gebhart/patrepeval huggingface dataset:
Protonated base pairs explain the a properties of 06-methylguanine (hydrogen bonding/DNA structure/protonated cytosine/mutagenesi (2016)

The base-pairing interactions of promutagen- ic 06-methylguanine (06-MeGua) with cytosine and thymine in deuterated chloroform were investigated by 1H NMR spectros- copy. Nucleosides were derivatized at hydroxyl positions with triisopropylsilyl groups to obtain solubility in nonaqueous solvents and to prevent the ribose hydroxyls from forming hydrogen bonds. We were able to observe hydrogen-bonding interactions between nucleic acid bases in a solvent of low dielectric constant, a condition that approximates the hydro- phobic interior of the DNA helix. 06-MeGua was observed to form a hydrogen-bonded mispair with thymine. Whereas 06-MeGua did not form hydrogen bonds with cytosine (via usual, wobble, or unusual tautomeric structures), it did form a 1:1 hydrogen-bonded complex with protonated cytosine. The pairing of unprotonated cytosine in chloroform is thus consist- ent with the known preference of 06-MeGua for thymine over cytosine in polymerase reactions. In contrast, the pairing of protonated cytosine is consistent with the greater stability of oligonucleotide duplexes containing cytosine'06-MeGua as compared with thymine0O6-MeGua base pairs (Gaffney, B. L., Markey, L. A. & Jones, R. A. (1984) Biochemistry 23, 5686- 5691). Our observation that cytosine must be protonated in order to pair with 06-MeGua suggests that the cytosine0 6- MeGua base pair in DNA is stabilized by protonation of cytosine. Through this mechanism, methylation at the 06 position of guanine in double-stranded DNA could promote cross-strand deamination of cytosine (or 5-methylcytosine) to produce uracil (or thymine).
Dielectric properties of alumina-filled poly (ethylene-co-butyl acrylate) nanocomposites Part I - dry studies (2012)

The dielectric properties of poly (ethylene-co-butyl acrylate) with 13 wt% of butyl acrylate (EBA) filled with alumina nanoparticles were studied as a function of particle size, particle coating, filler content (2, 6 or 12wt%) and temperature. The particles were either unmodified or surface-treated with either aminopropyltriethoxy silane or octyltriethoxy silane. The complex permittivity was measured with frequencies varying between 1 mHz and up to 1 kHz at different temperatures (25, 45 and 65°C). Measurements were performed in dry conditions. From the dielectric spectroscopy measurements it can be seen that the tan δ for the dry samples is almost independent of the type of the particle coating used. It does, however, depend on the particle size, filler content and temperature.
Investigating a Simulated Model of 2.5 GHz 64 Channel 140 kmDWDM System Using EDFAand Raman Amplifier Considering Self-Phase Modulation (2015)

In this paper a 2.5 GHz 64 channel DWDM fiber optic transmission system is investigated with 140km of fiber length.For comparative analysis, both EDFA and Raman areused for amplification purposes but in consideration with self-phase modulation. The model of DWDM grid frequency ranged from193.1 THz to 199.4 THz (1552.52 nm to 1503.47 nm in wavelength) and with 100GHz (0.8nm) of channel spacing. This range covers most of the C-band and a portion of the S-band.The simulationresults show that the system with Raman Amplifiers yieldedahighest gain of 12.36 dB whereas the system withEDFA produced ahighest gain of 13.01dBat C band region and it was further reduced to 5dB entering S band region. It isalso shown thatRaman Amplifier networks are less prone to crosstalk and inter symbol interference than EDFA networks.
Differential Expression of CHL1 Gene during Development of Major Human Cancers (2011)

Our results suggested that CHL1 is involved in the development of different human cancers. Initially, during the primary tumor growth CHL1 could act as a putative tumor suppressor and is silenced to facilitate in situ tumor growth for 11 cancer types. We also suggested that re-expression of the gene on the edge of tumor mass might promote local invasive growth and enable further metastatic spread in ovary, colon and breast cancer. Our data also supported the role of CHL1 as a potentially novel specific biomarker in the early pathogenesis of two major histological types of renal cancer.
ChemInform Abstract: A Direct Route to Triazole Boronic Esters and Their Application in the Synthesis of Small Molecule Arrays. (2009)

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.
Supplementary Figure 4 from Endogenous Two-Photon Fluorescence Imaging Elucidates Metabolic Changes Related to Enhanced Glycolysis and Glutamine Consumption in Precancerous Epithelial Tissues (2023)

