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  1. Book ; Online: Three-dimensional receptivity of hypersonic sharp and blunt cones to free-stream planar waves using hierarchical input-output analysis

    Cook, David A. / Nichols, Joseph W.

    2023  

    Abstract: Understanding the receptivity of hypersonic flows to free-stream disturbances is crucial for predicting laminar to turbulent boundary layer transition. Input-output analysis as a receptivity tool considers which free-stream disturbances lead to the ... ...

    Abstract Understanding the receptivity of hypersonic flows to free-stream disturbances is crucial for predicting laminar to turbulent boundary layer transition. Input-output analysis as a receptivity tool considers which free-stream disturbances lead to the largest response from the boundary layer using the global linear dynamics. Two technical challenges are addressed. First, we extend recent work by Kamal et al. (Kamal, 2023) and restrict the allowable forcing to physically realizable inputs via a free-stream boundary modification to the classic input-output formulation. Second, we develop a hierarchical input-output (H-IO) analysis which allows us to solve the three-dimensional problem at a fraction of the computational cost otherwise associated with directly inverting the fully three-dimensional resolvent operator. Next, we consider Mach 5.8 flows over a sharp cone and two blunt cones with 3.6 mm and 7.2 mm spherically blunt tips. H-IO correctly predicts that the sharp cone boundary layer is most receptive to slow acoustic waves at an optimal incidence angle of 10 degrees, validating the method. We then investigate the effect of free-stream disturbances on the blunt cone boundary layer, and identify two distinct vorticity-dominated receptivity mechanisms for the oblique first mode instability at 10 kHz and an entropy layer instability at 40 and 70 kHz. Our results reveal these receptivity processes to be highly three-dimensional in nature, involving both the nose-tip and excitation along narrow bands at certain azimuthal angles along the oblique shock downstream. We interpret these processes in terms of critical angles from linear shock/perturbation interaction theory. Finally, we show how these novel receptivity processes vary with frequency and nose tip bluntness, and demonstrate how this methodology might be applied to transition prediction from first principles.

    Comment: Submitted to Physical Review Fluids
    Keywords Physics - Fluid Dynamics
    Subject code 551
    Publishing date 2023-06-05
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: CRISPR-based engineering of RNA viruses.

    Nemudryi, Artem / Nemudraia, Anna / Nichols, Joseph E / Scherffius, Andrew M / Zahl, Trevor / Wiedenheft, Blake

    Science advances

    2023  Volume 9, Issue 37, Page(s) eadj8277

    Abstract: CRISPR RNA-guided endonucleases have enabled precise editing of DNA. However, options for editing RNA remain limited. Here, we combine sequence-specific RNA cleavage by CRISPR ribonucleases with programmable RNA repair to make precise deletions and ... ...

    Abstract CRISPR RNA-guided endonucleases have enabled precise editing of DNA. However, options for editing RNA remain limited. Here, we combine sequence-specific RNA cleavage by CRISPR ribonucleases with programmable RNA repair to make precise deletions and insertions in RNA. This work establishes a recombinant RNA technology with immediate applications for the facile engineering of RNA viruses.
    MeSH term(s) Engineering ; RNA Viruses/genetics ; Technology ; Endonucleases/genetics ; RNA
    Chemical Substances Endonucleases (EC 3.1.-) ; RNA (63231-63-0)
    Language English
    Publishing date 2023-09-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.adj8277
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: CRISPR-based engineering of RNA viruses.

    Nemudryi, Artem / Nemudraia, Anna / Nichols, Joseph E / Scherffius, Andrew M / Zahl, Trevor / Wiedenheft, Blake

    bioRxiv : the preprint server for biology

    2023  

    Abstract: CRISPR RNA-guided endonucleases have enabled precise editing of DNA. However, options for editing RNA remain limited. Here, we combine sequence-specific RNA cleavage by CRISPR ribonucleases with programmable RNA repair to make precise deletions and ... ...

    Abstract CRISPR RNA-guided endonucleases have enabled precise editing of DNA. However, options for editing RNA remain limited. Here, we combine sequence-specific RNA cleavage by CRISPR ribonucleases with programmable RNA repair to make precise deletions and insertions in RNA. This work establishes a new recombinant RNA technology with immediate applications for the facile engineering of RNA viruses.
    One-sentence summary: Programmable CRISPR RNA-guided ribonucleases enable recombinant RNA technology.
    Language English
    Publishing date 2023-05-20
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.19.541219
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The hard x-ray nanotomography microscope at the advanced light source.

    Nichols, Joseph B / Voltolini, Marco / Gilbert, Benjamin / MacDowell, Alastair A / Czabaj, Michael W

    The Review of scientific instruments

    2022  Volume 93, Issue 2, Page(s) 23704

    Abstract: Beamline 11.3.1 at the Advanced Light Source is a tender/hard (6-17 keV) x-ray bend magnet beamline recently re-purposed with a new full-field, nanoscale transmission x-ray microscope. The microscope is designed to image composite and porous materials ... ...

