gebhart/patrepeval huggingface dataset:
Synthesis of C8‐N‐Arylamine‐Modified 2′‐Deoxyguanosine‐5′‐Triphosphates and Their Effects on Primer Extension by DNA Polymerases (2015)

C8-N-arylamine adducts of 2'-deoxyguanosine (2'-dG) play an important role in the induction of the chemical carcinogenesis caused by aromatic amines. C8-N-acetyl-N-arylamine dG adducts that differ in their substitution pattern in the aniline moiety were converted by cycloSal technology into the corresponding C8-N-acetyl-N-arylamine-2'-deoxyguanosine-5'-triphosphates and C8-NH-arylamine-2'-deoxyguanosine-5'-triphosphates. Their conformation preference has been investigated by NOE spectroscopy and DFT calculations. The substrate properties of the C8-dG adducts were studied in primer-extension assays by using Klenow fragment exo(-) of Escherichia coli DNA polymerase I and human DNA polymerase β. It was shown that the incorporation was independent of the substitution pattern in the aryl moiety and the N-acetyl group. Although the triphosphates were poor substrates for the human polymerases, they were incorporated twice before the termination of the elongation process occurred; this might demonstrate the importance of C8-N-arylamine-2'-deoxyguanosine-5'-triphosphates in chemical carcinogenesis.
Chimie bio-inspirée et nanosciences : vers de nouveaux catalyseurs pour la production et l’oxydation de l’hydrogène (2010)

Il ne fait pas de doute que la source d’énergie renouvelable la plus abondante, très largement supérieure aux contributions potentielles de l’énergie éolienne, géothermique ou hydroélectrique par exemple, est l’énergie solaire. Une façon d’exploiter cette énergie est de la transformer en énergie chimique, de la stocker sous la forme d’un carburant, par exemple l’hydrogène. Ce dernier est, on le sait, une alternative prometteuse à l’utilisation du pétrole, à la fois en raison de la grande quan...
The Soul as the Root, the Ground, and the Flowering Dance of Religious Dialogue: Toward a Worldview of Evolving Equanimity (2019)

In 2010
Heterogeneous InP on SOI Integration for the Realization of All-Optical Logic Devices (2010)

InP-based microdisk lasers, heterogeneously integrated onto SOI waveguides, can be used as generic non-linear devices for realizing all-optical logic. We will discuss the performance of individual microdisk lasers, and the implementation of more complex circuits.
Batch Optimization for DNA Synthesis (2021)

Large pools of synthetic DNA molecules have been recently used to reliably store significant volumes of digital data. While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently severely limited because of the high cost and low throughput of available DNA synthesis technologies. We study the role of batch optimization in reducing the cost of large scale DNA synthesis, which translates to the following algorithmic task. Given a large pool <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$S$</tex> of random quaternary strings of fixed length, partition <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$S$</tex> into batches in a way that minimizes the sum of the lengths of the shortest common supersequences across batches. We introduce two ideas for batch optimization that both improve (in different ways) upon a naive baseline: (1) using both (ACGT)* and its reverse (TGCA)* as reference strands, and batching appropriately, and (2) batching via the quantiles of an appropriate ordering of the strands. We also prove asymptotically matching lower bounds on the cost of DNA synthesis, showing that one cannot improve upon these two ideas. Our results uncover a surprising separation between two cases that naturally arise in the context of DNA data storage: the asymptotic cost savings of batch optimization are significantly greater in the case where strings in <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$S$</tex> do not contain repeats of the same character (homopolymers), as compared to the case where strings in <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$S$</tex> are unconstrained. A full version of this paper is accessible at: https://arxiv.org/abs/2011.14532
Data from Biomarker Assessment of HR Deficiency, Tumor <i>BRCA1/2</i> Mutations, and <i>CCNE1</i> Copy Number in Ovarian Cancer: Associations with Clinical Outcome Following Platinum Monotherapy (2023)

