985,668 research outputs found
Cubical Type Theory: A Constructive Interpretation of the Univalence Axiom
This paper presents a type theory in which it is possible to
directly manipulate -dimensional cubes (points, lines, squares,
cubes, etc.) based on an interpretation of dependent type theory in
a cubical set model. This enables new ways to reason about identity
types, for instance, function extensionality is directly provable in
the system. Further, Voevodsky\u27s univalence axiom is provable in
this system. We also explain an extension with some higher inductive
types like the circle and propositional truncation. Finally we
provide semantics for this cubical type theory in a constructive
meta-theory
Cubical Type Theory: a constructive interpretation of the univalence axiom
International audienceThis paper presents a type theory in which it is possible to directly manipulate n-dimensional cubes (points, lines, squares, cubes, etc.) based on an interpretation of dependent type theory in a cubical set model. This enables new ways to reason about identity types, for instance, function extensionality is directly provable in the system. Further, Voevodsky's univalence axiom is provable in this system. We also explain an extension with some higher inductive types like the circle and propositional truncation. Finally we provide semantics for this cubical type theory in a constructive meta-theory
Association of YY1 with maternal mRNAs in oocyte mRNPs
Early embryonic development in vertebrates is directed in part by maternal mRNAs
expressed in oocytes and stored in cytoplasmic messenger ribonucleoprotein particles (mRNPs).
Abundant evidence demonstrates the importance of mRNPs in embryonic development and in
post-embryonic cellular function; however their characterization has been hampered by lack of
suitable methodologies. The Xenopus oocyte has been the primary model system for studies of
mRNPs. YY1 is a well-studied transcriptional regulatory factor that is sequestered in the oocyte cytoplasm and present entirely in cytoplasmic oocyte mRNPs. The objective of this thesis was to examine the biochemistry of YY1 association with maternal mRNA molecules in order to shed light on the role of YY1 in development and the poorly understood biology of oocyte mRNPs.
The initial working hypotheses were that association of YY1 with mRNPs is dependent on
sequence-specific RNA-binding activity and, therefore, that YY1 associates with a definite
subset of maternal mRNA. A number of unique methods were developed in this study to address
these hypotheses. RNA immunoprecipitation-DNA microarray (RIP-CHIP) analysis establishes
that YY1 associates with a subset of mRNAs in the oocyte pool. A novel sequence-specific
RNA-binding activity of the YY1 protein is demonstrated, and the RNA-binding activity of YY1
is shown to be required for its association with oocyte mRNPs in vivo. The functional roles of
YY1 mRNA substrates are discussed in the context of embryological development and the
biological function of YY1 in oocyte mRNPs. Extension of the experimental approaches
developed in this thesis to the entire set of mRNP proteins would significantly advance our
understanding of mRNP composition and heterogeneity, as well as the biological function of maternal mRNAs and mRNPs in development
Sequence-dependent thermodynamics of a coarse-grained DNA model
We introduce a sequence-dependent parametrization for a coarse-grained DNA
model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134,
085101 (2011)] originally designed to reproduce the properties of DNA molecules
with average sequences. The new parametrization introduces sequence-dependent
stacking and base-pairing interaction strengths chosen to reproduce the melting
temperatures of short duplexes. By developing a histogram reweighting
technique, we are able to fit our parameters to the melting temperatures of
thousands of sequences. To demonstrate the flexibility of the model, we study
the effects of sequence on: (a) the heterogeneous stacking transition of single
strands, (b) the tendency of a duplex to fray at its melting point, (c) the
effects of stacking strength in the loop on the melting temperature of
hairpins, (d) the force-extension properties of single strands and (e) the
structure of a kissing-loop complex. Where possible we compare our results with
experimental data and find a good agreement. A simulation code called oxDNA,
implementing our model, is available as free software.Comment: 15 page
Pressure-dependent EPANET extension
In water distribution systems (WDSs), the available flow at a demand node is dependent on the pressure at that node. When a network is lacking in pressure, not all consumer demands will be met in full. In this context, the assumption that all demands are fully satisfied regardless of the pressure in the system becomes unreasonable and represents the main limitation of the conventional demand driven analysis (DDA) approach to WDS modelling. A realistic depiction of the network performance can only be attained by considering demands to be pressure dependent. This paper presents an extension of the renowned DDA based hydraulic simulator EPANET 2 to incorporate pressure-dependent demands. This extension is termed âEPANET-PDXâ (pressure-dependent extension) herein. The utilization of a continuous nodal pressure-flow function coupled with a line search and backtracking procedure greatly enhance the algorithmâs convergence rate and robustness. Simulations of real life networks consisting of multiple sources, pipes, valves and pumps were successfully executed and results are presented herein. Excellent modelling performance was achieved for analysing both normal and pressure deficient conditions of the WDSs. Detailed computational efficiency results of EPANET-PDX with reference to EPANET 2 are included as well
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