&lt;p&gt;PDF file - 516KB, TPEF images and quantitative data from cells exposed to KSFM, Low Glu (low glucose), No Glu (no glucose), and Low Oxy (low O2) media.&lt;/p&gt;
Arsenic determination at submicrogram levels by arsine evolution and flameless atomic absorption spectrophotometric technique (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTArsenic determination at submicrogram levels by arsine evolution and flameless atomic absorption spectrophotometric techniqueRichard C. Chu, George P. Barron, and Paul A. W. BaumgarnerCite this: Anal. Chem. 1972, 44, 8, 1476–1479Publication Date (Print):July 1, 1972Publication History Published online1 May 2002Published inissue 1 July 1972https://pubs.acs.org/doi/10.1021/ac60316a042https://doi.org/10.1021/ac60316a042research-articleACS PublicationsRequest reuse permissionsArticle Views214Altmetric-Citations86LEARN 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
Application of Sonar-Based, Clamp-on Flow Meter in Oilsand Processing (2004)

Data is presented demonstrating the applicability of sonar-based, clamp-on flow measurement to several, long-standing flow measurement challenges within the oilsands industry, including hydrotransport, coarse tailings, and bitumen froth flow lines. Sonar-based flow measurement technology was developed and field proven in the oil and gas production industry over the last five years and provides robust, accurate volumetric flow rate measurement for a broad range of process fluids, slurries, pipes sizes and flow conditions. Sonar-based flow metering technology utilizes an array of sensors to listen to, and interpret, unsteady pressure fields within process flow lines. The methodology is implemented using strain-based sensors which clamp-on to existing process piping. Sonar-based flow monitoring systems determine volumetric flow rate by measuring the speed at which self-generated, coherent flow structures convect past the sensor array. Using similar sonar-based array processing techniques as those used for volumetric flow, sonar-based flow meters can also determine entrained air (or any other gas) levels by measuring the speed at which sound propagates within the process flow lines. The speed of sound in the process flow lines provides an accurate and robust, clamp-on method for determining entrained air levels in aerated liquids. Data is presented showing entrained air levels on a 16-inch diameter froth line exiting a steam-driven deaerator.
Cross-platform FPGA accelerator development using CoRAM and CONNECT (2013)

The CoRAM memory architecture is an easy-to-use and portable abstraction for FPGA accelerator development [1, 2]. Using the CoRAM framework, FPGA developers can write their applications once and re-target them automatically to different FPGA platforms and devices (e.g., Xilinx ML605, Altera DE4, ZYNQ-702, etc). In this tutorial, participants will learn the key concepts of the CoRAM Virtual Architecture and the underlying CONNECT Network-on-Chip generation framework [3]. The tutorial is organized into three parts. The first part will provide an overview of the CoRAM Virtual Architecture and include a hands-on section where participants will work on a small example to get first-hand experience with the CoRAM development flow. The second part of the tutorial will provide a beneath-the-hood look at CoRAM and cover more advanced topics. These topics include memory loading, user I/O, debugging, as well as a segment on the CONNECT NoC generation framework which serves as the on-chip interconnect for CoRAM. The final part of the tutorial will be devoted to more advanced exercises and demos, as well as a Q&A session for CoRAM and CONNECT. The tutorial assumes a basic understanding of RTL design and C programming. To join in on the hands-on exercise, the attendees need laptops with 15GB of free space and VirtualBox installed. Please visit http://www.ece.cmu.edu/~coram for information about CoRAM and updates on this tutorial.
Eigenvalue based SNR estimation for cognitive radio in presence of channel correlation (2013)

In addition to spectrum sensing capability required by a Cognitive Radio (CR), Signal to Noise Ratio (SNR) estimation of the primary signals is crucial in order to adapt its coverage area dynamically using underlay techniques. Furthermore, in practical scenarios, the fading channel may be correlated due to various causes such as insufficient scattering in the propagation path and antenna mutual coupling. In this context, we consider the SNR estimation problem for a CR in the presence of channel correlation. We study an eigenvalue-based SNR estimation technique for large-scale CR networks using asymptotic Random Matrix Theory (RMT). We carry out detailed theoretical analysis of the signal plus noise hypothesis to derive the asymptotic eigenvalue probability distribution function (a.e.p.d.f.) of the received signal's covariance matrix in the presence of the correlated channel. Then an SNR estimation technique based on the derived a.e.p.d.f. is proposed for PU SNR in the presence of channel correlation and its performance is evaluated in terms of normalized Mean Square Error (MSE). It is shown that the PU SNR can be accurately estimated in the presence of channel correlation using the proposed technique even in low SNR region.
High-throughput approaches to uncover synergistic drug combinations in leukemia (2023)