&lt;div&gt;Abstract&lt;p&gt;The current study evaluated three biomarkers [homologous recombination deficiency (HRD), tumor BRCA1/2 (tBRCA) mutations, and CCNE1 copy-number variation (CNV)] in ovarian tumors from patients enrolled on the SCOTROC4 clinical trial for associations with outcome following carboplatin monotherapy. Ovarian tumors (&lt;i&gt;n&lt;/i&gt; = 250), with high-grade serous (HGSOC) subgroup analysis (&lt;i&gt;n&lt;/i&gt; = 179) were classified as HRD positive (HRD score ≥42 or tBRCA mutation) and as CCNE1 amplification positive (CCNE1 CNV score &gt;2.4). Seventy-four (30%) tumors were HRD positive, including 34 (14%) with tBRCA mutations. Forty-seven (19%) were CCNE1 amplification positive, all of which were tBRCA wild-type. HRD and tBRCA, but not CCNE1 amplification, were significantly associated with CA125 complete response in the entire cohort (HRD, &lt;i&gt;P&lt;/i&gt; = 0.00015; tBRCA &lt;i&gt;P&lt;/i&gt; = 0.0096), and the HGSOC subgroup (HRD, &lt;i&gt;P&lt;/i&gt; = 0.0016; tBRCA &lt;i&gt;P&lt;/i&gt; = 0.032). HRD and lack of CCNE1 amplification were associated with improved progression-free survival (PFS) and overall survival (OS) in the full cohort and HGSOC subgroup (HRD, &lt;i&gt;P&lt;/i&gt; = 0.00021; CCNE1 status &lt;i&gt;P&lt;/i&gt; = 0.038). HRD remained significant for OS and PFS after adjusting for clinical factors, while CCNE1 status only remained significant for PFS. Patients with HRD-positive tumors had greater PFS and OS benefit from platinum dose intensification than HRD-negative tumors (&lt;i&gt;P&lt;/i&gt; = 0.049 and &lt;i&gt;P&lt;/i&gt; = 0.035, respectively). An alternative exploratory HRD score threshold (≥33 or tBRCA mutation) was also significantly associated with both PFS and OS in the HGSOC subset.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Implications:&lt;/b&gt; HRD, tumor BRCA1/2 mutations, and absence of CCNE1 amplification are associated with improved survival of ovarian cancer patients treated with platinum monotherapy and HRD-positive patients may benefit from platinum dose intensification. &lt;i&gt;Mol Cancer Res; 16(7); 1103–11. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
High performance sieving of biomolecules in a capillary-well motif (2015)

We report a novel artificial sieve featuring a periodic array of 70-nm capillaries interleaved with deep wells: the capillary-well motif. Integration of cylindrical capillaries and subsequent scaling of their diameter are achieved by standard fabrication techniques and surface tension driven shape transformation of a doped glass layer on silicon. High resolution rapid sieving of DNA and proteins within broad size ranges is presented in continuous-flow as well as batch separation modes. The high performance attained is ascribed to the vastly steep entropic barriers imposed by capillaries and their capacity to handle increased fields (1000 V/cm).
Branched KLVFF Tetramers Strongly Potentiate Inhibition of β‐Amyloid Aggregation (2007)

The key pathogenic event in the onset of Alzheimer's disease (AD) is the aggregation of beta-amyloid (Abeta) peptides into toxic aggregates. Molecules that interfere with this process might act as therapeutic agents for the treatment of AD. The amino acid residues 16-20 (KLVFF) are known to be essential for the aggregation of Abeta. In this study, we have used a first-generation dendrimer as a scaffold for the multivalent display of the KLVFF peptide. The effect of four KLVFF peptides attached to the dendrimer (K(4)) on Abeta aggregation was compared to the effect of monomeric KLVFF (K(1)). Our data show that K(4) very effectively inhibits the aggregation of low-molecular-weight and protofibrillar Abeta(1-42) into fibrils, in a concentration-dependent manner, and much more potently than K(1). Moreover, we show that K(4) can lead to the disassembly of existing aggregates. Our data lead us to propose that conjugates that bear multiple copies of KLVFF might be useful as therapeutic agents for the treatment of Alzheimer's disease.
A modular, analytical throughput model for modern disk arrays (2002)

Enterprise storage systems depend on disk arrays for their capacity and availability needs. To design and maintain storage systems that efficiently satisfy evolving requirements, it is critical to be able to evaluate configuration alternatives without having to physically implement them. In this paper, we describe an analytical model to predict disk array throughput, based on a hierarchical decomposition of the internal array architecture. We validate the model against a state-of-the-art disk array for a variety of synthetic workloads and array configurations. To our knowledge, no previously published analytical model has either incorporated the combined effects of the complex optimizations present in modern disk arrays, or been validated against a real, commercial array. Our results are quite encouraging for an analytical model: predictions are accurate in most cases within 32% of the observed array performance (15% on the average) for our set of experiments.
A high-fidelity airbus benchmark for system fault detection and isolation and flight control law clearance (2013)

This paper presents a high-fidelity generic twin engine civil aircraft model developed by Airbus for advanced flight control system research. The main features of this benchmark are described to make the reader aware of the model complexity and representativeness. It is a complete representation including the nonlinear rigid-body aircraft model with a full set of control surfaces, actuator models, sensor models, flight control laws (FCL), and pilot inputs. Two applications of this benchmark in the framework of European projects are presented: FCL clearance using optimization and advanced fault detection and diagnosis (FDD).
Wear and Shelling Behavior in Pearlitic and Bainitic Rail Steels with Various Tensile Strengths (2000)

