gebhart/patrepeval huggingface dataset:
Introduction (1995)

Exploration seismology deals with the use of artificially generated elastic waves to locate mineral deposits (including hydrocarbons, ores, water, geothermal reservoirs, etc.), archaeological sites, and to obtain geological information for engineering. Exploration seismology provides data that, when used in conjunction with other geophysical, borehole, and geological data and with concepts of physics and geology, can provide information about the structure and distribution of rock types. Usually, seismic exploration is part of a commercial venture and, hence, economics is an ever-present concern. Seismic methods alone cannot determine many of the features that make for a profitable venture and, even when supplemented by other data, a unique interpretation is rarely evident. Seismic exploration usually stops long before unambiguous answers are obtained and before all has been learned that might possibly be learned, because in someone's judgment further information is better obtained in some other way, such as by drilling a well. Seismic methods are in continual economic competition with other methods.
Differential serological immune imprinting following SARS-CoV-2 infection, vaccination, and breakthrough infection (2022)

Abstract Extensive efforts have been made to study the human immune response following SARS-CoV-2 infection. Recent work by our lab provided insights into the molecular-level composition of the circulating IgG antibody repertoire evoked by SARS-CoV-2 primary infection and revealed key properties of the spike-directed antibodies and the epitopes they target in convalescent plasma (Voss et al., Science 2021). We showed that the antibody response in mild SARS-CoV-2 infection is directed to epitopes outside the RBD and primarily to the S2 domain of the spike glycoprotein. The continual emergence of globally circulating SARS-CoV-2 variants underscores the need for an ongoing study of the long-term evolution of our adaptive immune response to this virus. Collective knowledge about the molecular composition of human serological IgG memory to SARS-CoV-2 is limited. Our research uses single-cell sequencing and plasma IgG proteomics to better understand the evolving plasma antibody response to infection, vaccination, and breakthrough infection. In volunteers with a primary infection prior to vaccination, we can identify the serological recall of somatically mutated, pre-existing IgG antibodies targeting the S2 domain of the SARS-CoV-2 spike that cross-react with conserved epitopes expressed by endemic β-coronaviruses, indicating the existence of serological immune imprinting by prior infections. In contrast, in volunteers who received a full vaccine regimen and then had a breakthrough infection, the serological recall is markedly different—as shall be discussed. Collectively, these data reveal that the molecular nature of serological IgG recall appears to depend on the sequence and mode of exposure to SARS-CoV-2 spike antigen. Supported by NIH NCI COVID-19 SeroNet grant U54-CA260543 (R.S.B.)
ChemInform Abstract: Synthesis of Taxoids. Part 2. Synthesis and Antitumor Activity of Water‐Soluble Taxoids. (1998)

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.
Interactions of CCCH Zinc Finger Proteins with mRNA (2001)

The CCCH family of tandem zinc finger proteins has recently been shown to promote the turnover of certain mRNAs containing class II AU-rich elements (AREs). In the case of one member of this family, tristetraprolin (TTP), absence of the protein in knockout mice leads to stabilization of two mRNAs containing AREs of this type, those encoding tumor necrosis factor alpha (TNFalpha) and granulocyte-macrophage colony-stimulating factor. To begin to decipher the mechanism by which these zinc finger proteins stimulate the breakdown of this class of mRNAs, we co-transfected TTP and its related CCCH proteins into 293 cells with vectors encoding full-length TNFalpha, granulocyte-macrophage colony-stimulating factor, and interleukin-3 mRNAs. Co-expression of the CCCH proteins caused the rapid turnover of these ARE-containing mRNAs and also promoted the accumulation of stable breakdown intermediates that were truncated at the 3'-end of the mRNA, even further 5' than the 5'-end of the poly(A) tail. To determine whether an intact poly(A) tail was necessary for TTP to promote this type of mRNA degradation, we inserted the TNFalpha ARE into a nonpolyadenylated histone mRNA and also attached a histone 3'-end-processing sequence to the 3'-end of nonpolyadenylated interleukin-3 and TNFalpha mRNAs. In all three cases, TTP stimulated the turnover of the ARE-containing mRNAs, despite the demonstrated absence of a poly(A) tail. These studies indicate that members of this class of CCCH proteins can promote class II ARE-containing mRNA turnover even in the absence of a poly(A) tail, suggesting that the processive removal of the poly(A) tail may not be required for this type of CCCH protein-stimulated mRNA turnover.
A genome‐wide linkage study in families with major depression and co‐morbid unexplained swelling (2007)