    Abstract Beamline 11.3.1 at the Advanced Light Source is a tender/hard (6-17 keV) x-ray bend magnet beamline recently re-purposed with a new full-field, nanoscale transmission x-ray microscope. The microscope is designed to image composite and porous materials possessing a submicrometer structure and compositional heterogeneity that determine materials' performance and geologic behavior. The theoretical and achieved resolutions are 55 and <100 nm, respectively. The microscope is used in tandem with a <25 nm eccentricity rotation stage for high-resolution volume imaging using nanoscale computed tomography. The system also features a novel bipolar illumination condenser for the illumination of an ∼100 μm spot of interest on the sample, followed by a phase-type zone plate magnifying objective of ∼52 µm field of view and a phase detection ring. The zone plate serves as the system objective and magnifies the sample with projection onto an indirect x-ray detection system, consisting of a polished single crystal CsI(Tl) scintillator and a range of high-quality Plan Fluorite visible light objectives. The objectives project the final visible light image onto a water-cooled CMOS 2048 × 2048-pixel
    Language English
    Publishing date 2022-03-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209865-9
    ISSN 1089-7623 ; 0034-6748
    ISSN (online) 1089-7623
    ISSN 0034-6748
    DOI 10.1063/5.0076322
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: A second golden age of aeroacoustics?

    Lele, Sanjiva K / Nichols, Joseph W

    Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

    2014  Volume 372, Issue 2022, Page(s) 20130321

    Abstract: In 1992, Sir James Lighthill foresaw the dawn of a second golden age in aeroacoustics enabled by computer simulations (Hardin JC, Hussaini MY (eds) 1993 Computational aeroacoustics, New York, NY: Springer (doi:10.1007/978-1-4613-8342-0)). This review ... ...

    Abstract In 1992, Sir James Lighthill foresaw the dawn of a second golden age in aeroacoustics enabled by computer simulations (Hardin JC, Hussaini MY (eds) 1993 Computational aeroacoustics, New York, NY: Springer (doi:10.1007/978-1-4613-8342-0)). This review traces the progress in large-scale computations to resolve the noise-source processes and the methods devised to predict the far-field radiated sound using this information. Keeping focus on aviation-related noise sources a brief account of the progress in simulations of jet noise, fan noise and airframe noise is given highlighting the key technical issues and challenges. The complex geometry of nozzle elements and airframe components as well as the high Reynolds number of target applications require careful assessment of the discretization algorithms on unstructured grids and modelling compromises. High-fidelity simulations with 200-500 million points are not uncommon today and are used to improve scientific understanding of the noise generation process in specific situations. We attempt to discern where the future might take us, especially if exascale computing becomes a reality in 10 years. A pressing question in this context concerns the role of modelling in the coming era. While the sheer scale of the data generated by large-scale simulations will require new methods for data analysis and data visualization, it is our view that suitable theoretical formulations and reduced models will be even more important in future.
    Language English
    Publishing date 2014-08-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 208381-4
    ISSN 1471-2962 ; 1364-503X ; 0080-4614 ; 0264-3820 ; 0264-3952
    ISSN (online) 1471-2962
    ISSN 1364-503X ; 0080-4614 ; 0264-3820 ; 0264-3952
    DOI 10.1098/rsta.2013.0321
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Winnable battles: family physicians play an essential role in addressing tobacco use and obesity.

    Nichols, Joseph / Bazemore, Andrew

    American family physician

    2014  Volume 89, Issue 11, Page(s) 872

    MeSH term(s) Family Practice ; Humans ; Mass Screening ; Obesity/prevention & control ; Physician's Role ; Tobacco Use/prevention & control
    Language English
    Publishing date 2014-06-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 412694-4
    ISSN 1532-0650 ; 0002-838X ; 0572-3612
    ISSN (online) 1532-0650
    ISSN 0002-838X ; 0572-3612
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: EPR: Evidence and fallacy.

    Nichols, Joseph W / Bae, You Han

    Journal of controlled release : official journal of the Controlled Release Society

    2014  Volume 190, Page(s) 451–464

    Abstract: The enhanced permeability and retention (EPR) of nanoparticles in tumors has long stood as one of the fundamental principles of cancer drug delivery, holding the promise of safe, simple and effective therapy. By allowing particles preferential access to ... ...

