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  1. Article: Copernico e la fondazione del cosmo eliocentrico.

    De Pace, Anna

    Isis; an international review devoted to the history of science and its cultural influences

    2013  Volume 103, Issue 3, Page(s) 564; author reply 564–5

    MeSH term(s) Astronomical Phenomena ; Astronomy/history ; History, 15th Century ; History, 16th Century ; Science/history
    Language English
    Publishing date 2013-01-02
    Publishing country United States
    Document type Historical Article ; Letter
    ZDB-ID 3190-2
    ISSN 1545-6994 ; 0021-1753
    ISSN (online) 1545-6994
    ISSN 0021-1753
    DOI 10.1086/667980
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4769: Show issues Location:
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  2. Article ; Online: Information Integration and Energy Expenditure in Gene Regulation.

    Estrada, Javier / Wong, Felix / DePace, Angela / Gunawardena, Jeremy

    Cell

    2016  Volume 166, Issue 1, Page(s) 234–244

    Abstract: The quantitative concepts used to reason about gene regulation largely derive from bacterial studies. We show that this bacterial paradigm cannot explain the sharp expression of a canonical developmental gene in response to a regulating transcription ... ...

    Abstract The quantitative concepts used to reason about gene regulation largely derive from bacterial studies. We show that this bacterial paradigm cannot explain the sharp expression of a canonical developmental gene in response to a regulating transcription factor (TF). In the absence of energy expenditure, with regulatory DNA at thermodynamic equilibrium, information integration across multiple TF binding sites can generate the required sharpness, but with strong constraints on the resultant "higher-order cooperativities." Even with such integration, there is a "Hopfield barrier" to sharpness; for n TF binding sites, this barrier is represented by the Hill function with the Hill coefficient n. If, however, energy is expended to maintain regulatory DNA away from thermodynamic equilibrium, as in kinetic proofreading, this barrier can be breached and greater sharpness achieved. Our approach is grounded in fundamental physics, leads to testable experimental predictions, and suggests how a quantitative paradigm for eukaryotic gene regulation can be formulated.
    MeSH term(s) DNA/metabolism ; Energy Metabolism ; Gene Expression Regulation ; Models, Genetic ; Transcription Factors/metabolism
    Chemical Substances Transcription Factors ; DNA (9007-49-2)
    Language English
    Publishing date 2016-07-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2016.06.012
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    Zs.A 1167: Show issues Location:
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    Zs.MG 58: Show issues

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  3. Article ; Online: Leadership.

    Bowdish, Dawn / Desai, Tejal A / DePace, Angela / Haswell, Elizabeth S / Baltrus, David / García, Andrés J / Deans, Tara / Lage, Kasper / Wittkopp, Patricia

    Cell systems

    2021  Volume 12, Issue 1, Page(s) 1–4

    Abstract: We asked group leaders how they foster mutually reinforcing research productivity and psychological safety in their teams. ...

    Abstract We asked group leaders how they foster mutually reinforcing research productivity and psychological safety in their teams.
    MeSH term(s) Biomedical Research ; Leadership ; Set, Psychology
    Language English
    Publishing date 2021-01-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2854138-8
    ISSN 2405-4720 ; 2405-4712
    ISSN (online) 2405-4720
    ISSN 2405-4712
    DOI 10.1016/j.cels.2020.12.004
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  4. Article ; Online: Glauber isovector spin responses for (p

    De Pace A

    Physical review letters

    1995  Volume 75, Issue 1, Page(s) 29–32

    Language English
    Publishing date 1995-07-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 208853-8
    ISSN 1079-7114 ; 0031-9007
    ISSN (online) 1079-7114
    ISSN 0031-9007
    DOI 10.1103/PhysRevLett.75.29
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  5. Article: Quasielastic nuclear response.

    De Pace A / Viviani

    Physical review. C, Nuclear physics

    1993  Volume 48, Issue 6, Page(s) 2931–2945

    Language English
    Publishing date 1993-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209771-0
    ISSN 1089-490X ; 0556-2813 ; 2469-9985
    ISSN (online) 1089-490X
    ISSN 0556-2813 ; 2469-9985
    DOI 10.1103/physrevc.48.2931
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    In stock of ZB MED Bonn / Germany

    Z 71/750: Show issues

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  6. Article ; Online: Heavy flavour in nucleus-nucleus collisions at RHIC and LHC

    Beraudo A. / De Pace A. / Monteno M. / Prino F. / Alberico W.M. / Molinari A. / Nardi M.

