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  1. Book ; Online: A Proof of the Weak Simplex Conjecture

    Pastore, Adriano

    2023  

    Abstract: We solve a long-standing open problem about the optimal codebook structure of codes in $n$-dimensional Euclidean space that consist of $n+1$ codewords subject to a codeword energy constraint, in terms of minimizing the average decoding error probability. ...

    Abstract We solve a long-standing open problem about the optimal codebook structure of codes in $n$-dimensional Euclidean space that consist of $n+1$ codewords subject to a codeword energy constraint, in terms of minimizing the average decoding error probability. The conjecture states that optimal codebooks are formed by the $n+1$ vertices of a regular simplex (the $n$-dimensional generalization of a regular tetrahedron) inscribed in the unit sphere. A self-contained proof of this conjecture is provided that hinges on symmetry arguments and leverages a relaxation approach that consists in jointly optimizing the codebook and the decision regions, rather than the codeword locations alone.

    Comment: 7 pages, submitted for peer review
    Keywords Computer Science - Information Theory ; Mathematics - Metric Geometry
    Publishing date 2023-06-23
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article: The Complementarity of Nuclear Magnetic Resonance and Native Mass Spectrometry in Probing Protein-Protein Interactions.

    Erba, Elisabetta Boeri / Pastore, Annalisa

    Advances in experimental medicine and biology

    2024  Volume 3234, Page(s) 109–123

    Abstract: Nuclear magnetic resonance (NMR) and native mass spectrometry (MS) are mature physicochemical techniques with long histories and important applications. NMR spectroscopy provides detailed information about the structure, dynamics, interactions, and ... ...

    Abstract Nuclear magnetic resonance (NMR) and native mass spectrometry (MS) are mature physicochemical techniques with long histories and important applications. NMR spectroscopy provides detailed information about the structure, dynamics, interactions, and chemical environment of biomolecules. MS is an effective approach for determining the mass of biomolecules with high accuracy, sensitivity, and speed. The two techniques offer unique advantages and provide solid tools for structural biology. In the present review, we discuss their individual merits in the context of their applications to structural studies in biology with specific focus on protein interactions and evaluate their limitations. We provide specific examples in which these techniques can complement each other, providing new information on the same scientific case. We discuss how the field may develop and what challenges are expected in the future. Overall, the combination of NMR and MS plays an increasingly important role in integrative structural biology, assisting scientists in deciphering the three-dimensional structure of composite macromolecular assemblies.
    MeSH term(s) Mass Spectrometry/methods ; Magnetic Resonance Spectroscopy ; Magnetic Resonance Imaging ; Macromolecular Substances/chemistry ; Nuclear Magnetic Resonance, Biomolecular/methods
    Chemical Substances Macromolecular Substances
    Language English
    Publishing date 2024-03-20
    Publishing country United States
    Document type Review ; Journal Article
    ZDB-ID 410187-X
    ISSN 0065-2598
    ISSN 0065-2598
    DOI 10.1007/978-3-031-52193-5_8
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3192: Show issues Location:
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  3. Article ; Online: From sequence to structure to mechanism to phenotype: The new frontiers of structural biology.

    Pastore, Annalisa / Shakhnovitch, Eugene

    Current opinion in structural biology

    2023  Volume 82, Page(s) 102674

    MeSH term(s) Molecular Biology ; Phenotype ; Biology
    Language English
    Publishing date 2023-08-08
    Publishing country England
    Document type Editorial
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2023.102674
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3206: Show issues Location:
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  4. Article ; Online: Unfolding under Pressure: An NMR Perspective.

    Pastore, Annalisa / Temussi, Piero Andrea

    Chembiochem : a European journal of chemical biology

    2023  Volume 24, Issue 16, Page(s) e202300164

    Abstract: This review aims to analyse the role of solution nuclear magnetic resonance spectroscopy in pressure-induced in vitro studies of protein unfolding. Although this transition has been neglected for many years because of technical difficulties, it provides ... ...

    Abstract This review aims to analyse the role of solution nuclear magnetic resonance spectroscopy in pressure-induced in vitro studies of protein unfolding. Although this transition has been neglected for many years because of technical difficulties, it provides important information about the forces that keep protein structure together. We first analyse what pressure unfolding is, then provide a critical overview of how NMR spectroscopy has contributed to the field and evaluate the observables used in these studies. Finally, we discuss the commonalities and differences between pressure-, cold- and heat-induced unfolding. We conclude that, despite specific peculiarities, in both cold and pressure denaturation the important contribution of the state of hydration of nonpolar side chains is a major factor that determines the pressure dependence of the conformational stability of proteins.
    MeSH term(s) Protein Denaturation ; Proteins/chemistry ; Magnetic Resonance Spectroscopy/methods ; Protein Unfolding ; Protein Conformation ; Thermodynamics ; Protein Folding ; Cold Temperature
    Chemical Substances Proteins
    Language English
    Publishing date 2023-07-25
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 2020469-3
    ISSN 1439-7633 ; 1439-4227
    ISSN (online) 1439-7633
    ISSN 1439-4227
    DOI 10.1002/cbic.202300164
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  5. Article ; Online: Dimeric structures of DNA ATTTC repeats promoted by divalent cations.