    Abstract The enhanced permeability and retention (EPR) of nanoparticles in tumors has long stood as one of the fundamental principles of cancer drug delivery, holding the promise of safe, simple and effective therapy. By allowing particles preferential access to tumors by virtue of size and longevity in circulation, EPR provided a neat rationale for the trend toward nano-sized drug carriers. Following the discovery of the phenomenon by Maeda in the mid-1980s, this rationale appeared to be well justified by the flood of evidence from preclinical studies and by the clinical success of Doxil. Clinical outcomes from nano-sized drug delivery systems, however, have indicated that EPR is not as reliable as previously thought. Drug carriers generally fail to provide superior efficacy to free drug systems when tested in clinical trials. A closer look reveals that EPR-dependent drug delivery is complicated by high tumor interstitial fluid pressure (IFP), irregular vascular distribution, and poor blood flow inside tumors. Furthermore, the animal tumor models used to study EPR differ from clinical tumors in several key aspects that seem to make EPR more pronounced than in human patients. On the basis of this evidence, we believe that EPR should only be invoked on a case-by-case basis, when clinical evidence suggests the tumor type is susceptible.
    MeSH term(s) Animals ; Antineoplastic Agents/administration & dosage ; Antineoplastic Agents/history ; Drug Carriers/chemistry ; Drug Carriers/history ; History, 20th Century ; Humans ; Maleic Anhydrides/administration & dosage ; Maleic Anhydrides/chemistry ; Maleic Anhydrides/history ; Nanoparticles/chemistry ; Neoplasms/drug therapy ; Neoplasms/pathology ; Permeability ; Polystyrenes/administration & dosage ; Polystyrenes/chemistry ; Polystyrenes/history ; Zinostatin/administration & dosage ; Zinostatin/analogs & derivatives ; Zinostatin/chemistry ; Zinostatin/history
    Chemical Substances Antineoplastic Agents ; Drug Carriers ; Maleic Anhydrides ; Polystyrenes ; poly(maleic acid-styrene)neocarzinostatin ; Zinostatin (9014-02-2)
    Language English
    Publishing date 2014-09-28
    Publishing country Netherlands
    Document type Historical Article ; Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 632533-6
    ISSN 1873-4995 ; 0168-3659
    ISSN (online) 1873-4995
    ISSN 0168-3659
    DOI 10.1016/j.jconrel.2014.03.057
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: CRISPR-Cas, Argonaute proteins and the emerging landscape of amplification-free diagnostics

    Santiago-Frangos, Andrew / Nemudryi, Artem / Nemudraia, Anna / Wiegand, Tanner / Nichols, Joseph E. / Krishna, Pushya / Scherffius, Andrew M. / Zahl, Trevor R. / Wilkinson, Royce A. / Wiedenheft, Blake

    Methods. 2022 Sept., v. 205

    2022  

    Abstract: Polymerase Chain Reaction (PCR) is the reigning gold standard for molecular diagnostics. However, the SARS-CoV-2 pandemic reveals an urgent need for new diagnostics that provide users with immediate results without complex procedures or sophisticated ... ...

    Abstract Polymerase Chain Reaction (PCR) is the reigning gold standard for molecular diagnostics. However, the SARS-CoV-2 pandemic reveals an urgent need for new diagnostics that provide users with immediate results without complex procedures or sophisticated equipment. These new demands have stimulated a tsunami of innovations that improve turnaround times without compromising the specificity and sensitivity that has established PCR as the paragon of diagnostics. Here we briefly introduce the origins of PCR and isothermal amplification, before turning to the emergence of CRISPR-Cas and Argonaute proteins, which are being coupled to fluorimeters, spectrometers, microfluidic devices, field-effect transistors, and amperometric biosensors, for a new generation of nucleic acid-based diagnostics.
    Keywords CRISPR-Cas systems ; Severe acute respiratory syndrome coronavirus 2 ; biosensors ; diagnostic techniques ; landscapes ; pandemic ; polymerase chain reaction ; tsunamis
    Language English
    Dates of publication 2022-09
    Size p. 1-10.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2022.06.002
    Database NAL-Catalogue (AGRICOLA)

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  9. Book ; Online: Safe collateral, arm's-length credit

    Black, Lamont / Krainer, John / Nichols, Joseph B

    evidence from the commercial real estate market

    (Working papers series / Federal Reserve Bank of San Francisco ; 2017, 19)

    2017  

    Author's details Lamont Black (DePaul University), John Krainer (Federal Reserve Bank of San Francisco), Joseph Nichols (Federal Reserve Board of Governors)
    Series title Working papers series / Federal Reserve Bank of San Francisco ; 2017, 19
    Keywords Kreditsicherung ; Asset-Backed Securities ; Gewerbeimmobilien ; Fremdkapital ; USA
    Language English
    Size 1 Online-Ressource (circa 43 Seiten), Illustrationen
    Document type Book ; Online
    Database ECONomics Information System

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  10. Book ; Online: Safe collateral, arm's-length credit

    Black, Lamont / Krainer, John / Nichols, Joseph B

    evidence from the commercial real estate mortgage market

    (Finance and economics discussion series ; 2017, 056)

    2017  

    Author's details Lamont Black, John Krainer, and Joseph Nichols
    Series title Finance and economics discussion series ; 2017, 056
    Keywords Kreditsicherung ; Asset-Backed Securities ; Gewerbeimmobilien ; Fremdkapital ; USA
    Language English
    Size 1 Online-Ressource (circa 42 Seiten), Illustrationen
    Document type Book ; Online
    Database ECONomics Information System

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