    EPJ Web of Conferences, Vol 66, p

    a Langevin approach

    2014  Volume 04004

    Abstract: A snapshot of the results for heavy-flavour observables in heavy-ion (AA) collisions at RHIC and LHC obtained with our transport calculations is displayed. The initial charm and beauty production is simulated through pQCD tools (POWHEG+PYTHIA) and is ... ...

    Abstract A snapshot of the results for heavy-flavour observables in heavy-ion (AA) collisions at RHIC and LHC obtained with our transport calculations is displayed. The initial charm and beauty production is simulated through pQCD tools (POWHEG+PYTHIA) and is validated through the comparison with data from pp collisions. The propagation of c and b quarks in the medium formed in heavy-ion collisions is studied through a transport setup based on the relativistic Langevin equation. With respect to past works we perform a more systematic study, providing results with different choices of transport coefficients, either from weak-coupling calculations or from lattice-QCD simulations. Our findings are compared to a rich set of experimental data (D-mesons, non-photonic electrons, non-prompt J/ψ’s) which have meanwhile become accessible.
    Keywords Physics ; QC1-999 ; Science ; Q
    Language English
    Publishing date 2014-03-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
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  7. Article ; Online: Heavy flavors in nucleus-nucleus collisions at RHIC and LHC

    Nardi Marzia / Alberico W.M. / Molinari A. / Beraudo A. / De Pace A. / Monteno M. / Prino F. / Sitta M.

    EPJ Web of Conferences, Vol 71, p

    2014  Volume 00098

    Abstract: A multi-step setup for heavy-flavor studies in high-energy nucleus-nucleus (AA) collisions — addressing within a comprehensive framework the initial QQ¯$Q\overline Q $ production, the propagation in the hot medium until decoupling and the final ... ...

    Abstract A multi-step setup for heavy-flavor studies in high-energy nucleus-nucleus (AA) collisions — addressing within a comprehensive framework the initial QQ¯$Q\overline Q $ production, the propagation in the hot medium until decoupling and the final hadronization and decays — is presented. The propagation of the heavy quarks in the medium is described in a framework provided by the relativistic Langevin equation and the corresponding numerical results are compared to experimental data from RHIC and the LHC. In particular, outcomes for the nuclear modification factor RAA and for the elliptic flow υ2 of D/B mesons, heavy-flavor electrons and non-prompt J/ψ’s are displayed.
    Keywords Physics ; QC1-999 ; Science ; Q
    Language English
    Publishing date 2014-04-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
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  8. Article: MulteeSum: a tool for comparative spatial and temporal gene expression data.

    Meyer, Miriah / Munzner, Tamara / DePace, Angela / Pfister, Hanspeter

    IEEE transactions on visualization and computer graphics

    2010  Volume 16, Issue 6, Page(s) 908–917

    Abstract: Cells in an organism share the same genetic information in their DNA, but have very different forms and behavior because of the selective expression of subsets of their genes. The widely used approach of measuring gene expression over time from a tissue ... ...

    Abstract Cells in an organism share the same genetic information in their DNA, but have very different forms and behavior because of the selective expression of subsets of their genes. The widely used approach of measuring gene expression over time from a tissue sample using techniques such as microarrays or sequencing do not provide information about the spatial position within the tissue where these genes are expressed. In contrast, we are working with biologists who use techniques that measure gene expression in every individual cell of entire fruitfly embryos over an hour of their development, and do so for multiple closely-related subspecies of Drosophila. These scientists are faced with the challenge of integrating temporal gene expression data with the spatial location of cells and, moreover, comparing this data across multiple related species. We have worked with these biologists over the past two years to develop MulteeSum, a visualization system that supports inspection and curation of data sets showing gene expression over time, in conjunction with the spatial location of the cells where the genes are expressed--it is the first tool to support comparisons across multiple such data sets. MulteeSum is part of a general and flexible framework we developed with our collaborators that is built around multiple summaries for each cell, allowing the biologists to explore the results of computations that mix spatial information, gene expression measurements over time, and data from multiple related species or organisms. We justify our design decisions based on specific descriptions of the analysis needs of our collaborators, and provide anecdotal evidence of the efficacy of MulteeSum through a series of case studies.
    MeSH term(s) Animals ; Computer Graphics ; Drosophila/embryology ; Drosophila/genetics ; Gene Expression Profiling/statistics & numerical data ; Gene Expression Regulation, Developmental ; Genes, Insect
    Language English
    Publishing date 2010-11
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1077-2626
    ISSN 1077-2626
    DOI 10.1109/TVCG.2010.137
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  9. Book ; Online: Relativistic viscous hydrodynamics for heavy-ion collisions with ECHO-QGP

    Del Zanna, L. / Chandra, V. / Inghirami, G. / Rolando, V. / Beraudo, A. / De Pace, A. / Pagliara, G. / Drago, A. / Becattini, F.