    Trajkovski, Marko / Pastore, Annalisa / Plavec, Janez

    Nucleic acids research

    2024  Volume 52, Issue 4, Page(s) 1591–1601

    Abstract: Structural studies of repetitive DNA sequences may provide insights why and how certain repeat instabilities in their number and nucleotide sequence are managed or even required for normal cell physiology, while genomic variability associated with repeat ...

    Abstract Structural studies of repetitive DNA sequences may provide insights why and how certain repeat instabilities in their number and nucleotide sequence are managed or even required for normal cell physiology, while genomic variability associated with repeat expansions may also be disease-causing. The pentanucleotide ATTTC repeats occur in hundreds of genes important for various cellular processes, while their insertion and expansion in noncoding regions are associated with neurodegeneration, particularly with subtypes of spinocerebellar ataxia and familial adult myoclonic epilepsy. We describe a new striking domain-swapped DNA-DNA interaction triggered by the addition of divalent cations, including Mg2+ and Ca2+. The results of NMR characterization of d(ATTTC)3 in solution show that the oligonucleotide folds into a novel 3D architecture with two central C:C+ base pairs sandwiched between a couple of T:T base pairs. This structural element, referred to here as the TCCTzip, is characterized by intercalative hydrogen-bonding, while the nucleobase moieties are poorly stacked. The 5'- and 3'-ends of TCCTzip motif are connected by stem-loop segments characterized by A:T base pairs and stacking interactions. Insights embodied in the non-canonical DNA structure are expected to advance our understanding of why only certain pyrimidine-rich DNA repeats appear to be pathogenic, while others can occur in the human genome without any harmful consequences.
    MeSH term(s) Adult ; Humans ; Cations, Divalent ; DNA/genetics ; DNA/chemistry ; Repetitive Sequences, Nucleic Acid/genetics ; Spinocerebellar Ataxias/genetics ; Base Sequence ; Microsatellite Repeats
    Chemical Substances Cations, Divalent ; DNA (9007-49-2)
    Language English
    Publishing date 2024-01-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkae052
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
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  6. Article ; Online: A fluorescent probe with an ultra-rapid response to nitric oxide.

    Parisi, Cristina / Pastore, Arianna / Stornaiuolo, Mariano / Sortino, Salvatore

    Journal of materials chemistry. B

    2024  

    Abstract: Nitric oxide (NO) is a diatomic inorganic free radical ubiquitous in mammalian tissues and cells that plays a multifaceted role in a variety of physiological and pathophysiological processes. The strict dependence of the biological effects of NO on its ... ...

    Abstract Nitric oxide (NO) is a diatomic inorganic free radical ubiquitous in mammalian tissues and cells that plays a multifaceted role in a variety of physiological and pathophysiological processes. The strict dependence of the biological effects of NO on its concentration makes its real-time monitoring crucial. In view of the reactivity of NO with multiple bio-targets, the development of NO sensors that associate a fast response rate with selectivity and sensitivity is very challenging. Herein we report a fluorescent NO probe based on a BODIPY fluorogenic unit covalently linked to a trimethoxy aniline derivative through a flexible spacer. NO leads to effective nitrosation of the highly electron-rich amino active site of the probe through the secondary oxide N
    Language English
    Publishing date 2024-04-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2702241-9
    ISSN 2050-7518 ; 2050-750X
    ISSN (online) 2050-7518
    ISSN 2050-750X
    DOI 10.1039/d4tb00064a
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  7. Book: Patologia molecolare nei carcinomi delle VADS

    Pastore, A.

    stato dell'arte = Molecolar alterations in head and neck carcinoma

    (Acta otorhinolaryngologica Italica : Supplemento ; 54)

    1996  

    Title variant Molecolar alterations in head and neck carcinoma
    Author's details a cura di A. Pastore
    Series title Acta otorhinolaryngologica Italica : Supplemento ; 54
    Acta otorhinolaryngologica italica
    Acta otorhinolaryngologica Italica ; Supplemento
    Collection Acta otorhinolaryngologica italica
    Acta otorhinolaryngologica Italica ; Supplemento
    Keywords Head and Neck Neoplasms
    Language Italian
    Size 38 S. : graph. Darst.
    Publisher Pacini Med
    Publishing place Pisa
    Publishing country Italy
    Document type Book
    HBZ-ID HT007437558
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Zs B 2608 -Suppl.54- verfügbar in Königswinter Königswinter

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  8. Article ; Online: The Protein Unfolded State: One, No One and One Hundred Thousand.