Resistance to wear and surface damaging (shelling) in pearlitic and bainitic steel rails with various tensile strengths ranging from 850 to 1400 MPa were examined by wear and rotating contact fatigue tests. The pearlitic steels showed better wear resistance than the bainitic steels for all the test conditions tested, although the amount of wear varied according to the strength range and contact pressure used in the wear tests. The wear behavior of the pearlitic steels was roughly described by a Holm's-type equation (W=kP/H; where W: amount of wear, P: contact pressure, H: hardness and k: constant), while that of the bainitic steels showed complex dependencies on the strength and contact pressure. The bainitic steels, however, showed superior damage resistance to the pearlitic steels for all the test conditions tested: at a fixed tensile strength of 850 MPa, significant shelling was observed in the pearlitic steel after 200 h testing, while no damage was detected in the bainitic steel even after 500 h. The resistance to shelling of the pearlitic steels was improved by strengthening, but the opposite trend was obtained in the bainitic steels. These results were analyzed taking work hardening on the sample surface into consideration. Additionally, the formation behavior of the "white phase", which was the martensite phase formed on the rail-head surface by friction between rails and wheels, was compared in pearlitic and bainitic steels and discussed metallurgically.
Year-round daylight savings: an equation predicting carbon monoxide violations (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleYear-round daylight savings: an equation predicting carbon monoxide violationsKaren K. Francis, Cecilia Hellstadius, and Donald H. StedmanCite this: Environ. Sci. Technol. 1989, 23, 9, 1168–1170Publication Date (Print):September 1, 1989Publication History Published online1 May 2002Published inissue 1 September 1989https://pubs.acs.org/doi/10.1021/es00067a016https://doi.org/10.1021/es00067a016research-articleACS PublicationsRequest reuse permissionsArticle Views23Altmetric-Citations-LEARN 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
Heparin‐Based Nanocapsules as Potential Drug Delivery Systems (2015)

Herein, the synthesis and characterization of heparin-based nanocapsules (NCs) as potential drug delivery systems is described. For the synthesis of the heparin-based NCs, the versatile method of miniemulsion polymerization at the droplets interface was achieved resulting in narrowly distributed NCs with 180 nm in diameter. Scanning and transmission electron microscopy images showed clearly NC morphology. A highly negative charge density for the heparin-based NCs was determined by measuring the electro-kinetic potential. Measuring the activated clotting time demonstrated the biological intactness of the polymeric shell. The ability of heparin-based NCs to bind to antithrombin (AT III) was investigated using isothermal titration calorimetry and dynamic light scattering experiments. The chemical stability of the NCs was studied in physiological protein-containing solutions and also in medically interesting fluids such as sodium chloride 0.9%, Ringer's solution, and phosphate buffer saline using dynamic light scattering and measuring the fluorescence intensity. The impressive uptake of NCs in different cells was confirmed by fluorescence-activated cell sorting, confocal laser scanning microscopy, and transmission electron microscopy. The low toxicity of all types of NCs was demonstrated.
Low-driving-voltage band-operation LiNbO 3 modulator with lightwave reflection and double-stub structure (2002)

A reflection-type Mach-Zehnder LiNbO3 optical modulator with a double-stub structure that can modulate both forward and backward lightwave to achieve low-driving-voltage optical modulation for band-operation is developed. Using optical reflection the modulation efficiency is doubled. The halfwave-voltage of the fabricated modulator was 2.9 V at 7 GHz.
Teaching and implementing autonomous robotic lab walkthroughs in a biotech laboratory through model-based visual tracking (2009)

After utilizing robots for more than 30 years for classic industrial automation applications, service robots form a constantly increasing market, although the big breakthrough is still awaited. Our approach to service robots was driven by the idea of supporting lab personnel in a biotechnology laboratory. After initial development in Germany, a mobile robot platform extended with an industrial manipulator and the necessary sensors for indoor localization and object manipulation, has been shipped to Bayer HealthCare in Berkeley, CA, USA, a global player in the sector of biopharmaceutical products, located in the San Francisco bay area. The determined goal of the mobile manipulator is to support the off-shift staff to carry out completely autonomous or guided, remote controlled lab walkthroughs, which we implement utilizing a recent development of our computer vision group: OpenTL - an integrated framework for model-based visual tracking.
Status of the AIMS(TM) EUV Project (2012)

In previous conferences the status of the AIMS™ EUV project has been presented in which the basic layout scheme and preliminary design have been shown along with the targeted performance specification levels to be met. Presently the final design milestone of the project has been successfully completed and assembly of the prototype tool is underway. The final design concept will be presented along with the current status of the tool and simulated performance data.
Feasibility and efficacy of bypassing the right ventricle and pulmonary circulation to treat right ventricular failure: an experimental study (2012)