    2013  

    Abstract: We present ECHO-QGP, a numerical code for $(3+1)$-dimensional relativistic viscous hydrodynamics designed for the modeling of the space-time evolution of the matter created in high energy nuclear collisions. The code has been built on top of the \emph{ ... ...

    Abstract We present ECHO-QGP, a numerical code for $(3+1)$-dimensional relativistic viscous hydrodynamics designed for the modeling of the space-time evolution of the matter created in high energy nuclear collisions. The code has been built on top of the \emph{Eulerian Conservative High-Order} astrophysical code for general relativistic magneto-hydrodynamics [\emph{Del Zanna et al., Astron. Astrophys. 473, 11, 2007}] and here it has been upgraded to handle the physics of the Quark-Gluon Plasma. ECHO-QGP features second-order treatment of causal relativistic viscosity effects in both Minkowskian or Bjorken coordinates; partial or complete chemical equilibrium of hadronic species before kinetic freeze-out; initial conditions based on the optical Glauber model, including a Monte-Carlo routine for event-by-event fluctuating initial conditions; a freeze-out procedure based on the Cooper-Frye prescription. The code is extensively validated against several test problems and results always appear accurate, as guaranteed by the combination of the conservative (shock-capturing) approach and the high-order methods employed. ECHO-QGP can be extended to include evolution of the electromagnetic fields coupled to the plasma.

    Comment: 25 pages, two column, Final version: accepted for publication in European Physical Journal C
    Keywords Nuclear Theory ; Astrophysics - High Energy Astrophysical Phenomena ; High Energy Physics - Phenomenology
    Subject code 621
    Publishing date 2013-05-30
    Publishing country us
    Document type Book ; Online
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  10. Article: Rapid confirmation of enzyme multiplied immunoassay technique (EMIT) cocaine positive urine samples by capillary gas-liquid chromatography/nitrogen phosphorus detection (GLC/NPD).

    Verebey, K / DePace, A

    Journal of forensic sciences

    1989  Volume 34, Issue 1, Page(s) 46–52

    Abstract: A rapid gas-liquid chromatographic (GLC) method was developed for the confirmation of benzoylecgonine (BE) positive urine samples screened by the enzyme multiplied immunoassay technique (EMIT) assay. The procedure is performed by solvent extraction of BE ...

    Abstract A rapid gas-liquid chromatographic (GLC) method was developed for the confirmation of benzoylecgonine (BE) positive urine samples screened by the enzyme multiplied immunoassay technique (EMIT) assay. The procedure is performed by solvent extraction of BE from 0.1 or 0.2 mL of urine, followed by an aqueous wash of the solvent and evaporation. The dried residue was derivatized with 50 microL of pentafluoropropionic anhydride and 25 microL of pentafluoropropropanol at 90 degrees C for 15 min. The derivatizing reagents were evaporated to dryness, and the derivatized BE, and cocaine if present, were reconstituted and injected into the gas chromatograph. The column was a 15-m by 0.2-mm fused silica capillary column, coated with 0.25 micron of DB-1, terminating in a nitrogen phosphorus detector (NPD). Cocaine and the pentafluoro BE derivatives retention times were 3.2 and 2.6 min, respectively. Nalorphine was used as reference or internal standard with a retention time of 4.78 min. The complete procedure can be performed in approximately 1.5 h. The EMIT cutoff between positive and negative urine samples is 300 ng/mL of BE. The lower limit of sensitivity of this method is 25 ng of BE extracted from urine. Validation studies resulted in confirmation of 101 out of 121 EMIT cocaine positive urine samples that could not be confirmed by thin-layer chromatography (TLC). This represents 84% confirmation efficiency.
    MeSH term(s) Chromatography, Gas ; Cocaine/analogs & derivatives ; Cocaine/pharmacokinetics ; Cocaine/urine ; Humans ; Immunoenzyme Techniques ; Substance-Related Disorders/urine
    Chemical Substances benzoylecgonine (5353I8I6YS) ; Cocaine (I5Y540LHVR)
    Language English
    Publishing date 1989-01
    Publishing country United States
    Document type Comparative Study ; Journal Article
    ZDB-ID 219216-0
    ISSN 1556-4029 ; 0022-1198
    ISSN (online) 1556-4029
    ISSN 0022-1198
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