Major depressive disorder (MDD) is a common heritable condition. The diversity of the phenotype coupled with aetiological and genetic heterogeneity present formidable obstacles in the search for causative genetic loci. Studies of large families with many affected individuals, and the selection of well-defined clinical subgroups of depression, are two ways to reduce this complexity. Unexplained swelling symptoms (USS) are common in women and many patients give a strong personal and family history of depression. Co-morbid depression and swelling symptoms define a useful sub-phenotype for investigating genetic factors in depression. We have completed a genome-wide linkage analysis using 371 microsatellite markers in four families where MDD is co-morbid with USS. Of 47 affected individuals, 28 had both MDD and unexplained swelling, 11 had symptoms of swelling alone, and 8 had MDD alone. Parametric marker-specific analysis identified one suggestive locus, D8S260 (LOD = 2.02) and non-parametric multipoint variance component analysis identified a region on 7p (LOD = 2.10). A 47 cM suggestive linkage region on chromosome 14q (identified by both parametric and non-parametric methods) was identified and investigated further with fine-mapping markers but the evidence for linkage to this region decreased with increased marker information content.
Photodynamic Therapy with Fullerenes In Vivo : Reality or a Dream? (2011)

Photodynamic therapy (PDT) employs the combination of nontoxic photosensitizers and visible light that is absorbed by the chromophore to produce long-lived triplet states that can carry out photochemistry in the presence of oxygen to kill cells. The closed carbon-cage structure found in fullerenes can act as a photosensitizer, especially when functionalized to impart water solubility. Although there are reports of the use of fullerenes to carry out light-mediated destruction of viruses, microorganisms and cancer cells in vitro, the use of fullerenes to mediate PDT of diseases such as cancer and infections in animal models is less well developed. It has recently been shown that fullerene PDT can be used to save the life of mice with wounds infected with pathogenic Gram-negative bacteria. Fullerene PDT has also been used to treat mouse models of various cancers including disseminated metastatic cancer in the peritoneal cavity. In vivo PDT with fullerenes represents a new application in nanomedicine.
Efficacy of D‐RaCe and ProTaper Universal Retreatment NiTi instruments and hand files in removing gutta‐percha from curved root canals – a micro‐computed tomography study (2012)

D-RaCe instruments were associated with significantly less residual filling material than ProTaper Universal Retreatment instruments and hand files. Hedström files removed significantly less dentine than both rotary NiTi systems. Retreatment with rotary NiTi systems resulted in a high incidence of procedural errors.
Correction to A Selection for Assembly Reveals That a Single Amino Acid Mutant of the Bacteriophage MS2 Coat Protein Forms a Smaller Virus-like Particle (2016)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to A Selection for Assembly Reveals That a Single Amino Acid Mutant of the Bacteriophage MS2 Coat Protein Forms a Smaller Virus-like ParticleMichael A. Asensio, Norma M. Morella, Christopher M. Jakobson, Emily C. Hartman, Jeff E. Glasgow, Banumathi Sankaran, Peter H. Zwart, and Danielle Tullman-Ercek*Cite this: Nano Lett. 2016, 16, 12, 8034Publication Date (Web):November 10, 2016Publication History Published online10 November 2016Published inissue 14 December 2016https://pubs.acs.org/doi/10.1021/acs.nanolett.6b04653https://doi.org/10.1021/acs.nanolett.6b04653correctionACS PublicationsCopyright © 2016 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views683Altmetric-Citations3LEARN 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 PDF (112 KB) Get e-Alertsclose Get e-Alerts
Compact Dual-Polarization Silicon Integrated Couplers for Multicore Fibers (2021)