We report a comprehensive drug synergy study in acute myeloid leukemia (AML). In this work, we investigate a panel of cell lines spanning both MLL-rearranged and non-rearranged subtypes. The work comprises a resource for the community, with many synergistic drug combinations that could not have been predicted a priori, and open source code for automation and analyses. We base our definitions of drug synergy on the Chou-Talalay method, which is useful for visualizations of synergy experiments in isobolograms, and median-effects plots, among other representations. Our key findings include drug synergies affecting the chromatin state, specifically in the context of regulation of the modification state of histone H3 lysine-27. We report open source high throughput methodology such that multidimensional drug screening can be accomplished with equipment that is accessible to most laboratories. This study will enable preclinical investigation of new drug combinations in a lethal blood cancer, with data analysis and automation workflows freely available to the community.
90% &lt;i&gt;SNR&lt;/i&gt; Improvement with Multi-Port Hall Plates (2020)

For Hall plates, the ratio of signal over thermal noise is determined by material properties, thickness, layout geometry, magnetic field, and the electric power at which the plate is operated. For traditional Hall plates with four contacts, the optimum choice is a symmetrical device with medium-sized contacts. This paper shows that the signal-to-noise-ratio (SNR) can be further increased by up to 90% for Hall plates with more than four contacts. Supply currents flow through several pairs of contacts, while a signal conditioning circuit taps output voltages at all pairs of contacts and sums them up. We compute the total thermal noise of the sum of correlated noise voltages and relate it to the total magnetic sensitivity. We also prove that for electrically linear devices a spinning current scheme cancels out zero point errors (offset errors) in a strict sense. All our investigations use the definite resistance matrix of multi-port Hall plates. We develop an analytical theory based on recent advances in the theory of Hall plates, and then we compute the integrals and matrices numerically for symmetrical Hall plates with six to 40 contacts. We also present measurements in accordance with our theory.
Oncogenes and Mammary Carcinogenesis (1999)

Breast cancer is the most common malignancy among women in the United States, accounting for nearly 32% ofall cancers and for nearly 20% ofall cancer deaths in women (1). Breast cancer is a multifactorial disease, and several factors are thought to influence the risk of breast cancer development, including geography, radiation exposure, and reproductive and family history. A family history of breast cancer constitutes the major risk factor, although familial breast cancer accounts for only 5% of all cases (1). Although breast cancer deaths declined by 5% between 1989 and 1992 (2), the incidence of breast cancer is expected to increase by 2–3% annually (1), and efforts to decrease mortality significantly, including new therapeutic approaches and early diagnosis, have been relatively unsuccessful. One of the critical factors in determining the therapeutic approach to breast cancer, along with the presence or absence of lymph node metastasis, is the estrogen and progesterone receptor (ER and PR) status of the tumor. Indeed, ER- and/or PR-positive tumors have been found to be more likely to respond to endocrine therapy and are associated with a better prognosis (1). An understanding of the genetic changes involved in breast cancer and of its biologic behavior, including possible interactions between hormones and oncogenes or tumor suppressor genes, will undoubtedly aid in the design of new therapies as well as in prevention and diagnosis of this disease.
Aeroacoustic Sensitivity Analysis and Its Application for Noise Barrier Design (2002)

An automated design optimization method is demonstrated by computationally modeling the wheel-on-rail noise. The noise propagation is simulated by solving the wave equation using the boundary element method and compared with field test data. Then, the computational model was coupled with an optimization methodology through finite-differenced sensitivities. Using this method, a number of new designs was obtained and evaluated for their relative effectiveness. Three new designs were found to improve the insertion loss within the design space delineated by the given geometrical constraints. Finally, for improved computational efficiency, a continuous adjoint sensitivity methodology was applied to the wave equation to obtain the shape sensitivity derivatives of the acoustic pressure field. Its accuracy and validity are demonstrated for objectives defined on the barrier surface and out in the acoustic field.
Molecular and Genetic Mechanisms Involved in the Pathogenesis of Cardiorenal Cross Talk (2016)

The term 'cardiorenal syndrome' (CRS) encloses a scenario of clinical interactions in which cardiac and renal dysfunctions coexist. The cross talk between the heart and the kidney is clearly evidenced but not fully understood. Indeed, different factors have been shown to be involved in the pathogenesis of CRS, such as systemic inflammation, oxidative stress, apoptosis and immune dysregulation. Recently, considerable attention has been paid to the role of new alternative mechanisms which may be implicated in the pathogenesis of cardiorenal cross talk. In this review, we will focus on epigenetics, prenatal programming, small noncoding RNAs and extracellular vesicles, aiming to elucidate their possible role in heart and kidney diseases.
Hepcidin: the Missing Link between Hemochromatosis andInfections (2003)

The aphrodisiacal potential of oysters is the stuff of maritime folklore, having roots in tales of Aphrodite (literally “foam born”), the goddess of love, said to have arisen from the sea on an oyster shell. However, mariners' tales chronicling oysters' lethal potential, despite having abounded
Automated 3D reconstruction of coronary artery tree based on stochastic branch and bound (2005)

