401 research outputs found
An Analysis of Phase Transition in NK Landscapes
In this paper, we analyze the decision version of the NK landscape model from
the perspective of threshold phenomena and phase transitions under two random
distributions, the uniform probability model and the fixed ratio model. For the
uniform probability model, we prove that the phase transition is easy in the
sense that there is a polynomial algorithm that can solve a random instance of
the problem with the probability asymptotic to 1 as the problem size tends to
infinity. For the fixed ratio model, we establish several upper bounds for the
solubility threshold, and prove that random instances with parameters above
these upper bounds can be solved polynomially. This, together with our
empirical study for random instances generated below and in the phase
transition region, suggests that the phase transition of the fixed ratio model
is also easy
Alien Registration- Culberson, Dorothy J. (Presque Isle, Aroostook County)
https://digitalmaine.com/alien_docs/33792/thumbnail.jp
Consistency and Random Constraint Satisfaction Models
In this paper, we study the possibility of designing non-trivial random CSP
models by exploiting the intrinsic connection between structures and
typical-case hardness. We show that constraint consistency, a notion that has
been developed to improve the efficiency of CSP algorithms, is in fact the key
to the design of random CSP models that have interesting phase transition
behavior and guaranteed exponential resolution complexity without putting much
restriction on the parameter of constraint tightness or the domain size of the
problem. We propose a very flexible framework for constructing problem
instances withinteresting behavior and develop a variety of concrete methods to
construct specific random CSP models that enforce different levels of
constraint consistency. A series of experimental studies with interesting
observations are carried out to illustrate the effectiveness of introducing
structural elements in random instances, to verify the robustness of our
proposal, and to investigate features of some specific models based on our
framework that are highly related to the behavior of backtracking search
algorithms
Seawater alkalinity determination by the pH method
The coefficient fH used in the seawater alkalinity method of Anderson and Robinson (1946), has been redetermined at 25°C. We have found that fH = 0.741 ±0,005 for salinities between 30‰ and 41‰…
Random Graph Coloring - a Statistical Physics Approach
The problem of vertex coloring in random graphs is studied using methods of
statistical physics and probability. Our analytical results are compared to
those obtained by exact enumeration and Monte-Carlo simulations. We critically
discuss the merits and shortcomings of the various methods, and interpret the
results obtained. We present an exact analytical expression for the 2-coloring
problem as well as general replica symmetric approximated solutions for the
thermodynamics of the graph coloring problem with p colors and K-body edges.Comment: 17 pages, 9 figure
Ploidy Reductions in Murine Fusion-Derived Hepatocytes
We previously showed that fusion between hepatocytes lacking a crucial liver enzyme, fumarylacetoacetate hydrolase (FAH), and wild-type blood cells resulted in hepatocyte reprogramming. FAH expression was restored in hybrid hepatocytes and, upon in vivo expansion, ameliorated the effects of FAH deficiency. Here, we show that fusion-derived polyploid hepatocytes can undergo ploidy reductions to generate daughter cells with one-half chromosomal content. Fusion hybrids are, by definition, at least tetraploid. We demonstrate reduction to diploid chromosome content by multiple methods. First, cytogenetic analysis of fusion-derived hepatocytes reveals a population of diploid cells. Secondly, we demonstrate marker segregation using ß-galactosidase and the Y-chromosome. Approximately 2–5% of fusion-derived FAH-positive nodules were negative for one or more markers, as expected during ploidy reduction. Next, using a reporter system in which ß-galactosidase is expressed exclusively in fusion-derived hepatocytes, we identify a subpopulation of diploid cells expressing ß-galactosidase and FAH. Finally, we track marker segregation specifically in fusion-derived hepatocytes with diploid DNA content. Hemizygous markers were lost by ≥50% of Fah-positive cells. Since fusion-derived hepatocytes are minimally tetraploid, the existence of diploid hepatocytes demonstrates that fusion-derived cells can undergo ploidy reduction. Moreover, the high degree of marker loss in diploid daughter cells suggests that chromosomes/markers are lost in a non-random fashion. Thus, we propose that ploidy reductions lead to the generation of genetically diverse daughter cells with about 50% reduction in nuclear content. The generation of such daughter cells increases liver diversity, which may increase the likelihood of oncogenesis
Network conduciveness with application to the graph-coloring and independent-set optimization transitions
We introduce the notion of a network's conduciveness, a probabilistically
interpretable measure of how the network's structure allows it to be conducive
to roaming agents, in certain conditions, from one portion of the network to
another. We exemplify its use through an application to the two problems in
combinatorial optimization that, given an undirected graph, ask that its
so-called chromatic and independence numbers be found. Though NP-hard, when
solved on sequences of expanding random graphs there appear marked transitions
at which optimal solutions can be obtained substantially more easily than right
before them. We demonstrate that these phenomena can be understood by resorting
to the network that represents the solution space of the problems for each
graph and examining its conduciveness between the non-optimal solutions and the
optimal ones. At the said transitions, this network becomes strikingly more
conducive in the direction of the optimal solutions than it was just before
them, while at the same time becoming less conducive in the opposite direction.
