gebhart/patrepeval huggingface dataset:
The extrachromosomal elements of the Naegleria genus: How little we know (2021)

There are currently 47 characterized species in the Naegleria genus of free-living amoebae. Each amoeba has thousands of extrachromosomal elements that are closed circular structures comprised of a single ribosomal DNA (rDNA) copy and a large non-rDNA sequence. Despite the presence of putative open reading frames and introns, ribosomal RNA is the only established transcript. A single origin of DNA replication (ori) has been mapped within the non-rDNA sequence for one species (N. gruberi), a finding that strongly indicates that these episomes replicate independently of the cell's chromosomal DNA component. This article reviews that which has been published about these interesting DNA elements and by analyzing available sequence data, discusses the possibility that different phylogenetically related clusters of Naegleria species individually conserve ori structures and suggests where the rRNA promoter and termination sites may be located.
Recent progress in nonpolar LEDs as polarized light emitters (2008)

Abstract The present article provides an overview of developments in nonpolar‐oriented GaN‐based materials as polarized light emitters over the past 15 years. The strong interest in nonpolar materials emerged around 1996, but nonpolar‐oriented light‐emitting diodes were not demonstrated until 2004. The later technological key achievement was the commercialization of nonpolar‐oriented bulk GaN substrates; it is now feasible to discuss the electronic band structure of such high‐quality nonpolar GaN as well as device applications of polarized light emitters. (© 2009 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Thionation Using Fluorous Lawesson′s Reagent. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Single-photon detection beyond 1 μm: performance of commercially available germanium photodiodes (1994)

Germanium avalanche photodiodes (APD's) working biased above the breakdown voltage detect single optical photons in the near-infrared wavelength range. We give guidelines for the selection of devices suitable for photon-counting applications among the commercial samples, and we discuss in detail how the devices should be operated to achieve the best performance, both in terms of noise-equivalent power (NEP) and the timing-equivalent bandwidth. We introduce the driving electronics and we show that, in the measurements of fast optical signals, the adoption of single-photon techniques is very favorable, notwithstanding that presently available photodiodes are not designed for this purpose. On the contrary, in the detection of cw signals, the lower NEP values achieved in photon counting may not be sufficient to justify the replacement of conventional analog p-i-n germanium detectors, which offer comparable performance with a definitely larger sensitive area. Finally, we show that, by properly choosing theoperating conditions, some selected APD's achieve an 85-ps time resolution in the detection of optical photons at a 1.3-µm wavelength, which corresponds to a timing-equivalent bandwidth of 1.8 GHz. To the best of our knowledge, this time resolution is the lowest reported to date for single-photon detectors in the near infrared.
AAV8-antiVEGFfab Ocular Gene Transfer for Neovascular Age-Related Macular Degeneration (2017)

Sustained suppression of VEGF is needed in many patients with neovascular age-related macular degeneration (NVAMD), and gene transfer of a VEGF-neutralizing protein is a promising approach to achieve it. Initial clinical trials testing this approach have shown encouraging signals, but evidence of robust transgene expression and consistent antiangiogenic and antipermeability activity has been lacking. In this study, we demonstrate expression of an anti-human VEGF antibody fragment (antiVEGFfab) after subretinal injection of AAV8-antiVEGFfab. In transgenic mice expressing human VEGF in retina (rho/VEGF mice), a model of type 3 choroidal neovascularization (NV), eyes injected with ≥1 × 10<sup>7</sup> gene copies (GC) of AAV8-antiVEGFfab had significantly less mean area of NV than null vector-injected eyes. A dose-dependent response was observed with modest reduction of NV with ≤3 × 10<sup>7</sup>, >50% reduction with ≥1 × 10<sup>8</sup> GC and almost complete elimination of NV with 3 × 10<sup>9</sup> or 1 × 10<sup>10</sup> GC. In Tet/opsin/VEGF mice, in which doxycycline-induced high expression of VEGF leads to severe vascular leakage and exudative retinal detachment (RD), reduction of total RD by 70%-80% occurred with 3 × 10<sup>9</sup> or 1 × 10<sup>10</sup> GC of AAV8-antiVEGFfab, an effect that was sustained for at least a month. These data strongly support initiating clinical trials testing subretinal injection of AAV8-antiVEGFfab in patients with NVAMD.
Results on the gravity of quantum Fermi pressure of localized matter: A new test of general relativity (2006)