The paper discusses a new method for reconstructing vessel trees from biplane X-Ray projections. The used method reconstructs corresponding points in less than a second and is thus ideally suited for interventional procedures where time is essential. Biplane reconstruction is a two-fold problem: find corresponding points in both images and reconstruct the vessel segments between successive corresponding points in 3D. In this paper we solve the first problem using a new branch and bound technique based on Bayesian networks. With epipolar geometry we assign each of the vessel bifurcation/crossing/endpoint in one image a set of corresponding points in the second image. Starting with the vessel of largest diameter as root node we successively build up a tree of all possible solutions. Branches are cut according to probabilistic conditions (branch&bound based global search for the best solution). Each node is thus a possible partial tree for which we assign a conditional probability that the assignment of corresponding points is correct. The probability is the joint probability of having the correct topology, connectivity, tree and segment shape, characteristics of bifurcations. The respective probabilities for each bifurcation are measured from CTA data of real patients and the probability of the node is computed via a Bayesian network. If the assigned probability is too small, the branch is pruned. Further, for performance reasons we use A*-search where the most probable solution gets favored. All corresponding points are found in less then one second and both, topology and vessel crossings, are identified correctly. This method is thus by orders of magnitude faster than competing ones. This approach is therefore focused on both an automatic and robust method for 3D biplane reconstruction on one hand and an interactive method on the other hand. Further, it can be trained on a typical set of patients in order to obtain as reliable information as possible about the 3D vascular tree.
Infectious amplification of wild-type human immunodeficiency virus from patients' lymphocytes and modulation by reverse transcriptase inhibitors in vitro (1993)

The relative in vitro potency of nine human immunodeficiency virus (HIV) type 1 reverse transcriptase inhibitors was evaluated in a coculture assay which measures the frequencies of infectious primary cells from HIV-positive patients by the limiting dilution technique and measures their apparent reduction under increasing concentrations of drugs. An advantage of this assay is that it utilizes a variety of wild-type viruses not selected by in vitro propagation. Potency ranking placed the (-)-L-enantiomer of 2',3'-dideoxy-5-fluoro-3'-thiacytidine [(-)-FTC], an oxathiolane pyrimidine nucleoside analog (90% effective concentration = 55 nM), before 2',3'-dideoxycytidine (DDC) (74 nM), (-)-2',3'-dideoxy-3'-thiacytidine (3TC) (300 nM), 3'-azido-3'-deoxythymidine (AZT) (530 nM), TIBO R82913 (670 nM), and 2',3'-dideoxyinosine (DDI) (6,400 nM). HIV from AZT-naive patients' lymphocytes was more sensitive to the inhibitory effect of (-)-FTC, 3TC, or DDC than was highly AZT-resistant HIV obtained from AZT-treated patients' cells, indicating partial cross-resistance between thymidine and cytidine analogs. Combined inhibitory concentrations of AZT with (-)-FTC, 3TC, DDC, and DDI produced synergistic interactions as determined by the multiple-drug effect analysis. Synergistic interactions were demonstrable with AZT plus (-)-FTC or with AZT plus DDC with cells bearing AZT-resistant HIV. The inhibitory concentrations of AZT established by this cell-to-cell virus transmission assay are closer than those determined by the conventional assay system to the extracellular AZT concentrations required in patients' plasma to achieve comparable levels of HIV inhibition in vivo.
Tolerance to Small Delay Defects by Adaptive Clock Stretching (2007)

Bridging defects typically manifest themselves as increased path delays instead of stuck-at failures. On the other hand, parametric variations (both inter- and intra-die) increase the spread of the circuit delay. Low power design techniques such as voltage scaling, dual-Vth etc. deteriorate the delay spread further. These mechanisms for delay variations in nanoscaled technologies significantly affect the parametric yield. We propose a new design methodology to tolerate subtle delay failures that arise both due to manufacturing defects and parameter fluctuations. We synthesize the circuit to (a) isolate and predict the critical paths of a circuit; (b) create timing slack between critical and off-critical paths and ensure that they are activated rarely; and, (c) avoid the delay failures in these paths by adaptively stretching the clock period. Since critical paths are the most sensitive section of the circuit in terms of delay defects, we ensure fault-free operation by isolating them and providing extra computation time by predicting their activation. This allows us to achieve the required yield with small performance penalty (due to occasional clock stretching under critical path activation). We present application of the proposed methodology for both linear and non-linear pipeline designs. We also suggest two possible circuit-level implementations of clock stretching using clock gating and handshaking, respectively. Simulations on MCNC benchmark circuits with BPTM 70 nm devices show that the proposed technique can achieve good yield by tolerating increased path delays (under variations and bridging defects of various sizes) with small overhead in performance and ~14% die-area compared to the conventional design. For performance analysis, we have implemented the proposed methodology in simple <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in-order</i> pipeline in Simplescalar. Simulation results on SPEC2000 benchmarks show less that 2% of IPC (instructions-per-cycle) degradation.