Bypassing the right ventricle and pulmonary circulation with an oxygenating assist device, which may offer the advantages of enhanced right ventricular decompression and augmented left atrial filling, is feasible and effective in the treatment of acute RVF. Long time experiments are needed.
A parallel algorithm for fingerprint matching (2003)

A parallel algorithm for fingerprint matching is presented. The algorithm is implemented on a systolic array processor. Improvement in the speed of the matching process relative to a sequential algorithm is found to be significant.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
RETRACTED: Chitosan-Based Microparticles Enhance Ellagic Acid’s Colon Targeting and Proapoptotic Activity (2020)

This study aimed at improving the targeting and cytotoxic effect of ellagic acid (EA) on colon cancer cells. EA was encapsulated in chitosan (CHIT) polymers then coated by eudragit S100 (ES100) microparticles. The release of EA double-coated microparticles (MPs) was tested at simulative pH values. Maximum release was observed at 24 h and pH 7.4. The cytotoxicity of EA MPs on HCT 116 colon cancer cells was synergistically improved as compared with raw EA. Cell-cycle analysis by flow cytometry suggested enhanced G2-M phase colon cancer cell accumulation. In addition, a significantly higher cell fraction was observed in the pre-G phase, which highlighted the enhancement of the proapoptotic activity of EA formulated in the double-coat mixture. Annexin-V staining was used for substantiation of the observed cell-death-inducing activity. Cell fractions were significantly increased in early, late, and total cell death. This was backed by high elevation in cellular content of caspase 3. Effectiveness of the double-coated EA to target colonic tissues was confirmed using real-time iohexol dye X-ray radiography. In conclusion, CHIT loaded with EA and coated with ES100 formula exhibits improved colon targeting as well as enhanced cytotoxic and proapoptotic activity against HCT 116 colon cancer when compared with the administration of raw EA.
Monovalent and bivalent cations exchange isotherms for faujasites X and Y (2017)

This study addresses the modeling of exchange isotherms for faujasite-type zeolites X and Y with K<sup>+</sup>, Cs<sup>+</sup>, Ca<sup>2+</sup> and Ba<sup>2+</sup> cations based on a large experimental dataset obtained under operating conditions of 0.5 N total normality and an exchange temperature of 80 °C. The isotherm models are based on the mass action law. Ideal solution phase is assumed. Heterogeneity of the solid phase is taken into account by using Barrer and Klinowski's approach to multi-site exchange. Three types of exchange sites are identified on these zeolites. To each exchange site j corresponds a fitted selectivity coefficient K<sub>j</sub>. These parameters, estimated by least square method, evaluate the affinity of the studied cations for the identified exchange site. Globally, these fitted coefficients show that the cations considered present better affinity than Na<sup>+</sup>, especially for type III sites in faujasite X and type II sites in faujasite Y. For bivalent cations, an exchange with Ba<sup>2+</sup> is always more favorable than with Ca<sup>2+</sup>. On faujasite X, type II sites are more strongly preferred by monovalent cations (with the exception of Cs<sup>+</sup>) than by bivalent ones. The opposite trend is observed on faujasite Y, even for Cs<sup>+</sup>. These conclusions have been confirmed and are supported by bibliographic data.
Highly birefringent hollow-core photonic bandgap fiber (2005)

A highly birefringent hollow-core photonic bandgap fiber is fabricated and characterized. The fiber group birefringence is found to be 0.025 at 1550 nm through wavelength scanning method and direct measurement of differential group delay.
Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma (2021)

Sarcomatoid and rhabdoid (S/R) renal cell carcinoma (RCC) are highly aggressive tumors with limited molecular and clinical characterization. Emerging evidence suggests immune checkpoint inhibitors (ICI) are particularly effective for these tumors, although the biological basis for this property is largely unknown. Here, we evaluate multiple clinical trial and real-world cohorts of S/R RCC to characterize their molecular features, clinical outcomes, and immunologic characteristics. We find that S/R RCC tumors harbor distinctive molecular features that may account for their aggressive behavior, including BAP1 mutations, CDKN2A deletions, and increased expression of MYC transcriptional programs. We show that these tumors are highly responsive to ICI and that they exhibit an immune-inflamed phenotype characterized by immune activation, increased cytotoxic immune infiltration, upregulation of antigen presentation machinery genes, and PD-L1 expression. Our findings build on prior work and shed light on the molecular drivers of aggressivity and responsiveness to ICI of S/R RCC.
Implementation and optimization of a real-time PAC codec (2002)

The authors describe an implementation of the perceptual audio coding (PAC) audio compression algorithm on PowerPC hardware designed to support simultaneous real-time compression and decompression of audio for transmission over a network. They describe the algorithm variant used, the target hardware and software development tools, and then describe the various optimizations that reduced the complexity sufficiently to allow the algorithm to run in real-time. They conclude by describing a scheduling algorithm that allows them to manage the complexity associated with the compression of 'difficult' music.