Recently Ehlers, Ozsv\'ath, and Schucking discussed whether pressure contributes to active gravitational mass as required by general relativity. They pointed out that there is no experimental information on this available, though precision measurement of the gravitational constant should provide a test of this foundational aspect of gravity. We had used a similar argument earlier to test the contribution of leptons to the active gravitational mass. In this paper we use the result from the Z\"urich gravitational constant experiment to provide the first adequate experimental input regarding the active gravitational mass of Fermi pressure. Apart from confirming the equality of the passive and active gravitational roles of the pressure term in general relativity within an accuracy of 5%, our results are consistent with the theoretical expectation of the cancellation of the gravity of pressure by the gravity of the surface tension of confined matter. This result on the active gravitational mass of the quantum zero-point Fermi pressure in the atomic nucleus is also interesting from the point of view of studying the interplay between quantum physics and classical gravity.
Physiologic Levels of β‐Amyloid Activate Phosphatidylinositol 3‐Kinase with the Involvement of Tyrosine Phosphorylation (1996)

The beta-amyloid protein (A beta) peptide plays an important role in Alzheimer's disease, but the potential actions of physiologic levels of A beta (225-625 pM) have not been explored. We recently showed that picomolar doses of A beta can stimulate tyrosine phosphorylation of neuronal cells and now show that leads to the activation of the lipid kinase phosphatidylinositol 3-kinase (PI3 kinase). Three independent lines of evidence support the hypothesis that A beta is activating PI3 kinase through a tyrosine kinase-mediated mechanism. Immunoblotting studies show that A beta induces tyrosine phosphorylation of p85 as well as association of the p85 subunit of PI3 kinase with tyrosine-phosphorylated proteins. Studies of membrane proteins show that A beta induces a translocation of p85 to membrane-bound glycoproteins, which are likely to be receptors. Finally, direct studies of PI3 kinase activity in both anti-phosphotyrosine immunocomplexes and wheat germ agglutinin precipitates show that A beta increases formation of the product of PI3 kinase. Wortmannin, a selective inhibitor of PI3 kinase, blocks this A beta-stimulated PI3 kinase activity. Thus, physiologic levels of A beta stimulate tyrosine phosphorylation and PI3 kinase activity.
Moving Beyond Downstream Task Accuracy for Information Retrieval Benchmarking (2022)

Neural information retrieval (IR) systems have progressed rapidly in recent years, in large part due to the release of publicly available benchmarking tasks. Unfortunately, some dimensions of this progress are illusory: the majority of the popular IR benchmarks today focus exclusively on downstream task accuracy and thus conceal the costs incurred by systems that trade away efficiency for quality. Latency, hardware cost, and other efficiency considerations are paramount to the deployment of IR systems in user-facing settings. We propose that IR benchmarks structure their evaluation methodology to include not only metrics of accuracy, but also efficiency considerations such as a query latency and the corresponding cost budget for a reproducible hardware setting. For the popular IR benchmarks MS MARCO and XOR-TyDi, we show how the best choice of IR system varies according to how these efficiency considerations are chosen and weighed. We hope that future benchmarks will adopt these guidelines toward more holistic IR evaluation.
Selective Resistance of CD44hi T Cells to p53-Dependent Cell Death Results in Persistence of Immunologic Memory after Total Body Irradiation (2011)

Our previous studies showed that treatment of mice with total body irradiation (TBI) or total lymphoid tissue irradiation markedly changes the balance of residual T cell subsets to favor CD4(+)CD44(hi) NKT cells because of the differential resistance of the latter subset to cell death. The object of the current study was to further elucidate the changed balance and mechanisms of differential radioresistance of T cell subsets after graded doses of TBI. The experimental results showed that CD4(+) T cells were markedly more resistant than CD8(+) T cells, and CD44(hi) T cells, including NKT cells and memory T cells, were markedly more resistant than CD44(lo) (naive) T cells. The memory T cells immunized to alloantigens persisted even after myeloablative (1000 cGy) TBI and were able to prevent engraftment of bone marrow transplants. Although T cell death after 1000 cGy was prevented in p53(-/-) mice, there was progressive T cell death in p53(-/-) mice at higher doses. Although p53-dependent T cell death changed the balance of subsets, p53-independent T cell death did not. In conclusion, resistance of CD44(hi) T cells to p53-dependent cell death results in the persistence of immunological memory after TBI and can explain the immune-mediated rejection of marrow transplants in sensitized recipients.
Final step gallium-68 radiolabelling of silica-coated iron oxide nanorods as potential PET/MR multimodal imaging agents (2014)

