221 research outputs found
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Evi1 Counteracts Anti-Leukemic and Stem Cell Inhibitory Effects of All-Trans Retinoic Acid on Flt3-ITD/Npm1c-Driven Acute Myeloid Leukemia Cells.
All-trans retinoic acid (atRA) has a dramatic impact on the survival of patients with acute promyelocytic leukemia, but its therapeutic value in other types of acute myeloid leukemia (AML) has so far remained unclear. Given that AML is a stem cell-driven disease, recent studies have addressed the effects of atRA on leukemic stem cells (LSCs). atRA promoted stemness of MLL-AF9-driven AML in an Evi1-dependent manner but had the opposite effect in Flt3-ITD/Nup98-Hoxd13-driven AML. Overexpression of the stem cell-associated transcription factor EVI1 predicts a poor prognosis in AML, and is observed in different genetic subtypes, including cytogenetically normal AML. Here, we therefore investigated the effects of Evi1 in a mouse model for cytogenetically normal AML, which rests on the combined activity of Flt3-ITD and Npm1c mutations. Experimental expression of Evi1 on this background strongly promoted disease aggressiveness. atRA inhibited leukemia cell viability and stem cell-related properties, and these effects were counteracted by overexpression of Evi1. These data further underscore the complexity of the responsiveness of AML LSCs to atRA and point out the need for additional investigations which may lay a foundation for a precision medicine-based use of retinoids in AML
SAT-Based Synthesis Methods for Safety Specs
Automatic synthesis of hardware components from declarative specifications is
an ambitious endeavor in computer aided design. Existing synthesis algorithms
are often implemented with Binary Decision Diagrams (BDDs), inheriting their
scalability limitations. Instead of BDDs, we propose several new methods to
synthesize finite-state systems from safety specifications using decision
procedures for the satisfiability of quantified and unquantified Boolean
formulas (SAT-, QBF- and EPR-solvers). The presented approaches are based on
computational learning, templates, or reduction to first-order logic. We also
present an efficient parallelization, and optimizations to utilize reachability
information and incremental solving. Finally, we compare all methods in an
extensive case study. Our new methods outperform BDDs and other existing work
on some classes of benchmarks, and our parallelization achieves a super-linear
speedup. This is an extended version of [5], featuring an additional appendix.Comment: Extended version of a paper at VMCAI'1
On QBF Proofs and Preprocessing
QBFs (quantified boolean formulas), which are a superset of propositional
formulas, provide a canonical representation for PSPACE problems. To overcome
the inherent complexity of QBF, significant effort has been invested in
developing QBF solvers as well as the underlying proof systems. At the same
time, formula preprocessing is crucial for the application of QBF solvers. This
paper focuses on a missing link in currently-available technology: How to
obtain a certificate (e.g. proof) for a formula that had been preprocessed
before it was given to a solver? The paper targets a suite of commonly-used
preprocessing techniques and shows how to reconstruct certificates for them. On
the negative side, the paper discusses certain limitations of the
currently-used proof systems in the light of preprocessing. The presented
techniques were implemented and evaluated in the state-of-the-art QBF
preprocessor bloqqer.Comment: LPAR 201
Incremental QBF Solving
We consider the problem of incrementally solving a sequence of quantified
Boolean formulae (QBF). Incremental solving aims at using information learned
from one formula in the process of solving the next formulae in the sequence.
Based on a general overview of the problem and related challenges, we present
an approach to incremental QBF solving which is application-independent and
hence applicable to QBF encodings of arbitrary problems. We implemented this
approach in our incremental search-based QBF solver DepQBF and report on
implementation details. Experimental results illustrate the potential benefits
of incremental solving in QBF-based workflows.Comment: revision (camera-ready, to appear in the proceedings of CP 2014,
LNCS, Springer
CCancer: a birdās eye view on gene lists reported in cancer-related studies
CCancer is an automatically collected database of gene lists, which were reported mostly by experimental studies in various biological and clinical contexts. At the moment, the database covers 3369 gene lists extracted from 2644 papers published in ā¼80 peer-reviewed journals. As input, CCancer accepts a gene list. An enrichment analyses is implemented to generate, as output, a highly informative survey over recently published studies that report gene lists, which significantly intersect with the query gene list. A report on gene pairs from the input list which were frequently reported together by other biological studies is also provided. CCancer is freely available at http://mips.helmholtz-muenchen.de/proj/ccancer
Expressions 1986
https://openspace.dmacc.edu/expressions/1007/thumbnail.jp
Parameterized Synthesis with Safety Properties
Parameterized synthesis offers a solution to the problem of constructing
correct and verified controllers for parameterized systems. Such systems occur
naturally in practice (e.g., in the form of distributed protocols where the
amount of processes is often unknown at design time and the protocol must work
regardless of the number of processes). In this paper, we present a novel
learning based approach to the synthesis of reactive controllers for
parameterized systems from safety specifications. We use the framework of
regular model checking to model the synthesis problem as an infinite-duration
two-player game and show how one can utilize Angluin's well-known L* algorithm
to learn correct-by-design controllers. This approach results in a synthesis
procedure that is conceptually simpler than existing synthesis methods with a
completeness guarantee, whenever a winning strategy can be expressed by a
regular set. We have implemented our algorithm in a tool called L*-PSynth and
have demonstrated its performance on a range of benchmarks, including robotic
motion planning and distributed protocols. Despite the simplicity of L*-PSynth
it competes well against (and in many cases even outperforms) the
state-of-the-art tools for synthesizing parameterized systems.Comment: 18 page
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