We believe that, besides becoming useful also in other areas in which network
theory has a role to play, network conduciveness may become instrumental in
helping clarify further issues related to NP-hardness that remain poorly
understood
Iterative focused screening with biological fingerprints identifies selective Asc-1 inhibitors distinct from traditional high throughput screening
N-methyl-d-aspartate receptors (NMDARs) mediate glutamatergic signaling that is critical to cognitive processes in the central nervous system, and NMDAR hypofunction is thought to contribute to cognitive impairment observed in both schizophrenia and Alzheimer’s disease. One approach to enhance the function of NMDAR is to increase the concentration of an NMDAR coagonist, such as glycine or d-serine, in the synaptic cleft. Inhibition of alanine–serine–cysteine transporter-1 (Asc-1), the primary transporter of d-serine, is attractive because the transporter is localized to neurons in brain regions critical to cognitive function, including the hippocampus and cortical layers III and IV, and is colocalized with d-serine and NMDARs. To identify novel Asc-1 inhibitors, two different screening approaches were performed with whole-cell amino acid uptake in heterologous cells stably expressing human Asc-1: (1) a high-throughput screen (HTS) of 3 M compounds measuring 35S l-cysteine uptake into cells attached to scintillation proximity assay beads in a 1536 well format and (2) an iterative focused screen (IFS) of a 45 000 compound diversity set using a 3H d-serine uptake assay with a liquid scintillation plate reader in a 384 well format. Critically important for both screening approaches was the implementation of counter screens to remove nonspecific inhibitors of radioactive amino acid uptake. Furthermore, a 15 000 compound expansion step incorporating both on- and off-target data into chemical and biological fingerprint-based models for selection of additional hits enabled the identification of novel Asc-1-selective chemical matter from the IFS that was not identified in the full-collection HTS
Recognizing Treelike k-Dissimilarities
A k-dissimilarity D on a finite set X, |X| >= k, is a map from the set of
size k subsets of X to the real numbers. Such maps naturally arise from
edge-weighted trees T with leaf-set X: Given a subset Y of X of size k, D(Y) is
defined to be the total length of the smallest subtree of T with leaf-set Y .
In case k = 2, it is well-known that 2-dissimilarities arising in this way can
be characterized by the so-called "4-point condition". However, in case k > 2
Pachter and Speyer recently posed the following question: Given an arbitrary
k-dissimilarity, how do we test whether this map comes from a tree? In this
paper, we provide an answer to this question, showing that for k >= 3 a
k-dissimilarity on a set X arises from a tree if and only if its restriction to
every 2k-element subset of X arises from some tree, and that 2k is the least
possible subset size to ensure that this is the case. As a corollary, we show
that there exists a polynomial-time algorithm to determine when a
k-dissimilarity arises from a tree. We also give a 6-point condition for
determining when a 3-dissimilarity arises from a tree, that is similar to the
aforementioned 4-point condition.Comment: 18 pages, 4 figure
Polynomial iterative algorithms for coloring and analyzing random graphs
We study the graph coloring problem over random graphs of finite average
connectivity . Given a number of available colors, we find that graphs
with low connectivity admit almost always a proper coloring whereas graphs with
high connectivity are uncolorable. Depending on , we find the precise value
of the critical average connectivity . Moreover, we show that below
there exist a clustering phase in which ground states
spontaneously divide into an exponential number of clusters. Furthermore, we
extended our considerations to the case of single instances showing consistent
results. This lead us to propose a new algorithm able to color in polynomial
time random graphs in the hard but colorable region, i.e when .Comment: 23 pages, 10 eps figure
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