of type information between modules.
A Simple Method to Reduce both Lactic Acid and Ammonium Production in Industrial Animal Cell Culture (2018)

Fed-batch animal cell culture is the most common method for commercial production of recombinant proteins. However, higher cell densities in these platforms are still limited due to factors such as excessive ammonium production, lactic acid production, nutrient limitation, and/or hyperosmotic stress related to nutrient feeds and base additions to control pH. To partly overcome these factors, we investigated a simple method to reduce both ammonium and lactic acid production-termed Lactate Supplementation and Adaptation (LSA) technology-through the use of CHO cells adapted to a lactate-supplemented medium. Using this simple method, we achieved a reduction of nearly 100% in lactic acid production with a simultaneous 50% reduction in ammonium production in batch shaker flasks cultures. In subsequent fed-batch bioreactor cultures, lactic acid production and base addition were both reduced eight-fold. Viable cell densities of 35 million cells per mL and integral viable cell days of 273 million cell-days per mL were achieved, both among the highest currently reported for a fed-batch animal cell culture. Investigating the benefits of LSA technology in animal cell culture is worthy of further consideration and may lead to process conditions more favorable for advanced industrial applications.
Expression of TRX1 optimizes the antitumor functions of human CAR T cells and confers resistance to a pro-oxidative tumor microenvironment (2022)

Use of chimeric antigen receptor (CAR) T cells to treat B cell lymphoma and leukemia has been remarkably successful. Unfortunately, the therapeutic efficacy of CAR T cells against solid tumors is very limited, with immunosuppression by the pro-oxidative tumor microenvironment (TME) a major contributing factor. High levels of reactive oxygen species are well-tolerated by tumor cells due to their elevated expression of antioxidant proteins; however, this is not the case for T cells, which consequently become hypo-responsive. The aim of this study was to improve CAR T cell efficacy in solid tumors by empowering the antioxidant capacity of CAR T cells against the pro-oxidative TME. To this end, HER2-specific human CAR T cells stably expressing two antioxidant systems: thioredoxin-1 (TRX1), and glutaredoxin-1 (GRX1) were generated and characterized. Thereafter, antitumor functions of CAR T cells were evaluated under control or pro-oxidative conditions. To provide insights into the role of antioxidant systems, gene expression profiles as well as global protein oxidation were analyzed. Our results highlight that TRX1 is pivotal for T cell redox homeostasis. TRX1 expression allows CAR T cells to retain their cytolytic immune synapse formation, cytokine release, proliferation, and tumor cell-killing properties under pro-oxidative conditions. Evaluation of differentially expressed genes and the first comprehensive redoxosome analysis of T cells by mass spectrometry further clarified the underlying mechanisms. Taken together, enhancement of the key antioxidant TRX1 in human T cells opens possibilities to increase the efficacy of CAR T cell treatment against solid tumors.
Evaluation of SPN-Based Lightweight Crypto-Ciphers (2019)

Lightweight cryptography has recently emerged as a strong requirement for any highly constrained connected device; encryption/decryption processes must strike the balance between speed, area, power efficiency, and security robustness. The aim of this paper is to study the potential gains of the lightweight cryptography algorithms compared to the classic ones in hardware implementation. Advanced Encryption Standard (AES) as the standard, PRESENT and the very recently published GIFT are considered along with several optimized hardware versions of each one. Low- and high-security levels with 80- and 128-bit key length respectively are compared. They are all implemented on a Xilinx Kintex-7 FPGA, exploiting different slice configurations to evaluate their performances. The results show the expected benefits in terms of throughput and area, which allows selecting the best lightweight crypto-ciphers depending on the target device or application. In addition, correlation power analysis is performed on each cipher to estimate their resistance against side-channel analysis.
Experimental optical simulator of reconfigurable and complex quantum environment (2023)

No quantum system can be considered totally isolated from its environment. In most cases the interaction between the system of interest and the external degrees of freedom deeply changes its dynamics, as described by open quantum system theory. Nevertheless, engineered environment can be turned into beneficial effects for some quantum information tasks. Here we demonstrate an optical simulator of a quantum system coupled to an arbitrary and reconfigurable environment built as a complex network of quantum interacting systems. We experimentally retrieve typical features of open quantum system dynamics like the spectral density and quantum non-Markovianity, by exploiting squeezing and entanglement correlation of a continuous variables optical platform. This opens the way to the experimental tests of open quantum systems in reconfigurable environments that are relevant in, among others, quantum information, quantum thermodynamics, quantum transport and quantum synchronization.
Ultra-broadband THz time-domain spectroscopy of energetic materials (2017)

Ultra-broadband THz spectroscopy based on photomixing in air plasma allows to exploit an extended frequency range, up to 20 THz and beyond. In this work, we investigate the potential of this technique for chemical recognition of illicit substances like explosives and compare the experimental spectra with ab-inition DFT simulation results to get deeper insight to the physical nature of the observed spectral features.
Patient-reported outcomes in palliative gastrointestinal stenting: a Norwegian multicenter study (2011)

SEMS treatment is effective in relieving symptoms of malignant GI and biliary obstruction, as reported by patients and physicians. The physicians, however, reported a larger reduction in obstructive symptoms than did the patients. A prospective assessment of patient-reported outcomes is important in evaluating SEMS treatment.