The investigation of iron oxide-based positron emission tomography/magnetic resonance (PET/MR) multimodal imaging agents is an expanding field in which a variety of nanoparticle sizes, shapes, surface coatings and radioisotopes are open for exploration. This study develops iron oxide nanorods which are coated with various mixtures of poly(ethylene glycol) (PEG) and macrocyclic ligand (DO3A) via the formation of a silica layer on the surface. Gallium-68 radiolabelling of the nanorods was carried out in high radiochemical yields (RCY) and their stability in human serum was demonstrated for all constructs, even in the absence of the macrocyclic chelating unit. Further studies were carried out in an attempt to determine the appropriate amount of PEG coating to give optimal properties for future in vivo studies.
Characterizing batch reactions with in situ spectroscopic measurements, calorimetry and dynamic modeling (2003)

Abstract A method for fully characterizing consecutive batch reactions using self‐modeling curve resolution of in situ spectroscopic measurements and reaction energy profiles is reported. Simultaneous measurement of reaction temperature, reactor jacket temperature, reactor heater power and UV/visible spectra was made with a laboratory (50 ml capacity) batch reactor equipped with a UV/visible spectrometer and a fiber optic attenuated total reflectance (ATR) probe. Composition profiles and pure component spectra of reactants and products were estimated without the aid of reference measurements or standards from the in situ UV/visible spectra using non‐negative alternating least squares (ALS), a type of self‐modeling curve resolution (SMCR). Multiway SMCR analysis of consecutive batches permitted standardless comparisons of consecutive batches to determine which batch produced more or less product and which batch proceeded faster or slower. Dynamic modeling of batch energy profiles permitted mathematical resolution of the reaction dose heat and reaction heat. Kinetic fitting of the in situ reaction spectra was used to determine reaction rate constants. These three complementary approaches permitted simple and rapid characterization of the reaction's rate of reaction, energy balance and mass balance. Copyright © 2003 John Wiley &amp; Sons, Ltd.
A New Technique to Develop Rock Strength Correlation Using Artificial Intelligence Tools (2017)

Abstract Unconfined compressive strength (UCS) is the key parameter to; estimate the insitu stresses of the rock, design optimal hydraulic fracture geometry and avoid drilling problems like wellbore instability. UCS can be estimated by rock mechanical tests on core plugs retrieved from the depth of interest but retrieving reservoir rock samples throughout the depth of the reservoir section and performing laboratory tests on them are extremely expensive as well as time consuming. In absence of core plugs, UCS can be estimated from empirical correlations. Most of the empirical correlations for UCS prediction reported in the literature are based on elastic parameters or on compressional wave velocity. These correlations were developed using linear or non-linear regression techniques. Artificial intelligence tools once optimized for training can successfully model UCS since these tools can capture highly complex and non-linear relationship between input parameters and the output parameter. The objective of this research study is to accurately predict UCS of rock using basic geophysical well logs namely; bulk density, compressional, and shear wave velocities, by applying different artificial intelligence techniques namely; Support Vector Machine (SVM), Adaptive neuro fuzzy inference system (ANFIS) and Artificial neural network (ANN). The data set used in this study, comprised of 200 laboratory measured UCS values on core plugs and their corresponding well logs. The data were collected from 10 wells which were located in a giant carbonate reservoir. Based on minimum average absolute percentage error (AAPE) and highest coefficient of determination (R2) between actual and predicted data, ANN model proposed as the best model to predict UCS. A rigorous empirical correlation was developed using the weights and biases of ANN model to predict without the need of any software incorporating AI. A comparison of proposed model with other correlations to predict UCS on new data set also suggested that the proposed model gives less AAPE. Therefore, the proposed model seems very promising and can serve as a handy tool to help geo-mechanical engineers to determine the UCS of the carbonate rock.
Image sensor module and a method for evaluating an image sensor (2019)