    Pastore, Annalisa / Temussi, Piero Andrea

    Journal of the American Chemical Society

    2022  Volume 144, Issue 49, Page(s) 22352–22357

    Abstract: ... ...

    Abstract Many
    MeSH term(s) Protein Folding ; Proteins ; Protein Denaturation
    Chemical Substances Proteins
    Language English
    Publishing date 2022-11-30
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.2c07696
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    In stock of ZB MED Bonn / Germany

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  9. Article: Crowding revisited: Open questions and future perspectives.

    Pastore, Annalisa / Temussi, Piero Andrea

    Trends in biochemical sciences

    2022  Volume 47, Issue 12, Page(s) 1048–1058

    Abstract: Although biophysical studies have traditionally been performed in diluted solutions, it was pointed out in the late 1990s that the cellular milieu contains several other macromolecules, creating a condition of molecular crowding. How crowding affects ... ...

    Abstract Although biophysical studies have traditionally been performed in diluted solutions, it was pointed out in the late 1990s that the cellular milieu contains several other macromolecules, creating a condition of molecular crowding. How crowding affects protein stability is an important question heatedly discussed over the past 20 years. Theoretical estimations have suggested a 5-20°C effect of fold stabilisation. This estimate, however, is at variance with what has been verified experimentally that proposes only a limited increase of stability, opening the question whether some of the assumptions taken for granted should be reconsidered. The present review critically analyses the causes of this discrepancy and discusses the limitations and implications of the current concept of crowding.
    MeSH term(s) Protein Stability ; Macromolecular Substances ; Thermodynamics
    Chemical Substances Macromolecular Substances
    Language English
    Publishing date 2022-06-09
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 194216-5
    ISSN 1362-4326 ; 0968-0004 ; 0376-5067
    ISSN (online) 1362-4326
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2022.05.007
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    Zs.A 1207: Show issues Location:
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  10. Article ; Online: Positively Charged Organosilanes Covalently Linked to the Silica Network as Modulating Tools for the Salinity Correction of pH Values Obtained with Colorimetric Sensor Arrays (CSAs).

    Pastore, Andrea / Badocco, Denis / Cappellin, Luca / Tubiana, Mauro / Pastore, Paolo

    Sensors (Basel, Switzerland)

    2024  Volume 24, Issue 2

    Abstract: Seven increasing levels of water salinity from 0.029 to 0.600 M (as NaCl) were used to investigate the dependence of pH measurement, performed using colorimetric sensor arrays (CSAs), on ionic strength. The CSAs were arrays of sensing spots prepared in ... ...

    Abstract Seven increasing levels of water salinity from 0.029 to 0.600 M (as NaCl) were used to investigate the dependence of pH measurement, performed using colorimetric sensor arrays (CSAs), on ionic strength. The CSAs were arrays of sensing spots prepared in the form of sol-gel-embedding Bromothymol Blue (BB) and Bromocresol Green (BCG) in a porous nitrocellulose support. The support was impregnated over the entire thickness (≈100 µm), allowing for the signal (Hue) acquisition on the opposite side to the contact with the sample solution. Three CSAs were prepared, M1, M2, and M3. M1 contained a free cationic surfactant, hexadecyltrimethylammonium p-toluenesulfonate (CTApTs), for modulating the pKa of the indicators. In M2, the surfactant dimethyloctadecyl[3-(trimethoxysilyl)propyl]ammonium chloride (DTSACl) was covalently bonded to the sol-gel. M3 was prepared like M2 but using a larger amount of ethanol as the solvent for the synthesis. The modulation of the CTApTs or the DTSACl concentration enabled the tuning of the pKa. In general, the pKa modulation ability decreased with the increase in salinity. The presence of a surfactant covalently linked to the backbone partially reduced the competitiveness of the anionic species, improving the results. Nevertheless, the salt effect was still present, and a correction algorithm was required. Between pH 5.00 and 12.00, this correction could be made automatically by using spots taken as references to produce sensors independent of salinity. As the salt effect is virtually absent above 0.160 M, M2 and M3 can be used for future applications in seawater.
    Language English
    Publishing date 2024-01-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s24020417
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