3,281 research outputs found
Decidability of the Monadic Shallow Linear First-Order Fragment with Straight Dismatching Constraints
The monadic shallow linear Horn fragment is well-known to be decidable and
has many application, e.g., in security protocol analysis, tree automata, or
abstraction refinement. It was a long standing open problem how to extend the
fragment to the non-Horn case, preserving decidability, that would, e.g.,
enable to express non-determinism in protocols. We prove decidability of the
non-Horn monadic shallow linear fragment via ordered resolution further
extended with dismatching constraints and discuss some applications of the new
decidable fragment.Comment: 29 pages, long version of CADE-26 pape
Functional Derivative of the Zero Point Energy Functional from the Strong Interaction Limit of Density Functional Theory
We derive an explicit expression for the functional derivative of the
subleading term in the strong interaction limit expansion of the generalized
Levy--Lieb functional for the special case of two electrons in one dimension.
The expression is derived from the zero point energy (ZPE) functional, which is
valid if the quantum state reduces to strongly correlated electrons in the
strong coupling limit. The explicit expression is confirmed numerically and
respects the relevant sum-rule. We also show that the ZPE potential is able to
generate a bond mid-point peak for homo-nuclear dissociation and is properly of
purely kinetic origin. Unfortunately, the ZPE diverges for Coulomb systems,
whereas the exact peaks should be finite.Comment: 12 pages, 7 figure
Rat Monoclonal Antibodies Specific for LST1 Proteins
The LST1 gene is located in the human MHC class III region and encodes transmembrane and soluble isoforms that have been suggested to play a role in the regulation of the immune response and are associated with inflammatory diseases such as rheumatoid arthritis. Here we describe the generation and characterization of the first monoclonal antibodies against LST1. Two hybridoma lines secreting monoclonal antibodies designated 7E2 and 8D12 were established. The 7E2 antibody detects recombinant and endogenous LST1 by Western blot analysis while 8D12 reacts with recombinant and endogenous LST1 in immunoprecipitation and flow cytometry procedures. The newly established antibodies were used to survey LST1 protein expression in human cell lines, which was found to be tightly regulated, allowing the expression of transmembrane isoforms but suppressing soluble isoforms
Complexity of Equivalence and Learning for Multiplicity Tree Automata
We consider the complexity of equivalence and learning for multiplicity tree
automata, i.e., weighted tree automata over a field. We first show that the
equivalence problem is logspace equivalent to polynomial identity testing, the
complexity of which is a longstanding open problem. Secondly, we derive lower
bounds on the number of queries needed to learn multiplicity tree automata in
Angluin's exact learning model, over both arbitrary and fixed fields.
Habrard and Oncina (2006) give an exact learning algorithm for multiplicity
tree automata, in which the number of queries is proportional to the size of
the target automaton and the size of a largest counterexample, represented as a
tree, that is returned by the Teacher. However, the smallest
tree-counterexample may be exponential in the size of the target automaton.
Thus the above algorithm does not run in time polynomial in the size of the
target automaton, and has query complexity exponential in the lower bound.
Assuming a Teacher that returns minimal DAG representations of
counterexamples, we give a new exact learning algorithm whose query complexity
is quadratic in the target automaton size, almost matching the lower bound, and
improving the best previously-known algorithm by an exponential factor
Funktionsdiagnostik - State of the Art 2011: Vom Syndrom zur pathophysiologisch basierten Differenzialdiagnose
On Functionality of Visibly Pushdown Transducers
Visibly pushdown transducers form a subclass of pushdown transducers that
(strictly) extends finite state transducers with a stack. Like visibly pushdown
automata, the input symbols determine the stack operations. In this paper, we
prove that functionality is decidable in PSpace for visibly pushdown
transducers. The proof is done via a pumping argument: if a word with two
outputs has a sufficiently large nesting depth, there exists a nested word with
two outputs whose nesting depth is strictly smaller. The proof uses technics of
word combinatorics. As a consequence of decidability of functionality, we also
show that equivalence of functional visibly pushdown transducers is
Exptime-Complete.Comment: 20 page
Streaming Tree Transducers
Theory of tree transducers provides a foundation for understanding
expressiveness and complexity of analysis problems for specification languages
for transforming hierarchically structured data such as XML documents. We
introduce streaming tree transducers as an analyzable, executable, and
expressive model for transforming unranked ordered trees in a single pass.
Given a linear encoding of the input tree, the transducer makes a single
left-to-right pass through the input, and computes the output in linear time
using a finite-state control, a visibly pushdown stack, and a finite number of
variables that store output chunks that can be combined using the operations of
string-concatenation and tree-insertion. We prove that the expressiveness of
the model coincides with transductions definable using monadic second-order
logic (MSO). Existing models of tree transducers either cannot implement all
MSO-definable transformations, or require regular look ahead that prohibits
single-pass implementation. We show a variety of analysis problems such as
type-checking and checking functional equivalence are solvable for our model.Comment: 40 page
Single-molecule real-time sequencing combined with optical mapping yields completely finished fungal genome
Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio- generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism’s biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes. IMPORTANCE Studying whole-genome sequences has become an important aspect of biological research. The advent of nextgeneration sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBiogenerated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome sanalyses to facilitate functional studies into an organism’s biology
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