Compact fiber-to-chip couplers play an important role in optical interconnections, especially in data centers. However, the development of couplers has been mostly limited to standard single-mode fibers, with few devices compatible with multicore and multimode fibers. Through the use of state-of-the-art optimization algorithms, we designed a compact dual-polarization coupler to interface chips and dense multicore fibers, demonstrating, for the first time, coupling to both polarizations of all the cores, with measured coupling efficiency of -4.3 dB and with a 3 dB bandwidth of 48 nm. The dual-polarization coupler has a footprint of 200 mu m(2) per core, which makes it the smallest fiber-to-chip coupler experimentally demonstrated on a standard silicon-on-insulator platform. (C) 2021 Optical Society of America
Adaptive Radiation of the Flukes of the Family Fasciolidae Inferred from Genome-Wide Comparisons of Key Species (2019)

Liver and intestinal flukes of the family Fasciolidae cause zoonotic food-borne infections that impact both agriculture and human health throughout the world. Their evolutionary history and the genetic basis underlying their phenotypic and ecological diversity are not well understood. To close that knowledge gap, we compared the whole genomes of Fasciola hepatica, Fasciola gigantica, and Fasciolopsis buski and determined that the split between Fasciolopsis and Fasciola took place ∼90 Ma in the late Cretaceous period, and that between 65 and 50 Ma an intermediate host switch and a shift from intestinal to hepatic habitats occurred in the Fasciola lineage. The rapid climatic and ecological changes occurring during this period may have contributed to the adaptive radiation of these flukes. Expansion of cathepsins, fatty-acid-binding proteins, protein disulfide-isomerases, and molecular chaperones in the genus Fasciola highlights the significance of excretory-secretory proteins in these liver-dwelling flukes. Fasciola hepatica and Fasciola gigantica diverged ∼5 Ma near the Miocene-Pliocene boundary that coincides with reduced faunal exchange between Africa and Eurasia. Severe decrease in the effective population size ∼10 ka in Fasciola is consistent with a founder effect associated with its recent global spread through ruminant domestication. G-protein-coupled receptors may have key roles in adaptation of physiology and behavior to new ecological niches. This study has provided novel insights about the genome evolution of these important pathogens, has generated genomic resources to enable development of improved interventions and diagnosis, and has laid a solid foundation for genomic epidemiology to trace drug resistance and to aid surveillance.
Working Fluid Analysis for Supercritical Organic Rankine Cycles for Medium Geothermal Reservoir Temperatures (2017)

A steady state model of a supercritical organic Rankine cycle (SORC) was created in MATLAB and validated. Fluid properties were obtained using NIST REFPROP. Various working fluids were tested, including pentane (R601), isopentane (R601a), butane (R600), isobutane (R600a), butene, and cis-butene. Pentane and isopentane have not been of focus for SORCS at these temperatures. Varying turbine inlet temperatures ranging from 170 to 240°C were tested with the heat source provided by a medium temperature geothermal reservoir. A parametric analysis was performed on varying inlet pressure and turbine inlet temperature in comparison to first law efficiency, second law efficiency, effectiveness, and net work produced to analyze the overall and exergetic performance of each fluid. Optimum first law efficiency ranged from 17 to 22%. Cis-butene and pentane performed the best in all performance factors analyzed. Pentane and isopentane performed the best at pressures near or below their critical point. It was also found that near the critical temperature, a subcritical ORC has better performance than an SORC. This study is beneficial for not only geothermal energy but for applications that can provide operating temperatures between 170 to 240°C.
Sponsorit ja yhteistyökumppanit festivaalitapahtumassa (2012)