An Image Sensor Module (ISM) comprises an Image Sensor Chip (ISC) that typically does not contain information (ISC ID) about the manufacturer and specific process, as well as the data for failure analyses. Similar dice by different manufacturers may differ from each other by their quality and lifespan. Counterfeit ISMs usually exhibit lower performance and quality than the original ones. Installing a counterfeit ISM in an imaging device may dramatically reduce its functionality and reliability. The standard ISC ID technology assumes disassembly of the ISC from the ISM and reverse engineering, or a special electrical readout system, if the information was written in the embedded non- volatile memory. We suggest a simple ISC ID method that features Luminescent Composition (LC) introduced into the lenses and/or color filters of ISC. Chip identification is performed without disassembling of the ISM. In addition, the use of LC allows extending the spectral sensitivity of the ISM with silicon image sensor dice. The design is patented (US10210526) and ready for implementation in the new ISM generation.
Neutral Loss (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Supplementary Table 5 from Genome-Wide CpG Island Profiling of Intraductal Papillary Mucinous Neoplasms of the Pancreas (2023)

&lt;p&gt;XLS file - 59K&lt;/p&gt;
Two-Dimensional Siloxene Nanosheets: Impact of Morphology and Purity on Electrochemistry (2023)

Two-dimensional (2D) siloxene (Si<sub>6</sub>O<sub>3</sub>H<sub>6</sub>) has shown promise as a negative electrode material for Li-ion batteries due to its high gravimetric capacity and superior mechanical properties under (de)lithiation compared to bulk Si. In this work, we prepare purified siloxene nanosheets through the removal of bulk Si contaminants, use ultrasonication to control the lateral size and thickness of the nanosheets, and probe the effects of the resulting morphology and purity on the electrochemistry. The thin siloxene nanosheets formed after 4 h of ultrasonication deliver an average capacity of 810 mA h/g under a 1000 mA/g rate over 200 cycles with a capacity retention of 76%. Interestingly, the purified siloxene shows lower initial capacity but superior capacity retention over extended cycling. The 2D morphology benefit is illustrated where the parent siloxene nanosheet morphology and structure were largely maintained based on <i>operando</i> optoelectrochemistry, in situ Raman, ex situ scanning electron microscopy, and ex situ transmission electron microscopy. Furthermore, the purified siloxene-based electrode free from crystalline Si impurity experiences the least expansion upon (de)lithiation as visualized by cross-section electron microscopy of samples recovered post-cycling.
Oxidation-reduction equilibrium of cytochrome b5 (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxidation-reduction equilibrium of cytochrome b5Lorne S. Reid, Vernon T. Taniguchi, Harry B. Gray, and A. Grant MaukCite this: J. Am. Chem. Soc. 1982, 104, 26, 7516–7519Publication Date (Print):December 1, 1982Publication History Published online1 May 2002Published inissue 1 December 1982https://pubs.acs.org/doi/10.1021/ja00390a021https://doi.org/10.1021/ja00390a021research-articleACS PublicationsRequest reuse permissionsArticle Views255Altmetric-Citations67LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
FP7-CHEETAH Project Knowledge Exchange Portal: an Advanced Tool to Efficiently Bring Information to the European Photovoltaic RTD Community (2015)

FP7-CHEETAH is a combined collaborative project (CP) and coordination and support action (CSA) funded under the European Commission’s 7th Framework program and coordinated by ECN, NL with the aims to solve specific R&amp;D issues and to overcome fragmentation of European PV R&amp;D by intensifying the collaboration between R&amp;D providers and industry to accelerate the industrialization of innovations. The project is also tightly linked to the EERA-PV Joint Program. The CHEETAH Knowledge Exchange Area Portal (KEAP), in parallel to the project web site and other dissemination activities (newsletter, communication, etc), constitutes the pillar of the project to distribute information in a uniform and simple way. It is based on several very efficient ICT procedures by operating from the collection to management of information by dynamic data base matrix: any uploaded information is linked to all others. All interested browsers/readers can have efficient access to any stored data thanks to the utilization of a search engine/query keywords and user friendly graphic interfaces. Based on the implementation of SOPHi@webinar platform, the portal also offers its own e-learning platform. CHEETAH KEAP represents for its peculiarities a major breakthrough in the field with highly innovative contents and a substantial improvement in comparison with the state of the art of knowledge exchange on PV RTD.