Tämä opinnäytetyö on tehty kuvaamaan sponsoreiden ja yhteistyökumppaneiden\nhankintaprosessia festivaalitapahtumaan ja ennen kaikkea sitä kuinka sponsorien ja\nyhteistyökumppaneiden hankinta oli toteutettu The Winterfest musiikkifestivaalissa.\n\nTyön tavoitteena on antaa kattava kuva sponsorien ja yhteistyökumppanien hankinnasta\nja tähän prosessiin kuuluvista eri vaiheista. Työn esimerkkinä toimii The Winterfest\nmusiikkifestivaali ja sen toteutukseen liittynyt esivalmistelu. Lisäksi työssä kerrotaan\nmitä on sponsorointi, kuinka se on kehittynyt ja siitä kuinka sponsorointi eroaa\nmuista varainhankintakeinoista.\n\nOpinnäytetyö aloitettiin helmikuussa 2009 järjestetyn The Winterfest musiikkifestivaalin\njälkeen. Työ on toteutettu produktina ja siihen sisältyy tämän raportti osuuden\nlisäksi myös Internetissä julkaistu Non-profit – Kulttuuritapahtuman tuottamisen\nkäsikirja.\n\nOpinnäytetyön ja produktin tavoitteena oli tuottaa tietoa sponsoreiden ja yhteistyökumppaneiden hankinnasta uusille tapahtumanjärjestäjille. Työn avulla yhä useammat\ntapahtuma-alalla työskentelevät tai alalle pyrkivät saavat tietoa tapahtumanjärjestämisestä\nja sen eri osa-alueista sekä osaavat varautua paremmin erilaisiin heitä odottaviin\ntilanteisiin.
Time-Resolved Spectroscopic Studies of B12 Coenzymes:  The Photolysis of Methylcobalamin Is Wavelength Dependent (1999)

Femtosecond to nanosecond transient absorption spectroscopy has been used to investigate the primary photochemistry of the B12 coenzymes, methylcobalamin and 5‘-deoxyadenosylcobalamin. Photolysis at excitation wavelengths in the near UV (400 nm) and visible (520−530 nm) are compared. Measurements were performed with femtosecond time resolution covering time delays of up to 9 ns. The photochemistry of methylcobalamin is found to depend strongly on excitation wavelength, while the photochemistry of adenosylcobalamin is essentially wavelength independent over the range studied. Excitation of methylcobalamin at 400 nm results in a partitioning between prompt bond homolysis and formation of a metastable cob(III)alamin photoproduct as reported earlier [Walker, L. A., II; Jarrett, J. T.; Anderson, N. A.; Pullen, S. H.; Matthews, R. G.; Sension, R. J. J. Am. Chem. Soc. 1998, 120, 3597−3603]. Excitation of methylcobalamin at 520 nm in the visible αβ-band results only in formation of the metastable cob(III)alamin photoproduct. No prompt bond homolysis is observed. The metastable photoproduct partitions between formation of cob(II)alamin (14 ± 5%) and recovery of the methylcobalamin starting material (86 ± 5%) on a 1.0 ± 0.1 ns time scale. The quantum yield for bond homolysis in methylcobalamin is determined by the wavelength-dependent partitioning between prompt homolysis and formation of the metastable photoproduct and by the partitioning of the metastable photoproduct between bond homolysis and ground-state recovery. In contrast, excitation of adenosylcobalamin at both 400 and 520 nm results in the development of a difference spectrum characteristic of the formation of cob(II)alamin on a picosecond time scale. The quantum yield for bond homolysis in this case is determined primarily by the competition between geminate recombination and diffusion to form solvent-separated radical pairs. The caging fraction for adenosylcobalamin in aqueous solution at room temperature is 0.71 ± 0.05.
Effect of Aberrations in Femtosecond Laser Writing Using the Phase Mask Technique (2019)

The combined effect of chromatic dispersion and conical diffraction in femtosecond laser writing using the phase mask technique is characterized by measuring the axial intensity distribution. Optimum writing distance from the phase mask is experimentally determined.
Segmentation of breast masses on dedicated breast computed tomography and three-dimensional breast ultrasound images (2014)

We present and evaluate a method for the three-dimensional (3-D) segmentation of breast masses on dedicated breast computed tomography (bCT) and automated 3-D breast ultrasound images. The segmentation method, refined from our previous segmentation method for masses on contrast-enhanced bCT, includes two steps: (1) initial contour estimation and (2) active contour-based segmentation to further evolve and refine the initial contour by adding a local energy term to the level-set equation. Segmentation performance was assessed in terms of Dice coefficients (DICE) for 129 lesions on noncontrast bCT, 38 lesions on contrast-enhanced bCT, and 98 lesions on 3-D breast ultrasound (US) images. For bCT, DICE values of 0.82 and 0.80 were obtained on contrast-enhanced and noncontrast images, respectively. The improvement in segmentation performance with respect to that of our previous method was statistically significant ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>p</mml:mi> <mml:mo>=</mml:mo> <mml:mn>0.002</mml:mn></mml:mrow> </mml:math> ). Moreover, segmentation appeared robust with respect to the presence of glandular tissue. For 3-D breast US, the DICE value was 0.71. Hence, our method obtained promising results for both 3-D imaging modalities, laying a solid foundation for further quantitative image analysis and potential future expansion to other 3-D imaging modalities.
Model-based ethanol blend estimation in flexible-fuel vehicles (2011)

This paper presents a model-based strategy estimating the ethanol content of an ethanol–gasoline blended fuel in flexible fuel vehicles. A steady-state parametric model relating engine speed, throttle angle, and air–fuel ratio to the fuel injector pulse-width is developed from physics. The parameters of this model are adapted and linked to percentage of ethanol content via a suitably defined metric. The proposed steady-state model structure is experimentally validated on a 2005 5.4L V8 Ford engine. The developed ethanol content estimation methodology is justified based on the combustion chemistry and physics involved. The methodology developed has a distinct advantage over previously proposed methods as it uses only the existing sensor set on a production vehicle.
Chirurgische behandlung von intertrochant??ren h??ftfrakturen mit einhergehenden oberschenkelhalsfrakturen mittels einer h??ftgleitschraube (2005)

* Department of Orthopaedic Surgery, Hennepin County Medical Center, Minneapolis, MN; and †Department of Orthopaedics and Rehabilitation, Oregon Health & Sciences University, Portland, OR
Dispersion of Nanocrystalline Fe3O4 within Composite Electrodes: Insights on Battery-Related Electrochemistry (2016)

Aggregation of nanosized materials in composite lithium-ion-battery electrodes can be a significant factor influencing electrochemical behavior. In this study, aggregation was controlled in magnetite, Fe3O4, composite electrodes via oleic acid capping and subsequent dispersion in a carbon black matrix. A heat treatment process was effective in the removal of the oleic acid capping agent while preserving a high degree of Fe3O4 dispersion. Electrochemical testing showed that Fe3O4 dispersion is initially beneficial in delivering a higher functional capacity, in agreement with continuum model simulations. However, increased capacity fade upon extended cycling was observed for the dispersed Fe3O4 composites relative to the aggregated Fe3O4 composites. X-ray absorption spectroscopy measurements of electrodes post cycling indicated that the dispersed Fe3O4 electrodes are more oxidized in the discharged state, consistent with reduced reversibility compared with the aggregated sample. Higher charge-transfer resistance for the dispersed sample after cycling suggests increased surface-film formation on the dispersed, high-surface-area nanocrystalline Fe3O4 compared to the aggregated materials. This study provides insight into the specific effects of aggregation on electrochemistry through a multiscale view of mechanisms for magnetite composite electrodes.
Order-Optimal Consensus through Randomized Path Averaging (2008)

Gossip algorithms have recently received significant attention, mainly because they constitute simple and robust message-passing schemes for distributed information processing over networks. However for many topologies that are realistic for wireless ad-hoc and sensor networks (like grids and random geometric graphs), the standard nearest-neighbor gossip converges as slowly as flooding ($O(n^2)$ messages). A recently proposed algorithm called geographic gossip improves gossip efficiency by a $\sqrt{n}$ factor, by exploiting geographic information to enable multi-hop long distance communications. In this paper we prove that a variation of geographic gossip that averages along routed paths, improves efficiency by an additional $\sqrt{n}$ factor and is order optimal ($O(n)$ messages) for grids and random geometric graphs. We develop a general technique (travel agency method) based on Markov chain mixing time inequalities, which can give bounds on the performance of randomized message-passing algorithms operating over various graph topologies.